1
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Falanga AP, Massaro M, Borbone N, Notarbartolo M, Piccialli G, Liotta LF, Sanchez-Espejo R, Viseras Iborra C, Raymo FM, Oliviero G, Riela S. Carrier capability of halloysite nanotubes for the intracellular delivery of antisense PNA targeting mRNA of neuroglobin gene. J Colloid Interface Sci 2024; 663:9-20. [PMID: 38387188 DOI: 10.1016/j.jcis.2024.02.136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/28/2023] [Accepted: 02/17/2024] [Indexed: 02/24/2024]
Abstract
Peptide nucleic acid (PNA) is a DNA mimic that shows good stability against nucleases and proteases, forming strongly recognized complementary strands of DNA and RNA. However, due to its feeble ability to cross the cellular membrane, PNA activity and its targeting gene action is limited. Halloysite nanotubes (HNTs) are a natural and low-cost aluminosilicate clay. Because of their peculiar ability to cross cellular membrane, HNTs represent a valuable candidate for delivering genetic materials into cells. Herein, two differently charged 12-mer PNAs capable of recognizing as molecular target a 12-mer DNA molecule mimicking a purine-rich tract of neuroglobin were synthetized and loaded onto HNTs by electrostatic attraction interactions. After characterization, the kinetic release was also assessed in media mimicking physiological conditions. Resonance light scattering measurements assessed their ability to bind complementary single-stranded DNA. Furthermore, their intracellular delivery was assessed by confocal laser scanning microscopy on living MCF-7 cells incubated with fluorescence isothiocyanate (FITC)-PNA and HNTs labeled with a probe. The nanomaterials were found to cross cellular membrane and cell nuclei efficiently. Finally, it is worth mentioning that the HNTs/PNA can reduce the level of neuroglobin gene expression, as shown by reverse transcription-quantitative polymerase chain reaction and western blotting analysis.
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Affiliation(s)
- Andrea P Falanga
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy
| | - Marina Massaro
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | - Nicola Borbone
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy.
| | - Monica Notarbartolo
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | - Gennaro Piccialli
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy
| | - Leonarda F Liotta
- Istituto per lo Studio dei Materiali Nanostrutturati (ISMN)-CNR, Via Ugo La Malfa 153, Palermo 90146, Italy
| | - Rita Sanchez-Espejo
- University of Granada, Department of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, 18071 Granada, Spain
| | - Cesar Viseras Iborra
- University of Granada, Department of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, 18071 Granada, Spain; Andalusian Institute of Earth Sciences, CSIC-UGR, 18100 Armilla, Granada, Spain
| | - Françisco M Raymo
- Laboratory for Molecular Photonics, Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables 33146-0431, FL, United States
| | - Giorgia Oliviero
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Via Sergio Pansini 5, 80131 Napoli, Italy
| | - Serena Riela
- Dipartimento di Scienze Chimiche, Viale Andrea Doria 6, 95125 Catania, Italy.
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2
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Pals MJ, Wijnberg L, Yildiz Ç, Velema WA. Catechol-Siderophore Mimics Convey Nucleic Acid Therapeutics into Bacteria. Angew Chem Int Ed Engl 2024; 63:e202402405. [PMID: 38407513 DOI: 10.1002/anie.202402405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 02/23/2024] [Accepted: 02/24/2024] [Indexed: 02/27/2024]
Abstract
Antibacterial resistance is a major threat for human health. There is a need for new antibacterials to stay ahead of constantly-evolving resistant bacteria. Nucleic acid therapeutics hold promise as powerful antibiotics, but issues with their delivery hamper their applicability. Here, we exploit the siderophore-mediated iron uptake pathway to efficiently transport antisense oligomers into bacteria. We appended a synthetic siderophore to antisense oligomers targeting the essential acpP gene in Escherichia coli. Siderophore-conjugated PNA and PMO antisense oligomers displayed potent antibacterial properties. Conjugates bearing a minimal siderophore consisting of a mono-catechol group showed equally effective. Targeting the lacZ transcript resulted in dose-dependent decreased β-galactosidase production, demonstrating selective protein downregulation. Applying this concept to Acinetobacter baumannii also showed concentration-dependent growth inhibition. Whole-genome sequencing of resistant mutants and competition experiments with the endogenous siderophore verified selective uptake through the siderophore-mediated iron uptake pathway. Lastly, no toxicity towards mammalian cells was found. Collectively, we demonstrate for the first time that large nucleic acid therapeutics can be efficiently transported into bacteria using synthetic siderophore mimics.
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Affiliation(s)
- Mathijs J Pals
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Luuk Wijnberg
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Çağlar Yildiz
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Willem A Velema
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
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3
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MacLelland V, Kravitz M, Gupta A. Therapeutic and diagnostic applications of antisense peptide nucleic acids. Mol Ther Nucleic Acids 2024; 35:102086. [PMID: 38204913 PMCID: PMC10777018 DOI: 10.1016/j.omtn.2023.102086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Peptide nucleic acids (PNAs) are synthetic nucleic acid analogs with a neutral N-(2-aminoethyl) glycine backbone. PNAs possess unique physicochemical characteristics such as increased resistance to enzymatic degradation, ionic strength and stability over a wide range of temperatures and pH, and low intrinsic electrostatic repulsion against complementary target oligonucleotides. PNA has been widely used as an antisense oligonucleotide (ASO). Despite the favorable characteristics of PNA, in comparison with other ASO technologies, the use of antisense PNA for novel therapeutics has lagged. This review provides a brief overview of PNA, its antisense mechanisms of action, delivery strategies, and highlights successful applications of PNA, focusing on anti-pathogenic, anti-neurodegenerative disease, anti-cancer, and diagnostic agents. For each application, several studies are discussed focusing on the different target sites of the PNA, design of different PNAs and the therapeutic outcome in different cell lines and animal models. Thereafter, persisting limitations slowing the successful integration of antisense PNA therapeutics are discussed in order to highlight actionable next steps in the development and optimization of PNA as an ASO.
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Affiliation(s)
- Victoria MacLelland
- Department of Pharmaceutical Sciences, University of Saint Joseph, West Hartford, CT 06117, USA
| | - Madeline Kravitz
- Department of Pharmaceutical Sciences, University of Saint Joseph, West Hartford, CT 06117, USA
| | - Anisha Gupta
- Department of Pharmaceutical Sciences, University of Saint Joseph, West Hartford, CT 06117, USA
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4
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Sarkar S. Recent advancements in bionanomaterial applications of peptide nucleic acid assemblies. Biopolymers 2024; 115:e23567. [PMID: 37792292 DOI: 10.1002/bip.23567] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/02/2023] [Accepted: 09/19/2023] [Indexed: 10/05/2023]
Abstract
Peptide nucleic acid (PNA) is a unique combination of peptides and nucleic acids. PNA can exhibit hydrogen bonding interactions with complementary nucleobases like DNA/RNA. Also, its polyamide backbone allows easy incorporation of biomolecules like peptides and proteins to build hybrid molecular constructs. Because of chimeric structural properties, PNA has lots of potential to build diverse nanostructures. However, progress in the PNA material field is still immature compared with its massive applications in antisense oligonucleotide research. Examples of well-defined molecular assemblies have been reported with PNA amphiphiles, self-assembling guanine-PNA monomers/dimers, and PNA-decorated nucleic acids/ polymers/ peptides. All these works indicate the great potential of PNA to be used as bionanomaterials. The review summarizes the recent reports on PNA-based nanostructures and their versatile applications. Additionally, this review shares a perspective to promote a better understanding of controlling molecular assembly by the systematic structural modifications of PNA monomers.
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Affiliation(s)
- Srijani Sarkar
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
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5
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Malik S, Pradeep SP, Kumar V, Xiao Y, Deng Y, Fan R, Vasquez JC, Singh V, Bahal R. Antitumor efficacy of a sequence-specific DNA-targeted γ PNA-based c-Myc inhibitor. Cell Rep Med 2024; 5:101354. [PMID: 38183981 PMCID: PMC10829792 DOI: 10.1016/j.xcrm.2023.101354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 09/21/2023] [Accepted: 12/11/2023] [Indexed: 01/08/2024]
Abstract
Targeting oncogenes at the genomic DNA level can open new avenues for precision medicine. Significant efforts are ongoing to target oncogenes using RNA-targeted and protein-targeted platforms, but no progress has been made to target genomic DNA for cancer therapy. Here, we introduce a gamma peptide nucleic acid (γPNA)-based genomic DNA-targeted platform to silence oncogenes in vivo. γPNAs efficiently invade the mixed sequences of genomic DNA with high affinity and specificity. As a proof of concept, we establish that γPNA can inhibit c-Myc transcription in multiple cell lines. We evaluate the in vivo efficacy and safety of genomic DNA targeting in three pre-clinical models. We also establish that anti-transcription γPNA in combination with histone deacetylase inhibitors and chemotherapeutic drugs results in robust antitumor activity in cell-line- and patient-derived xenografts. Overall, this strategy offers a unique therapeutic platform to target genomic DNA to inhibit oncogenes for cancer therapy.
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Affiliation(s)
- Shipra Malik
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, USA
| | - Sai Pallavi Pradeep
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, USA
| | - Vikas Kumar
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, USA
| | - Yong Xiao
- Department of Biomedical Engineering, Yale University, New Haven, CT 06510, USA; Department of Neurosurgery, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Yanxiang Deng
- Department of Biomedical Engineering, Yale University, New Haven, CT 06510, USA; Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT 06510, USA; Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA; Human and Translational Immunology, Yale School of Medicine, New Haven, CT 06520, USA; Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Juan C Vasquez
- Department of Pediatrics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Vijender Singh
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
| | - Raman Bahal
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, USA.
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6
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Zhang P, Qin K, Gao K, Su F, Wang H, Liu J, Li Z. Multiple thermocycles followed by LAMP with only two primers for ultrasensitive colorimetric viral RNA testing and tracking at single-base resolution. Anal Chim Acta 2023; 1276:341621. [PMID: 37573111 DOI: 10.1016/j.aca.2023.341621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/06/2023] [Accepted: 07/12/2023] [Indexed: 08/14/2023]
Abstract
Rapid, accurate and high throughput measurement of infectious viruses is an urgent need to prevent viral transmission. Loop-mediated isothermal amplification (LAMP) is an attractive isothermal amplification method for nucleic acid detection, especially for point-of-care (POC) testing, but it needs at least four primers and its sensitivity is also limited when integrating with visual detection methods. Herein, by designing only two primers to precisely recognize the four regions of the target, we developed a multiple thermocycles-based LAMP method (MTC-LAMP) for sensitive and specific testing and tracking of viral RNA. We also introduced a novel SYBR Green I (SG)-assisted stable colorimetric assay induced by the amplification products through the charge neutralization effect of positively charged SG toward gold nanoparticles (AuNPs). The ultralow nonspecific background of the double exponential amplification improved the detection sensitivity to near single-molecule level (1 aM, 3 copies in 5 μL solution), which was higher than RT-PCR and RT-LAMP. After adding AuNPs, a significant color difference between target and blank was immediately observed by naked eye. By introducing a peptide nucleic acid (PNA) clamp into our colorimetric MTC-LAMP assay, the specific distinguish of virus variants at single-base resolution was observed without the requirement of any equipment. This assay shows great potential for large-scale screening and tracking of the threatening viruses with ultrahigh sensitivity and pronounced colorimetric output, which is of great importance for pandemic control.
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Affiliation(s)
- Pengbo Zhang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Ke Qin
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Kejian Gao
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Fengxia Su
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Hui Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
| | - Zhengping Li
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China.
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7
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Abt C, Gerlach LM, Bull J, Jacob A, Kreikemeyer B, Patenge N. Pyrenebutyrate Enhances the Antibacterial Effect of Peptide-Coupled Antisense Peptide Nucleic Acids in Streptococcus pyogenes. Microorganisms 2023; 11:2131. [PMID: 37763975 PMCID: PMC10537354 DOI: 10.3390/microorganisms11092131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 07/27/2023] [Accepted: 07/31/2023] [Indexed: 09/29/2023] Open
Abstract
Antisense peptide nucleic acids (PNAs) inhibit bacterial growth in several infection models. Since PNAs are not spontaneously taken up by bacteria, they are often conjugated to carriers such as cell-penetrating peptides (CPPs) in order to improve translocation. Hydrophobic counterions such as pyrenebutyrate (PyB) have been shown to facilitate translocation of peptides over natural and artificial membranes. In this study, the capability of PyB to support translocation of CPP-coupled antisense PNAs into bacteria was investigated in Streptococcus pyogenes and Streptococcus pneumoniae. PyB enhanced the antimicrobial activity of CPP-conjugated antisense PNAs in S. pyogenes. The most significant effect of PyB was observed in combination with K8-conjugated anti-gyrA PNAs. In contrast, no significant effect of PyB on the antimicrobial activity of CPP-conjugated PNAs in S. pneumoniae was detected. Uptake of K8-FITC into S. pyogenes, Escherichia coli, and Klebsiella pneumoniae could be improved by pre-incubation with PyB, indicating that PyB supports the antimicrobial effect of CPP-antisense PNAs in S. pyogenes by facilitating the translocation of peptides across the bacterial membrane.
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Affiliation(s)
- Corina Abt
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, 18057 Rostock, Germany (J.B.); (B.K.)
| | - Lisa Marie Gerlach
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, 18057 Rostock, Germany (J.B.); (B.K.)
| | - Jana Bull
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, 18057 Rostock, Germany (J.B.); (B.K.)
| | | | - Bernd Kreikemeyer
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, 18057 Rostock, Germany (J.B.); (B.K.)
| | - Nadja Patenge
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, 18057 Rostock, Germany (J.B.); (B.K.)
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8
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Kumpina I, Baskevics V, Nguyen KD, Katkevics M, Rozners E. Nucleobase and Linker Modification for Triple-Helical Recognition of Pyrimidines in RNA Using Peptide Nucleic Acids. Chembiochem 2023:e202300291. [PMID: 37321971 DOI: 10.1002/cbic.202300291] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/10/2023] [Accepted: 06/15/2023] [Indexed: 06/17/2023]
Abstract
Triple-helical recognition of any sequence of double-stranded RNA requires high affinity Hoogsteen hydrogen binding to pyrimidine interruptions of polypurine tracts. Because pyrimidines have only one hydrogen bond donor/acceptor on Hoogsteen face, their triple-helical recognition is a formidable problem. The present study explored various five-membered heterocycles and linkers that connect nucleobases to backbone of peptide nucleic acid (PNA) to optimize formation of X•C-G and Y•U-A triplets. Molecular modeling and biophysical (UV melting and isothermal titration calorimetry) results revealed a complex interplay between the heterocyclic nucleobase and linker to PNA backbone. While the five-membered heterocycles did not improve pyrimidine recognition, increasing the linker length by four atoms provided promising gains in binding affinity and selectivity. The results suggest that further optimization of heterocyclic bases with extended linkers to PNA backbone may be a promising approach to triple-helical recognition of RNA.
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Affiliation(s)
- Ilze Kumpina
- Binghamton University, Department of Chemistry, UNITED STATES
| | - Vladislavs Baskevics
- Latvian Institute of Organic Synthesis: Latvijas Organiskas sintezes instituts, Biologically Active Compound Synthesis Laboratory, LATVIA
| | - Khoi D Nguyen
- Binghamton University, Department of Chemistry, UNITED STATES
| | - Martins Katkevics
- Latvian Institute of Organic Synthesis: Latvijas Organiskas sintezes instituts, Biologically Active Compound Synthesis Laboratory, LATVIA
| | - Eriks Rozners
- Binghamton University, Department of Chemistry, 4400 Vestal Parkway East, 13902, Binghamton, UNITED STATES
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9
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Cailly L, Gruchet C, Maitre E, Guidez S, Delwail V, Systchenko T, Moya N, Sabirou F, Levy A, Bobin A, Gardeney H, Nsiala L, Vonfeld M, Chacon A, Pichon A, Bouyer S, Baslé C, Dindinnaud E, Chomel J, Raimbault A, Borde‐Mougenot F, Troussard X, Tomowiak C. Hairy cell leukemia with isolated bone lesions. Clin Case Rep 2023; 11:e7343. [PMID: 37207087 PMCID: PMC10188895 DOI: 10.1002/ccr3.7343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 03/24/2023] [Accepted: 04/28/2023] [Indexed: 05/21/2023] Open
Abstract
Key Clinical Message 18F-FDG PET/CT has clinical relevance in HCL at diagnosis and for the follow-up of patients treated, especially in case of atypical presentations such as bone involvements (which are probably underestimated) and poor bone marrow infiltration. Abstract Bone lesions are rarely reported in Hairy Cell Leukemia (HCL). We report two BRAFV600E mutated HCL patients presented bone lesions at foreground, poor bone marrow involvement, and the important role 18F-FDG PET/CT played in their management. We discuss the crucial role that 18F-FDG PET/CT could play in HCL routine practice.
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Affiliation(s)
- Laura Cailly
- Department of Hematology and Cellular Therapy, and INSERM CIC1402CHU La Miletrie, University HospitalPoitiersFrance
| | - Cécile Gruchet
- Department of Hematology and Cellular Therapy, and INSERM CIC1402CHU La Miletrie, University HospitalPoitiersFrance
| | - Elsa Maitre
- Department of Hematology, CHU Cote de NacreUniversity HospitalCaenFrance
| | - Stephanie Guidez
- Department of Hematology and Cellular Therapy, and INSERM CIC1402CHU La Miletrie, University HospitalPoitiersFrance
| | - Vincent Delwail
- Department of Hematology and Cellular Therapy, and INSERM CIC1402CHU La Miletrie, University HospitalPoitiersFrance
| | - Thomas Systchenko
- Department of Hematology and Cellular Therapy, and INSERM CIC1402CHU La Miletrie, University HospitalPoitiersFrance
| | - Niels Moya
- Department of Hematology and Cellular Therapy, and INSERM CIC1402CHU La Miletrie, University HospitalPoitiersFrance
| | - Florence Sabirou
- Department of Hematology and Cellular Therapy, and INSERM CIC1402CHU La Miletrie, University HospitalPoitiersFrance
| | - Anthony Levy
- Department of Hematology and Cellular Therapy, and INSERM CIC1402CHU La Miletrie, University HospitalPoitiersFrance
| | - Arthur Bobin
- Department of Hematology and Cellular Therapy, and INSERM CIC1402CHU La Miletrie, University HospitalPoitiersFrance
| | - Hélène Gardeney
- Department of Hematology and Cellular Therapy, and INSERM CIC1402CHU La Miletrie, University HospitalPoitiersFrance
| | - Laly Nsiala
- Department of Hematology and Cellular Therapy, and INSERM CIC1402CHU La Miletrie, University HospitalPoitiersFrance
| | - Mathilde Vonfeld
- Department of Hematology and Cellular Therapy, and INSERM CIC1402CHU La Miletrie, University HospitalPoitiersFrance
| | - Aurélia Chacon
- Department of Hematology and Cellular Therapy, and INSERM CIC1402CHU La Miletrie, University HospitalPoitiersFrance
| | - Aurélien Pichon
- Department of Hematology and Cellular Therapy, and INSERM CIC1402CHU La Miletrie, University HospitalPoitiersFrance
| | - Sabrina Bouyer
- Department of Biology, CHU La MiletrieUniversity HospitalPoitiersFrance
| | - Caroline Baslé
- Department of Biology, CHU La MiletrieUniversity HospitalPoitiersFrance
| | - Elodie Dindinnaud
- Department of Biology, CHU La MiletrieUniversity HospitalPoitiersFrance
| | | | - Anna Raimbault
- Department of Biology, CHU La MiletrieUniversity HospitalPoitiersFrance
| | | | - Xavier Troussard
- Department of Hematology, CHU Cote de NacreUniversity HospitalCaenFrance
| | - Cécile Tomowiak
- Department of Hematology and Cellular Therapy, and INSERM CIC1402CHU La Miletrie, University HospitalPoitiersFrance
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10
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Jarczewska M, Bojarski W, Majewska A, Drozd M, Ziółkowski R, Malinowska E. Studies on the application of single-stranded DNA and PNA probes for electrochemical detection of miRNA 141. Bioelectrochemistry 2023; 150:108363. [PMID: 36608369 DOI: 10.1016/j.bioelechem.2022.108363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 12/09/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022]
Abstract
The abnormal concentration of microRNAs (miRNAs) can be associated with occurrence of various diseases including cancer, cardiovascular and neurodegenerative, hence they can be considered as potential biomarkers. An attractive approach could be the application of electrochemical methods, particularly where hybridization event between single-stranded deoxyribonucleic acid (ssDNA) or peptide-nucleic acid (PNA) with miRNA strand happens. Recently, the use of various nanomaterials such as gold nanoparticles, graphene oxide, quantum dots as well as catalyzed hairpin assembly or hybridization chain reaction were proposed to further enhance the performance of elaborated sensors. Herein, we present the studies on selection of receptor layer composition for detection of miRNA 141. The possibility of formation of receptor layer and further duplex monolayer between ssDNA or PNA with miRNA was analyzed by atomic force microscopy (AFM) technique. The interaction of ssDNA and PNA probes with miRNA was further verified using surface plasmon resonance (SPR) and quartz - crystal microbalance (QCM) techniques. On the basis of impedance spectroscopy it was shown that the use of unlabelled ssDNA as receptor layer provided 0.1 pM detection limit. This shows that proposed biosensor that is simple in preparation and use is an attractive alternative to other recently presented approaches.
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11
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Pradeep SP, Malik S, Slack FJ, Bahal R. Unlocking the potential of chemically modified peptide nucleic acids for RNA-based therapeutics. RNA 2023; 29:434-445. [PMID: 36653113 PMCID: PMC10019372 DOI: 10.1261/rna.079498.122] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/12/2023] [Indexed: 05/27/2023]
Abstract
RNA therapeutics have emerged as next-generation therapy for the treatment of many diseases. Unlike small molecules, RNA targeted drugs are not limited by the availability of binding pockets on the protein, but rather utilize Watson-Crick (WC) base-pairing rules to recognize the target RNA and modulate gene expression. Antisense oligonucleotides (ASOs) present a powerful therapeutic approach to treat disorders triggered by genetic alterations. ASOs recognize the cognate site on the target RNA to alter gene expression. Nine single-stranded ASOs have been approved for clinical use and several candidates are in late-stage clinical trials for both rare and common diseases. Several chemical modifications, including phosphorothioates, locked nucleic acid, phosphorodiamidate, morpholino, and peptide nucleic acids (PNAs), have been investigated for efficient RNA targeting. PNAs are synthetic DNA mimics where the deoxyribose phosphate backbone is replaced by N-(2-aminoethyl)-glycine units. The neutral pseudopeptide backbone of PNAs contributes to enhanced binding affinity and high biological stability. PNAs hybridize with the complementary site in the target RNA and act by a steric hindrance--based mechanism. In the last three decades, various PNA designs, chemical modifications, and delivery strategies have been explored to demonstrate their potential as an effective and safe RNA-targeting platform. This review covers the advances in PNA-mediated targeting of coding and noncoding RNAs for a myriad of therapeutic applications.
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Affiliation(s)
- Sai Pallavi Pradeep
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Shipra Malik
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Frank J Slack
- HMS Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Raman Bahal
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269, USA
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12
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Lomae A, Preechakasedkit P, Hanpanich O, Ozer T, Henry CS, Maruyama A, Pasomsub E, Phuphuakrat A, Rengpipat S, Vilaivan T, Chailapakul O, Ruecha N, Ngamrojanavanich N. Label free electrochemical DNA biosensor for COVID-19 diagnosis. Talanta 2023; 253:123992. [PMID: 36228554 PMCID: PMC9546783 DOI: 10.1016/j.talanta.2022.123992] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 08/31/2022] [Accepted: 10/02/2022] [Indexed: 11/07/2022]
Abstract
The COVID-19 pandemic has significantly increased the development of the development of point-of-care (POC) diagnostic tools because they can serve as useful tools for detecting and controlling spread of the disease. Most current methods require sophisticated laboratory instruments and specialists to provide reliable, cost-effective, specific, and sensitive POC testing for COVID-19 diagnosis. Here, a smartphone-assisted Sensit Smart potentiostat (PalmSens) was integrated with a paper-based electrochemical sensor to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A disposable paper-based device was fabricated, and the working electrode directly modified with a pyrrolidinyl peptide nucleic acid (acpcPNA) as the biological recognition element to capture the target complementary DNA (cDNA). In the presence of the target cDNA, hybridization with acpcPNA probe blocks the redox conversion of a redox reporter, leading to a decrease in electrochemical response correlating to SARS-CoV-2 concentration. Under optimal conditions, a linear range from 0.1 to 200 nM and a detection limit of 1.0 pM were obtained. The PNA-based electrochemical paper-based analytical device (PNA-based ePAD) offers high specificity toward SARS-CoV-2 N gene because of the highly selective PNA-DNA binding. The developed sensor was used for amplification-free SARS-CoV-2 detection in 10 nasopharyngeal swab samples (7 SARS-CoV-2 positive and 3 SARS-CoV-2 negative), giving a 100% agreement result with RT-PCR.
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Affiliation(s)
- Atchara Lomae
- Electrochemistry and Optical Spectroscopy Center of Excellence (EOSCE), Department of Chemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Pattarachaya Preechakasedkit
- Metallurgy and Materials Science Research Institute, Chulalongkorn University, Soi Chula 12 Phayathai Rd., Pathumwan, Bangkok, 10330, Thailand
| | - Orakan Hanpanich
- Electrochemistry and Optical Spectroscopy Center of Excellence (EOSCE), Department of Chemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Tugba Ozer
- Department of Bioengineering, Faculty of Chemical-Metallurgical Engineering, Yildiz Technical University, 34220, Istanbul, Turkey
| | - Charles S. Henry
- Metallurgy and Materials Science Research Institute, Chulalongkorn University, Soi Chula 12 Phayathai Rd., Pathumwan, Bangkok, 10330, Thailand,Department of Chemistry, Colorado State University, Fort Collins, CO, 80523, USA
| | - Atsushi Maruyama
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259 B-57, Yokohama, 226-8501, Japan
| | - Ekawat Pasomsub
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Angsana Phuphuakrat
- Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Sirirat Rengpipat
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand,Qualified Diagnostic Development Center, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Orawon Chailapakul
- Electrochemistry and Optical Spectroscopy Center of Excellence (EOSCE), Department of Chemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Nipapan Ruecha
- Electrochemistry and Optical Spectroscopy Center of Excellence (EOSCE), Department of Chemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok, 10330, Thailand,Metallurgy and Materials Science Research Institute, Chulalongkorn University, Soi Chula 12 Phayathai Rd., Pathumwan, Bangkok, 10330, Thailand,Corresponding author. Metallurgy and Materials Science Research Institute, Chulalongkorn University, Soi Chula 12 Phayathai Rd., Pathumwan, Bangkok, 10330, Thailand
| | - Nattaya Ngamrojanavanich
- Electrochemistry and Optical Spectroscopy Center of Excellence (EOSCE), Department of Chemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok, 10330, Thailand,Institute of Biotechnology and Genetic Engineering, Chulalongkorn University, Bangkok, 10330, Thailand,Corresponding author. Institute of Biotechnology and Genetic Engineering, Chulalongkorn University, Bangkok, 10330, Thailand
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13
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Mecarelli E, Aigotti R, Asteggiano A, Giacobini P, Chasles M, Tillet Y, Dal Bello F, Medana C. Quantitation of endogenous GnRH by validated nano-HPLC-HRMS method: a pilot study on ewe plasma. Anal Bioanal Chem 2022; 414:7623-7634. [PMID: 36063171 PMCID: PMC9587114 DOI: 10.1007/s00216-022-04293-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/01/2022] [Accepted: 08/17/2022] [Indexed: 11/18/2022]
Abstract
Gonadotropin-releasing hormone isoform I (GnRH), a neuro-deca-peptide, plays a fundamental role in development and maintenance of the reproductive system in vertebrates. The anomalous release of GnRH is observed in reproductive disorder such as hypogonadotropic hypogonadism, polycystic ovary syndrome (PCOS), or following prenatal exposure to elevated androgen levels. Quantitation of GnRH plasma levels could help to diagnose and better understand these pathologies. Here, a validated nano-high-performance liquid chromatography–high-resolution mass spectrometry (HPLC-HRMS) method to quantify GnRH in ewe plasma samples is presented. Protein precipitation and solid-phase extraction (SPE) pre-treatment steps were required to purify and enrich GnRH and internal standard (lamprey-luteinizing hormone-releasing hormone-III, l-LHRH-III). For the validation process, a surrogate matrix approach was chosen following the International Council for Harmonisation (ICH) and FDA guidelines. Before the validation study, the validation model using the surrogate matrix was compared with those using a real matrix such as human plasma. All the tested parameters were analogous confirming the use of the surrogate matrix as a standard calibration medium. From the validation study, limit of detection (LOD) and limit of quantitation (LOQ) values of 0.008 and 0.024 ng/mL were obtained, respectively. Selectivity, accuracy, precision, recovery, and matrix effect were assessed with quality control samples in human plasma and all values were acceptable. Sixteen samples belonging to healthy and prenatal androgen (PNA) exposed ewes were collected and analyzed, and the GnRH levels ranged between 0.05 and 3.26 ng/mL. The nano-HPLC-HRMS developed here was successful in measuring GnRH, representing therefore a suitable technique to quantify GnRH in ewe plasma and to detect it in other matrices and species.
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Affiliation(s)
- Enrica Mecarelli
- Department of Molecular Biotechnology and Health Sciences, University of Turin, via Pietro Giuria 5, 10125, Turin, Italy
| | - Riccardo Aigotti
- Department of Molecular Biotechnology and Health Sciences, University of Turin, via Pietro Giuria 5, 10125, Turin, Italy
| | - Alberto Asteggiano
- Department of Molecular Biotechnology and Health Sciences, University of Turin, via Pietro Giuria 5, 10125, Turin, Italy
| | - Paolo Giacobini
- University Lille, Inserm, CHU Lille, Laboratory of Development and Plasticity of the Neuroendocrine Brain, Lille Neuroscience & Cognition, Inserm UMR-S1172, 59000, Lille, France
| | - Manon Chasles
- University of Tours, IFCE, Centre INRAE Val de Loire, 37380, Nouzilly, France
| | - Yves Tillet
- University of Tours, IFCE, Centre INRAE Val de Loire, 37380, Nouzilly, France
| | - Federica Dal Bello
- Department of Molecular Biotechnology and Health Sciences, University of Turin, via Pietro Giuria 5, 10125, Turin, Italy.
| | - Claudio Medana
- Department of Molecular Biotechnology and Health Sciences, University of Turin, via Pietro Giuria 5, 10125, Turin, Italy
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14
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Hausherr D, Niederdorfer R, Bürgmann H, Lehmann M, Magyar P, Mohn J, Morgenroth E, Joss A. Successful year-round mainstream partial nitritation anammox: Assessment of effluent quality, performance and N 2O emissions. Water Res X 2022; 16:100145. [PMID: 35789883 PMCID: PMC9250041 DOI: 10.1016/j.wroa.2022.100145] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 05/17/2022] [Accepted: 06/15/2022] [Indexed: 05/04/2023]
Abstract
For two decades now, partial nitritation anammox (PNA) systems were suggested to more efficiently remove nitrogen (N) from mainstream municipal wastewater. Yet to date, only a few pilot-scale systems and even fewer full-scale implementations of this technology have been described. Process instability continues to restrict the broad application of PNA. Especially problematic are insufficient anammox biomass retention, the growth of undesired aerobic nitrite-oxidizers, and nitrous oxide (N2O) emissions. In this study, a two-stage mainstream pilot-scale PNA system, consisting of three reactors (carbon pre-treatment, nitritation, anammox - 8 m3 each), was operated over a year, treating municipal wastewater. The aim was to test whether both, robust autotrophic N removal and high effluent quality, can be achieved throughout the year. A second aim was to better understand rate limiting processes, potentially affecting the overall performance of PNA systems. In this pilot study, excellent effluent quality, in terms of inorganic nitrogen, was accomplished (average effluent concentrations: 0.4 mgNH4-N/L, 0.1 mgNO2-N/L, 0.9 mgNO3-N/L) even at wastewater temperatures previously considered problematic (as low as 8 °C). N removal was limited by nitritation rates (84 ± 43 mgNH4-N/L/d), while surplus anammox activity was observed at all times (178 ± 43 mgN/L/d). Throughout the study, nitrite-oxidation was maintained at a low level (<2.5% of ammonium consumption rate). Unfortunately, high N2O emissions from the nitritation stage (1.2% of total nitrogen in the influent) were observed, and, based on natural isotope abundance measurements, could be attributed to heterotrophic denitrification. In situ batch experiments were conducted to identify the role of dissolved oxygen (DO) and organic substrate availability in N2O emission-mitigation. The addition of organic substrate, to promote complete denitrification, was not successful in decreasing N2O emission, but increasing the DO from 0.3 to 2.9 mgO2/L decreased N2O emissions by a factor of 3.4.
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Affiliation(s)
- D. Hausherr
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf 8600, Switzerland
- Corresponding author:
| | - R. Niederdorfer
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, 6047, Switzerland
| | - H. Bürgmann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, 6047, Switzerland
| | - M.F. Lehmann
- Department of Environmental Sciences, University of Basel, Aquatic and Isotope Biogeochemistry, Basel 4056, Switzerland
| | - P. Magyar
- Department of Environmental Sciences, University of Basel, Aquatic and Isotope Biogeochemistry, Basel 4056, Switzerland
| | - J. Mohn
- Empa, Swiss Federal Institute for Materials Science and Technology, Laboratory for Air Pollution / Environmental Technology, Dübendorf 8600, Switzerland
| | - E. Morgenroth
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf 8600, Switzerland
- ETH Zürich, Institute of Environmental Engineering, Zürich 8093, Switzerland
| | - A. Joss
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf 8600, Switzerland
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15
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Bryson SJ, Hunt KA, Stahl DA, Winkler MKH. Metagenomic Insights Into Competition Between Denitrification and Dissimilatory Nitrate Reduction to Ammonia Within One-Stage and Two-Stage Partial-Nitritation Anammox Bioreactor Configurations. Front Microbiol 2022; 13:825104. [PMID: 35547121 PMCID: PMC9083452 DOI: 10.3389/fmicb.2022.825104] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/30/2022] [Indexed: 11/13/2022] Open
Abstract
Anaerobic ammonia oxidizing bacteria (Anammox) are implemented in high-efficiency wastewater treatment systems operated in two general configurations; one-stage systems combine aerobic ammonia oxidizing bacteria (AOB) and Anammox within a single aerated reactor, whereas two-stage configurations separate these processes into discrete tanks. Within both configurations heterotrophic populations that perform denitrification or dissimilatory nitrate reduction to ammonia (DNRA) compete for carbon and nitrate or nitrite and can impact reactor performance because DNRA retains nitrogen in the system. Therefore, it is important to understand how selective pressures imposed by one-stage and two-stage reactor configurations impact the microbial community structure and associated nitrogen transforming functions. We performed 16S rRNA gene and metagenomic sequencing on different biomass fractions (granules, flocs, and suspended biomass) sampled from two facilities treating sludge dewatering centrate: a one-stage treatment facility (Chambers Creek, Tacoma, WA) and a two-stage system (Rotterdam, Netherlands). Similar microbial populations were identified across the different samples, but relative abundances differed between reactor configurations and biomass sources. Analysis of metagenome assembled genomes (MAGs) indicated different lifestyles for abundant heterotrophic populations. Acidobacteria, Bacteroidetes, and Chloroflexi MAGs had varying capacity for DNRA and denitrification. Acidobacteria MAGs possessed high numbers of glycosyl hydrolases and glycosyl transferases indicating a role in biomass degradation. Ignavibacteria and Phycosphaerae MAGs contributed to the greater relative abundance of DNRA associated nrf genes in the two-stage granules and contained genomic features suggesting a preference for an anoxic or microoxic niche. In the one-stage granules a MAG assigned to Burkholderiales accounted for much of the abundant denitrification genes and had genomic features, including the potential for autotrophic denitrification using reduced sulfur, that indicate an ability to adapt its physiology to varying redox conditions. Overall, the competition for carbon substrates between denitrifying and DNRA performing heterotrophs may be impacted by configuration specific selective pressures. In one-stage systems oxygen availability in the bulk liquid and the oxygen gradient within granules would provide a greater niche space for heterotrophic populations capable of utilizing both oxygen and nitrate or nitrite as terminal electron acceptors, compared to two-stage systems where a homogeneous anoxic environment would favor heterotrophic populations primarily adapted to anaerobic metabolism.
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Affiliation(s)
- Samuel J Bryson
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, United States
| | - Kristopher A Hunt
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, United States
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, United States
| | - Mari-Karoliina H Winkler
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, United States
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16
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Iubatti M, Gabas IM, Cavaco LM, Mood EH, Lim E, Bonanno F, Yavari N, Brolin C, Nielsen PE. Antisense Peptide Nucleic Acid-Diaminobutanoic Acid Dendron Conjugates with SbmA-Independent Antimicrobial Activity against Gram-Negative Bacteria. ACS Infect Dis 2022; 8:1098-1106. [PMID: 35436109 PMCID: PMC9112330 DOI: 10.1021/acsinfecdis.2c00089] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Precision antisense antibacterial agents may be developed into novel antibiotics in the fight against multidrug-resistant Gram-negative bacteria. In this study, a series of diaminobutanoic acid (DAB) dendrons are presented as novel carriers for the delivery of antisense antibacterial peptide nucleic acids (PNAs). The dendron-PNA conjugates targeting the essential acpP gene exhibit specific antisense antimicrobial bactericidal activity against Escherichia coli and Klebsiella pneumoniae at one-digit micromolar concentrations, while showing low toxicity to human cells. One compound selected from a structure-activity relationship series showed high stability in mouse and human serum (t1/2 ≫ 24 h) as well as in vivo activity against a multidrug-resistant, extended spectrum beta-lactamase-producing E. coli in a murine peritonitis model. The compound was also well tolerated in mice upon i.v. administration up to a dose of 20 mg/kg, and in vivo fluorescence imaging indicated clearance via renal excretion with slight accumulation in the kidneys and liver. Thus, DAB-based dendrons constitute a promising new chemistry platform for development of effective delivery agents for antibacterial drugs with possible in vivo use.
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Affiliation(s)
- Mirko Iubatti
- Center for Peptide-based Antibiotics, Department of Cellular and Molecular Medicine, The Panum Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen 2200, Denmark
| | - Isabel Maicas Gabas
- Center for Peptide-based Antibiotics, Department of Cellular and Molecular Medicine, The Panum Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen 2200, Denmark
| | - Lina M. Cavaco
- Department for Bacteria Parasites and Fungi, Statens Serum Institut, Copenhagen 2200, Denmark
| | - Elnaz Harifi Mood
- Center for Peptide-based Antibiotics, Department of Cellular and Molecular Medicine, The Panum Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen 2200, Denmark
| | - Ernest Lim
- Center for Peptide-based Antibiotics, Department of Cellular and Molecular Medicine, The Panum Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen 2200, Denmark
| | - Federica Bonanno
- Center for Peptide-based Antibiotics, Department of Cellular and Molecular Medicine, The Panum Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen 2200, Denmark
| | - Niloofar Yavari
- Center for Peptide-based Antibiotics, Department of Cellular and Molecular Medicine, The Panum Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen 2200, Denmark
| | - Camilla Brolin
- Center for Peptide-based Antibiotics, Department of Cellular and Molecular Medicine, The Panum Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen 2200, Denmark
| | - Peter E. Nielsen
- Center for Peptide-based Antibiotics, Department of Cellular and Molecular Medicine, The Panum Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen 2200, Denmark
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17
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Cimicata G, Fridkin G, Bose T, Eyal Z, Halfon Y, Breiner-Goldstein E, Fox T, Zimmerman E, Bashan A, de Val N, Wlodawer A, Yonath A. Structural Studies Reveal the Role of Helix 68 in the Elongation Step of Protein Biosynthesis. mBio 2022; 13:e0030622. [PMID: 35348349 PMCID: PMC9040758 DOI: 10.1128/mbio.00306-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 02/14/2022] [Indexed: 02/04/2023] Open
Abstract
The ribosome, a multicomponent assembly consisting of RNA and proteins, is a pivotal macromolecular machine that translates the genetic code into proteins. The large ribosomal subunit rRNA helix 68 (H68) is a key element in the protein synthesis process, as it coordinates the coupled movements of the actors involved in translocation, including the tRNAs and L1 stalk. Examination of cryo-electron microscopy (cryo-EM) structures of ribosomes incubated for various time durations at physiological temperatures led to the identification of functionally relevant H68 movements. These movements assist the transition of the L1 stalk between its open and closed states. H68 spatial flexibility and its significance to the protein synthesis process were confirmed through its effective targeting with antisense PNA oligomers. Our results suggest that H68 is actively involved in ribosome movements that are central to the elongation process. IMPORTANCE The mechanism that regulates the translocation step in ribosomes during protein synthesis is not fully understood. In this work, cryo-EM techniques used to image ribosomes from Staphylococcus aureus after incubation at physiological temperature allowed the identification of a conformation of the helix 68 that has never been observed so far. We then propose a mechanism in which such helix, switching between two different conformations, actively coordinates the translocation step, shedding light on the dynamics of ribosomal components. In addition, the relevance of helix 68 to ribosome function and its potential as an antibiotic target was proved by inhibiting Staphylococcus aureus ribosomes activity in vitro using oligomers with sequence complementarity.
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Affiliation(s)
- Giuseppe Cimicata
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Gil Fridkin
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
- Department of Organic Chemistry, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Tanaya Bose
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Zohar Eyal
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Yehuda Halfon
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Elinor Breiner-Goldstein
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Tara Fox
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Ella Zimmerman
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Anat Bashan
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Natalia de Val
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Alexander Wlodawer
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Ada Yonath
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
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18
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Shafi A, Bano S, Sharma L, Halder A, Sabir S, Khan MZ. Exploring multifunctional behaviour of g-C 3N 4 decorated BiVO 4/Ag 2CO 3 hierarchical nanocomposite for simultaneous electrochemical detection of two nitroaromatic compounds and water splitting applications. Talanta 2022; 241:123257. [PMID: 35114490 DOI: 10.1016/j.talanta.2022.123257] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 12/13/2021] [Accepted: 01/20/2022] [Indexed: 02/09/2023]
Abstract
Development of multifunctional ternary nanocomposite based electrocatalysts for detection of toxic elements and generation of renewable energy describes an environmentally sustainable technique to address the dual challenges of pollution and energy. Herein, we adopted microwave-assisted synthesis to design a multifunctional graphitic carbon nitride (g-C3N4) decorated BiVO4/Ag2CO3 (BVG@C) hierarchical ternary nanocomposite for sensing and water splitting applications. The morphological, structural and elemental characterizations demonstrate the successful decoration of carbon nitride on the composite surface. The electrochemical activity of BVG@C modified glassy carbon electrode reveals excellent redox behaviour towards simultaneous detection of 4-Nitrophenol (4-NP) and 4-Nitroaniline (PNA). The modified electrode shows rapid amperometric current response with high sensitivity of 2.368 μA mM cm-2 and 1.534 mA mM cm-2 and low detection limit of 0.012 μmol L-1and 0.028 μmol L-1, respectively for 4-NP and PNA. Moreover, the modified electrode was further investigated for hydrogen evolution and oxygen evolution reactions and the electrocatalytic results show admirable activity and good stability for oxygen evolution with very low overpotential of 136 mV in alkaline medium. It is worthwhile to mention that the excellent activity of electrocatalyst can be ascribed to the decoration and electronic interaction of g-C3N4 with the BiVO4/Ag2CO3 nanocomposite, increasing its surface area, active sites, charge transfer and decreasing resistance.
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Affiliation(s)
- Adil Shafi
- Environmental Research Laboratory, Department of Chemistry, Aligarh Muslim University, Aligarh, 202002, India
| | - Sayfa Bano
- Environmental Research Laboratory, Department of Chemistry, Aligarh Muslim University, Aligarh, 202002, India
| | - Lalita Sharma
- School of Basic Sciences, Indian Institute of Technology, Mandi, 175005, India
| | - Aditi Halder
- School of Basic Sciences, Indian Institute of Technology, Mandi, 175005, India
| | - Suhail Sabir
- Environmental Research Laboratory, Department of Chemistry, Aligarh Muslim University, Aligarh, 202002, India
| | - Mohammad Zain Khan
- Environmental Research Laboratory, Department of Chemistry, Aligarh Muslim University, Aligarh, 202002, India.
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19
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Farrera-Soler L, Gonse A, Kim KT, Barluenga S, Winssinger N. Combining recombinase polymerase amplification and DNA-templated reaction for SARS-CoV-2 sensing with dual fluorescence and lateral flow assay output. Biopolymers 2022; 113:e23485. [PMID: 35023571 PMCID: PMC9011641 DOI: 10.1002/bip.23485] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 12/17/2021] [Accepted: 12/20/2021] [Indexed: 12/17/2022]
Abstract
The early phase of the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) pandemic was exacerbated by a diagnostic challenge of unprecedented magnitude. In the absence of effective therapeutics or vaccines, breaking the chain of transmission through early disease detection and patient isolation was the only means to control the growing pandemic. While polymerase chain reaction (PCR)‐based methods and rapid‐antigen tests rose to the occasion, the analytical challenge of rapid and sequence‐specific nucleic acid‐sensing at a point‐of‐care or home setting stimulated intense developments. Herein we report a method that combines recombinase polymerase amplification and a DNA‐templated reaction to achieve a dual readout with either fluorescence (microtiter plate) or naked eye (lateral flow assay: LFA) detection. The nucleic acid templated reaction is based on an SNAr that simultaneously transfers biotin from one Peptide Nucleic Acid (PNA) strand to another PNA strand, enabling LFA detection while uncaging a coumarin for fluorescence readout. This methodology has been applied to the detection of a DNA or RNA sequence uniquely attributed to the SARS‐CoV‐2.
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Affiliation(s)
- Lluc Farrera-Soler
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Arthur Gonse
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Ki Tae Kim
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Sofia Barluenga
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
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20
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Zhan X, Deng L, Chen G. Mechanisms and applications of peptide nucleic acids selectively binding to double-stranded RNA. Biopolymers 2021; 113:e23476. [PMID: 34581432 DOI: 10.1002/bip.23476] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 12/11/2022]
Abstract
RNAs form secondary structures containing double-stranded base paired regions and single-stranded regions. Probing, detecting and modulating RNA structures and dynamics requires the development of molecular sensors that can differentiate the sequence and structure of RNAs present in viruses and cells, as well as in extracellular space. In this review, we summarize the recent progress on the development of chemically modified peptide nucleic acids (PNAs) for the selective recognition of double-stranded RNA (dsRNA) sequences over both single-stranded RNA (ssRNA) and double-stranded DNA (dsDNA) sequences. We also briefly discuss the applications of sequence-specific dsRNA-binding PNAs in sensing and stabilizing dsRNA structures and inhibiting dsRNA-protein interactions.
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Affiliation(s)
- Xuan Zhan
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, China
| | - Liping Deng
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, China
| | - Gang Chen
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, China
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21
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Xiang Z, Zhao J, Yi D, Di Z, Li L. PNA-Guided Peptide Engineering of Aptamer Sensor for Protease-Unlocked Molecular Imaging. Angew Chem Int Ed Engl 2021; 60:22659-22663. [PMID: 34355486 DOI: 10.1002/anie.202106639] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/22/2021] [Indexed: 11/11/2022]
Abstract
Protease-triggered control of functional DNA has remained unachieved, leaving a significant gap in activatable DNA biotechnology. Here we disclose the design of a protease-activatable aptamer technology that can perform molecular sensing and imaging function in a tumor-specific manner. The system is constructed by locking structure-switching activity of aptamer using a rationally designed PNA-peptide-PNA triblock copolymer. Highly selective cleavage of the peptide substrate is achieved by protease-mediated enzymatic reaction that result in reduced binding affinity of PNA to the aptamer module, with the subsequently recovering its biosensing function. We demonstrated that the DNA/peptide/PNA hybrid system not only allows for tumor cell-selective ATP imaging in vitro , but it also produce a fluorescent signal in vivo with improved tumor specificity. This work illustrates the potential of bridging the gap between functional DNA field and peptide area for precise biomedical applications.
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Affiliation(s)
- Zhichu Xiang
- NCNST: National Center for Nanoscience and Technology, the CAS key lab, CHINA
| | - Jian Zhao
- NCNST: National Center for Nanoscience and Technology, the CAS key lab, CHINA
| | - Deyu Yi
- NCNST: National Center for Nanoscience and Technology, the CAS key lab, CHINA
| | - Zhenghan Di
- NCNST: National Center for Nanoscience and Technology, the CAS key lab, CHINA
| | - Lele Li
- National Center for Nanoscience and Technology, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, 11 ZhongGuanCun BeiYiTiao, Haidian District, 100190, Beijing, CHINA
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22
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Cai L, He S, Zheng X, Li J, Wang H, Liu Y, Zhang L. Research on preparation and in vitro evaluation of the dendrimer-peptide nuclear acid conjugate for amplification pretargeting. J Labelled Comp Radiopharm 2021; 64:428-439. [PMID: 34330148 DOI: 10.1002/jlcr.3937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 07/07/2021] [Accepted: 07/20/2021] [Indexed: 11/07/2022]
Abstract
Amplification pretargeting has the potential to increase the tracer's accumulation in the tumor. This study aimed to develop a three-step amplification pretargeting strategy in nuclear medicine with a polymer conjugated with multiple copies of peptide nuclear acid (PNA). In this study, the tracer 18 F-labeled complementary PNA (18 F-cPNA) was prepared by click-chemistry with high radiochemical purity (>99%) and great stability in vitro. The PAMMA dendrimer generation 4 (G4) was conjugated with multiple copies of PNAs. The average number of PNA groups in the G4-PNA conjugate was determined by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and the accessibility to the 18 F-cPNA was identified by size-exclusion high-performance liquid chromatography (SE-HPLC). There were approximately 11.7 of 64 carboxyl groups modified with PNAs, of which more than 99% were accessible to 18 F-cPNA. 18 F-cPNA was added to a mixture of CC49-cPNA and G4-PNA, and the complex exhibited a single peak on high-performance liquid chromatography (HPLC) as evidence of complete hybridization between 18 F-cPNA and CC49-cPNA/G4-PNA. The LS174T tumor cells were incubated with CC49-cPNA followed by G4-PNA as an amplification platform before 18 F-cPNA was added to hybridize with CC49-cPNA/G4-PNA. Compared with conventional pretargeting without G4-PNA, the radioactivity signal was amplified about four times, which demonstrated that the dendrimer-PNA conjugate plays a crucial role in signal amplification.
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Affiliation(s)
- Le Cai
- Radiopharmaceuticals Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
- Shanghai Institute of Applied Physics, University of Chinese Academy of Sciences, Beijing, China
| | - Shuhua He
- Radiopharmaceuticals Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
- Shanghai Institute of Applied Physics, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaobei Zheng
- Radiopharmaceuticals Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
- Shanghai Institute of Applied Physics, University of Chinese Academy of Sciences, Beijing, China
| | - Jie Li
- Radiopharmaceuticals Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
- Shanghai Institute of Applied Physics, University of Chinese Academy of Sciences, Beijing, China
| | - Hong Wang
- Radiopharmaceuticals Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
- Shanghai Institute of Applied Physics, University of Chinese Academy of Sciences, Beijing, China
| | - Yuxia Liu
- Radiopharmaceuticals Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
| | - Lan Zhang
- Radiopharmaceuticals Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
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Brodyagin N, Katkevics M, Kotikam V, Ryan CA, Rozners E. Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications. Beilstein J Org Chem 2021; 17:1641-1688. [PMID: 34367346 PMCID: PMC8313981 DOI: 10.3762/bjoc.17.116] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/28/2021] [Indexed: 12/23/2022] Open
Abstract
Peptide nucleic acid (PNA) is arguably one of the most successful DNA mimics, despite a most dramatic departure from the native structure of DNA. The present review summarizes 30 years of research on PNA's chemistry, optimization of structure and function, applications as probes and diagnostics, and attempts to develop new PNA therapeutics. The discussion starts with a brief review of PNA's binding modes and structural features, followed by the most impactful chemical modifications, PNA enabled assays and diagnostics, and discussion of the current state of development of PNA therapeutics. While many modifications have improved on PNA's binding affinity and specificity, solubility and other biophysical properties, the original PNA is still most frequently used in diagnostic and other in vitro applications. Development of therapeutics and other in vivo applications of PNA has notably lagged behind and is still limited by insufficient bioavailability and difficulties with tissue specific delivery. Relatively high doses are required to overcome poor cellular uptake and endosomal entrapment, which increases the risk of toxicity. These limitations remain unsolved problems waiting for innovative chemistry and biology to unlock the full potential of PNA in biomedical applications.
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Affiliation(s)
- Nikita Brodyagin
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Martins Katkevics
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV-1006, Latvia
| | - Venubabu Kotikam
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Christopher A Ryan
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
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24
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Wu Y, Chanclón B, Micallef P, Stener-Victorin E, Wernstedt Asterholm I, Benrick A. Maternal adiponectin prevents visceral adiposity and adipocyte hypertrophy in prenatal androgenized female mice. FASEB J 2021; 35:e21299. [PMID: 33715227 DOI: 10.1096/fj.202002212r] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/26/2020] [Accepted: 12/07/2020] [Indexed: 01/17/2023]
Abstract
Hyperandrogenism is the main characteristic of polycystic ovary syndrome, which affects placental function and fetal growth, and leads to reproductive and metabolic dysfunction in female offspring. Adiponectin acts on the placenta and may exert endocrine effects on the developing fetus. This study aims to investigate if maternal and/or fetal adiponectin can prevent metabolic and reproductive dysfunction in prenatal androgenized (PNA) female offspring. Adiponectin transgenic (APNtg) and wild-type dams received dihydrotestosterone/vehicle injections between gestational days 16.5-18.5 to induce PNA offspring, which were followed for 4 months. Offspring from APNtg dams were smaller than offspring from wild-type dams, independent of genotype. Insulin sensitivity was higher in wild-type mice from APNtg dams compared to wild-types from wild-type dams, and insulin sensitivity correlated with fat mass and adipocyte size. PNA increased visceral fat% and adipocyte size in wild-type offspring from wild-type dams, while wild-type and APNtg offspring from APNtg dams were protected against this effect. APNtg mice had smaller adipocytes than wild-types and this morphology was associated with an increased expression of genes regulating adipogenesis (Ppard, Pparg, Cebpa, and Cebpb) and metabolism (Chrebp and Lpl). Anogenital distance was increased in all PNA-exposed wild-type offspring, but there was no increase in PNA APNtg offspring, suggesting that adiponectin overexpression protects against this effect. In conclusion, elevated adiponectin levels in utero improve insulin sensitivity, reduce body weight and fat mass gain in the adult offspring and protect against PNA-induced visceral adiposity. In conclusion, these data suggest that PNA offspring benefit from prenatal adiponectin supplementation.
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Affiliation(s)
- Yanling Wu
- Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Belén Chanclón
- Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Peter Micallef
- Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | | | - Ingrid Wernstedt Asterholm
- Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anna Benrick
- Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,School of Health Sciences, University of Skövde, Skövde, Sweden
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25
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Paillassa J, Troussard X. Patients with relapsed/refractory hairy-cell leukemia. Cancer Rep (Hoboken) 2021; 5:e1495. [PMID: 34250762 PMCID: PMC8955050 DOI: 10.1002/cnr2.1495] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/26/2021] [Accepted: 06/17/2021] [Indexed: 01/17/2023] Open
Abstract
Background Hairy cell leukemia (HCL) is a rare chronic B‐cell neoplasm with good long‐term prognosis. First and second‐line therapies include purine nucleoside analogues (PNAs) and rituximab, but until recently, limited alternative options were available for patients with two or more relapses. Aim The aim of this study is to describe our real‐life experience with HCL patients in third and fourth‐line therapies. Methods and Results Data from 49 HCL patients with two or more relapses, including 16 patients with three or more relapses, were collected from the French retrospective HCL cohort covering the period from 1980 until 2011. They were analyzed to assess hematological response, relapse free survival (RFS) and overall survival (OS) after third (L3) and fourth line (L4). The median age at diagnosis was 53 years. PNAs were the most frequently used treatments. As L3 therapy, 29 patients received PNAs (66%) and 15 (34%) other treatments (rituximab [11%] or interferon [7%] alone or in combination [16%]). The distribution of L4 treatments was similar. The overall hematological response rate (OHRR) after L3 was 97% (complete hematological response 86%) with a 40% five‐year cumulative incidence of relapse (CIR), a median RFS of 104 months, and a median OS of 235 months. After L4, the OHRR was 94% with a two‐year CIR of fourth relapse of 27%. Eleven secondary cancers (5‐year cumulative incidence of 12%) were diagnosed in 10 patients. Patients with ≥2 relapses experience frequent further relapses, with increasingly shorter time to next treatment as the number of treatment lines increases. Furthermore, treatment strategies are associated with substantial toxicities. Conclusion All these points lead to the need for novel treatments.
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Affiliation(s)
- Jérôme Paillassa
- Department of Hematology, Academic Hospital of Angers, Angers, France
| | - Xavier Troussard
- Laboratory of Hematology, Academic Hospital of Caen, Caen, France
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26
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Ditmangklo B, Sittiwong W, Boddaert T, Vilaivan T, Aitken DJ. Pyrrolidinyl peptide nucleic acids bearing hydroxy-modified cyclobutane building blocks: Synthesis and binding properties. Biopolymers 2021; 112:e23459. [PMID: 34101824 DOI: 10.1002/bip.23459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/25/2021] [Accepted: 05/27/2021] [Indexed: 12/19/2022]
Abstract
The conformationally constrained pyrrolidinyl PNA with a dipeptide consisting of an alternating nucleobase-modified D-proline and a cyclic β-amino acid "spacer" exhibited improved nucleic acid binding properties compared to the original PNA. The pyrrolidinyl PNA with the four-membered ring spacer (1S,2S)-2-aminocyclobutanecarboxylic acid (acbcPNA) are among the best performed members of the pyrrolidinyl PNA family. However, these PNA suffer some limitations such as aqueous solubility and non-specific interactions due to their extreme hydrophobicity. In the present work, a hydroxy group is introduced onto the cyclobutane ring spacer of the acbcPNA with the aim of decreasing its hydrophobicity. To this end, a Fmoc/tBu ether-protected 4-hydroxy-2-aminocyclobutanecarboxylic acid building block was synthesized and resolved by chiral HPLC. Each enantiomer was used to synthesize the hydroxy-modified acbcPNA employing Fmoc solid-phase peptide synthesis. DNA/RNA binding studies indicated that the introduction of the hydroxy group to the acbcPNA decreases the binding affinity toward complementary DNA and RNA while maintaining the sequence and directional specificity of unmodified acbcPNA. The hydrophobicity of the hydroxy-modified acbcPNA decreased with the number of hydroxy groups added as indicated by the decrease in the logP values. Only two modifications were sufficient to decrease the logP by an order of magnitude without excessively lowering the binding affinity nor the specificity. This work thus demonstrated that the specific structural modifications for this type of PNA model can be performed in a modular fashion, which paves the way toward the future realization of improving hydrophilicity and nucleic acid binding affinity as well as specificity.
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Affiliation(s)
- Boonsong Ditmangklo
- Department of Chemistry, Faculty of Science, Organic Synthesis Research Unit, Chulalongkorn University, Bangkok, Thailand
| | - Wantanee Sittiwong
- Department of Chemistry, Faculty of Science and Technology, Thammasat University, Rangsit Campus, Pathum Thani, Thailand
| | | | - Tirayut Vilaivan
- Department of Chemistry, Faculty of Science, Organic Synthesis Research Unit, Chulalongkorn University, Bangkok, Thailand
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Green CM, Hastman DA, Mathur D, Susumu K, Oh E, Medintz IL, Díaz SA. Direct and Efficient Conjugation of Quantum Dots to DNA Nanostructures with Peptide- PNA. ACS Nano 2021; 15:9101-9110. [PMID: 33955735 DOI: 10.1021/acsnano.1c02296] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
DNA nanotechnology has proven to be a powerful strategy for the bottom-up preparation of colloidal nanoparticle (NP) superstructures, enabling the coordination of multiple NPs with orientation and separation approaching nanometer precision. To do this, NPs are often conjugated with chemically modified, single-stranded (ss) DNA that can recognize complementary ssDNA on the DNA nanostructure. The limitation is that many NPs cannot be easily conjugated with ssDNA, and other conjugation strategies are expensive, inefficient, or reduce the specificity and/or precision with which NPs can be placed. As an alternative, the conjugation of nanoparticle-binding peptides and peptide nucleic acids (PNA) can produce peptide-PNA with distinct NP-binding and DNA-binding domains. Here, we demonstrate a simple application of this method to conjugate semiconductor quantum dots (QDs) directly to DNA nanostructures by means of a peptide-PNA with a six-histidine peptide motif that binds to the QD surface. With this method, we achieved greater than 90% capture efficiency for multiple QDs on a single DNA nanostructure while preserving both site specificity and precise spatial control of QD placement. Additionally, we investigated the effects of peptide-PNA charge on the efficacy of QD immobilization in suboptimal conditions. The results validate peptide-PNA as a viable alternative to ssDNA conjugation of NPs and warrant studies of other NP-binding peptides for peptide-PNA conjugation.
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Affiliation(s)
- Christopher M Green
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory Code 6900, Washington, DC 20375, United States
- National Research Council, 500 Fifth St NW, Washington, DC 20001, United States
| | - David A Hastman
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory Code 6900, Washington, DC 20375, United States
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
| | - Divita Mathur
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory Code 6900, Washington, DC 20375, United States
- College of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Kimihiro Susumu
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, Washington, DC 20375, United States
- Jacobs Corporation, Hanover, Maryland 21076, United States
| | - Eunkeu Oh
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, Washington, DC 20375, United States
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory Code 6900, Washington, DC 20375, United States
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory Code 6900, Washington, DC 20375, United States
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28
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Linden G, Janga H, Franz M, Nist A, Stiewe T, Schmeck B, Vázquez O, Schulte LN. Efficient antisense inhibition reveals microRNA-155 to restrain a late-myeloid inflammatory programme in primary human phagocytes. RNA Biol 2021; 18:604-618. [PMID: 33622174 PMCID: PMC8078538 DOI: 10.1080/15476286.2021.1885209] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/26/2021] [Accepted: 01/30/2021] [Indexed: 01/05/2023] Open
Abstract
A persisting obstacle in human immunology is that blood-derived leukocytes are notoriously difficult to manipulate at the RNA level. Therefore, our knowledge about immune-regulatory RNA-networks is largely based on tumour cell-line and rodent knockout models, which do not fully mimic human leukocyte biology. Here, we exploit straightforward cell penetrating peptide (CPP) chemistry to enable efficient loss-of-function phenotyping of regulatory RNAs in primary human blood-derived cells. The classical CPP octaarginine (R8) enabled antisense peptide-nucleic-acid (PNA) oligomer delivery into nearly 100% of human blood-derived macrophages without apparent cytotoxicity even up to micromolar concentrations. In a proof-of-principle experiment, we successfully de-repressed the global microRNA-155 regulome in primary human macrophages using a PNA-R8 oligomer, which phenocopies a CRISPR-Cas9 induced gene knockout. Interestingly, although it is often believed that fairly high concentrations (μM) are needed to achieve antisense activity, our PNA-R8 was effective at 200 nM. RNA-seq characterized microRNA-155 as a broad-acting riboregulator, feedback restraining a late myeloid differentiation-induced pro-inflammatory network, comprising MyD88-signalling and ubiquitin-proteasome components. Our results highlight the important role of the microRNA machinery in fine-control of blood-derived human phagocyte immunity and open the door for further studies on regulatory RNAs in difficult-to-transfect primary human immune cells.
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Affiliation(s)
- Greta Linden
- Department of Chemistry, Philipps University Marburg, Marburg, Germany
| | - Harshavardhan Janga
- Department of Medicine, Institute for Lung Research, Philipps University Marburg, Marburg, Germany
| | - Matthias Franz
- Department of Chemistry, Philipps University Marburg, Marburg, Germany
| | - Andrea Nist
- Genomics Core Facility, Philipps University Marburg, Marburg, Germany
| | - Thorsten Stiewe
- Genomics Core Facility, Philipps University Marburg, Marburg, Germany
- Department of Medicine, Institute of Molecular Oncology, Philipps University Marburg, Marburg, Germany
- German Center for Lung Research (DZL), Marburg, Germany
| | - Bernd Schmeck
- Department of Medicine, Institute for Lung Research, Philipps University Marburg, Marburg, Germany
- German Center for Lung Research (DZL), Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Marburg, Germany
- German Center for Infection Research (DZIF), Marburg, Germany
| | - Olalla Vázquez
- Department of Chemistry, Philipps University Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Marburg, Germany
| | - Leon N Schulte
- Department of Medicine, Institute for Lung Research, Philipps University Marburg, Marburg, Germany
- German Center for Lung Research (DZL), Marburg, Germany
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Abstract
Traditionally, RNA and DNA probes are used in fluorescence in situ hybridization (FISH) methods for microbial detection and characterization of communities' structure and diversity. However, the recent introduction of nucleic acid mimics (NAMs) has improved the robustness of the FISH methods in terms of sensitivity and specificity. Several NAMs have been used, of which the most relevant are peptide nucleic acid (PNA), locked nucleic acids (LNA), 2'-O-methyl RNA (2'OMe), and phosphorothioates (PS). In this chapter, we describe a protocol using PNA and LNA/2'OMe probes for microbial detection by FISH, pointing out the differences between them. These protocols are easily adapted to different microorganisms and different probe sequences.
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Affiliation(s)
- Ricardo Oliveira
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal.,INIAV - National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, Lugar da Madalena, Vairão, Vila do Conde, Portugal
| | - Andreia S Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal.,i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, University of Porto, Porto, Portugal.,CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Luzia Mendes
- FMDUP - Faculty of Dental Medicine, University of Porto, Porto, Portugal.
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30
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Tano H, Oroujeni M, Vorobyeva A, Westerlund K, Liu Y, Xu T, Vasconcelos D, Orlova A, Karlström AE, Tolmachev V. Comparative Evaluation of Novel 177Lu-Labeled PNA Probes for Affibody-Mediated PNA-Based Pretargeting. Cancers (Basel) 2021; 13:cancers13030500. [PMID: 33525578 PMCID: PMC7865858 DOI: 10.3390/cancers13030500] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/21/2021] [Accepted: 01/25/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Affibody molecules are small, engineered affinity proteins based on a nonimmunoglobulin scaffold. Affibody-based radionuclide imaging probes have demonstrated excellent tumor targeting. However, the renal clearance of affibody molecules is accompanied by high reabsorption and retention of activity in the kidney, which prevents their use for radionuclide therapy. We have previously shown the feasibility of overcoming the high renal uptake using a pretargeting approach for affibody-mediated therapy based on peptide nucleic acid (PNA) hybridization. In this study, we test the hypothesis that shortening the PNA pretargeting probes would further increase the difference between the accumulation of radiometals in tumor xenografts and in kidneys. A series of novel PNA probes has been designed and evaluated in vitro and in vivo. We have found that a variant containing 9 nucleobases enables a two-fold increase of the tumor-to-kidney dose ratio compared with a variant containing 15 nucleobases. This creates preconditions for more efficient therapy of cancer. Abstract Affibody-mediated PNA-based pretargeting is a promising approach to radionuclide therapy of HER2-expressing tumors. In this study, we test the hypothesis that shortening the PNA pretargeting probes would increase the tumor-to-kidney dose ratio. The primary probe ZHER2:342-SR-HP15 and the complementary secondary probes HP16, HP17, and HP18, containing 9, 12, and 15 nucleobases, respectively, and carrying a 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) chelator were designed, synthesized, characterized in vitro, and labeled with 177Lu. In vitro pretargeting was studied in HER2-expressing SKOV3 and BT474 cell lines. The biodistribution of these novel probes was evaluated in immunodeficient mice bearing SKOV3 xenografts and compared to the previously studied [177Lu]Lu-HP2. Characterization confirmed the formation of high-affinity duplexes between HP15 and the secondary probes, with the affinity correlating with the length of the complementary PNA sequences. All the PNA-based probes were bound specifically to HER2-expressing cells in vitro. In vivo studies demonstrated HER2-specific uptake of all 177Lu-labeled probes in xenografts in a pretargeting setting. The ratio of cumulated radioactivity in the tumor to the radioactivity in kidneys was dependent on the secondary probe’s size and decreased with an increased number of nucleobases. The shortest PNA probe, [177Lu]Lu-HP16, showed the highest tumor-to-kidney ratio. [177Lu]Lu-HP16 is the most promising secondary probe for affibody-mediated tumor pretargeting.
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Affiliation(s)
- Hanna Tano
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 106 91 Stockholm, Sweden; (H.T.); (K.W.); (D.V.)
| | - Maryam Oroujeni
- Department of Immunology, Genetics and Pathology, Dag Hammarskjölds väg 20, Uppsala University, 751 85 Uppsala, Sweden; (M.O.); (A.V.); (Y.L.); (T.X.); (V.T.)
| | - Anzhelika Vorobyeva
- Department of Immunology, Genetics and Pathology, Dag Hammarskjölds väg 20, Uppsala University, 751 85 Uppsala, Sweden; (M.O.); (A.V.); (Y.L.); (T.X.); (V.T.)
- Research Centrum for Oncotheranostics, Research School of Chemistry and Applied Biomedical Sciences, Tomsk Polytechnic University, 634050 Tomsk, Russia;
| | - Kristina Westerlund
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 106 91 Stockholm, Sweden; (H.T.); (K.W.); (D.V.)
| | - Yongsheng Liu
- Department of Immunology, Genetics and Pathology, Dag Hammarskjölds väg 20, Uppsala University, 751 85 Uppsala, Sweden; (M.O.); (A.V.); (Y.L.); (T.X.); (V.T.)
| | - Tianqi Xu
- Department of Immunology, Genetics and Pathology, Dag Hammarskjölds väg 20, Uppsala University, 751 85 Uppsala, Sweden; (M.O.); (A.V.); (Y.L.); (T.X.); (V.T.)
| | - Daniel Vasconcelos
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 106 91 Stockholm, Sweden; (H.T.); (K.W.); (D.V.)
| | - Anna Orlova
- Research Centrum for Oncotheranostics, Research School of Chemistry and Applied Biomedical Sciences, Tomsk Polytechnic University, 634050 Tomsk, Russia;
- Department of Medicinal Chemistry, Dag Hammarskjölds väg 14C, Uppsala University, 751 23 Uppsala, Sweden
| | - Amelie Eriksson Karlström
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 106 91 Stockholm, Sweden; (H.T.); (K.W.); (D.V.)
- Correspondence:
| | - Vladimir Tolmachev
- Department of Immunology, Genetics and Pathology, Dag Hammarskjölds väg 20, Uppsala University, 751 85 Uppsala, Sweden; (M.O.); (A.V.); (Y.L.); (T.X.); (V.T.)
- Research Centrum for Oncotheranostics, Research School of Chemistry and Applied Biomedical Sciences, Tomsk Polytechnic University, 634050 Tomsk, Russia;
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Altai M, Vorobyeva A, Tolmachev V, Karlström AE, Westerlund K. Preparation of Conjugates for Affibody-Based PNA-Mediated Pretargeting. Methods Mol Biol 2020; 2105:283-304. [PMID: 32088878 DOI: 10.1007/978-1-0716-0243-0_18] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Affibody molecules are small engineered scaffold proteins suitable for in vivo tumor targeting. Radionuclide molecular imaging using directly radiolabelled affibody molecules provides excellent imaging. However, affibody molecules have a high renal reabsorption, which complicates their use for radionuclide therapy. The high renal reabsorption is a common problem for the use of engineered scaffold proteins for radionuclide therapy. Affibody-based PNA-mediated pretargeting reduces dramatically the absorbed dose to the kidneys and makes affibody-based radionuclide therapy possible. This methodology might, hopefully, solve the problem of high renal reabsorption for radionuclide therapy mediated by other engineered scaffold proteins.
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Abstract
Duchenne muscular dystrophy (DMD) is the most common and severe form of muscular dystrophy and is caused by gene mutations that abolish production of functional dystrophin muscle protein. A promising new treatment exploits specifically targeted RNA-acting drugs that are able to partially restore the dystrophin protein. The mdx mouse model (animal model of DMD) serves as a good in vivo model for testing these antisense drugs. The simplest in vivo test, which circumvents the systemic circulation, is intramuscular administration of the compound. After 7 days it is possible to detect exon skipping by reverse transcriptase PCR, and newly synthesized dystrophin-positive fibers by immunohistochemistry and western blotting. All muscles, including the heart, are affected by the disease and must be treated. Therefore the use of antisense therapy for treatment of DMD requires systemic administration, and the model is also useful for systemic administration.
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Affiliation(s)
- Camilla Brolin
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Ernest Wee Kiat Lim
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peter E Nielsen
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Oliveira R, Almeida C, Azevedo NF. Detection of Microorganisms by Fluorescence In Situ Hybridization Using Peptide Nucleic Acid. Methods Mol Biol 2021; 2105:217-230. [PMID: 32088873 DOI: 10.1007/978-1-0716-0243-0_13] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Fluorescence in situ hybridization (FISH) is a 30-year-old technology that has evolved continuously and is now one of the most well-established molecular biology techniques. Traditionally, DNA probes are used for in situ hybridization. However, synthetic molecules are emerging as very promising alternatives, providing better hybridization performance and making FISH procedures easier and more efficient. In this chapter, we describe a universal FISH protocol, using nucleic acid probes, for the detection of bacteria. This protocol should be easily applied to different microorganisms as a way of identifying in situ relevant microorganisms (including pathogens) and their distribution patterns in different types of samples.
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Affiliation(s)
- Ricardo Oliveira
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal.,INIAV - National Institute for Agrarian and Veterinarian Research, Vairao, Portugal
| | - Carina Almeida
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal.,INIAV - National Institute for Agrarian and Veterinarian Research, Vairao, Portugal.,CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Nuno F Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal.
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Möllers PV, Ulku S, Jayarathna D, Tassinari F, Nürenberg D, Naaman R, Achim C, Zacharias H. Spin-selective electron transmission through self-assembled monolayers of double-stranded peptide nucleic acid. Chirality 2021; 33:93-102. [PMID: 33400337 DOI: 10.1002/chir.23290] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/06/2020] [Accepted: 12/01/2020] [Indexed: 12/19/2022]
Abstract
Monolayers of chiral molecules can preferentially transmit electrons with a specific spin orientation, introducing chiral molecules as efficient spin filters. This phenomenon is established as chirality-induced spin selectivity (CISS) and was demonstrated directly for the first time in self-assembled monolayers (SAMs) of double-stranded DNA (dsDNA)1 . Here, we discuss SAMs of double-stranded peptide nucleic acid (dsPNA) as a system which allows for systematic investigations of the influence of various molecular properties on CISS. In photoemission studies, SAMs of chiral, γ-modified PNA show significant spin filtering of up to P = (24.4 ± 4.3)% spin polarization. The polarization values found in PNA lacking chiral monomers are considerably lower at about P = 12%. The results confirm that the preferred spin orientation is directly linked to the molecular handedness and indicate that the spin filtering capacity of the dsPNA helices might be enhanced by introduction of chiral centers in the constituting peptide monomers.
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Affiliation(s)
- Paul Valerian Möllers
- Center for Soft Nanoscience (SoN), Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Selma Ulku
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Dilhara Jayarathna
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Francesco Tassinari
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Daniel Nürenberg
- Center for Soft Nanoscience (SoN), Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Ron Naaman
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Catalina Achim
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Helmut Zacharias
- Center for Soft Nanoscience (SoN), Westfälische Wilhelms-Universität Münster, Münster, Germany
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Abstract
Vitamin B12 (cobalamin, Cbl) is an essential nutrient for all mammals and some bacteria. From a chemical point of view, it is a highly functionalized molecule, which enables conjugation at multiple positions and attachment of various cargoes. Both mammalian and bacterial cells have developed a specific transport pathway for the uptake of vitamin B12, and as a consequence, cobalamin is an attractive candidate for the delivery of biologically relevant molecules into cells. Indeed, hybrid molecules containing vitamin B12 in their structure have found various applications in medicinal chemistry, diagnostics, and biological sciences.Herein, we describe synthetic strategies toward the synthesis of vitamin B12 conjugates with peptide nucleic acid (PNA ) oligomers. Such short-modified oligonucleotides targeted at bacterial DNA or RNA can act as antibacterial agents if efficiently taken up by bacterial cells. The uptake of such oligonucleotides is hindered by the bacterial cell envelope, but vitamin B12 was found to efficiently deliver antisense PNA into Escherichia coli and Salmonella Typhimurium cells. This paves the way to the use of vitamin B12-PNA conjugates in antibacterial and diagnostic applications.Vitamin B12-PNA conjugates can be prepared via copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) that gives access to covalently linked hybrids or via connecting both building blocks by reduction-sensitive disulfide bridge. Both approaches require prior modification of vitamin B12 by incorporation of the azide moiety or via transformation of the native functional group into a moiety reactive toward thiols. Conjugation of vitamin B12 with PNA-tagged substrates efficiently furnishes designed conjugates.
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Affiliation(s)
| | | | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Dorota Gryko
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland.
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Allkja J, Azevedo AS. Characterization of Social Interactions and Spatial Arrangement of Individual Bacteria in MultiStrain or Multispecies Biofilm Systems Using Nucleic Acid Mimics-Fluorescence In Situ Hybridization. Methods Mol Biol 2021; 2246:97-109. [PMID: 33576985 DOI: 10.1007/978-1-0716-1115-9_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Biofilms are often composed of different bacterial and fungal species/strains, which form complex structures based on social interactions with each other. Fluorescence in situ hybridization (FISH) can help us identify the different species/strains present within a biofilm , and when coupled with confocal scanning laser microscopy (CSLM), it enables the visualization of the three-dimensional (3D) structure of the biofilm and the spatial arrangement of each individual species/strain within it. In this chapter, we describe the protocol for characterizing multistrain or multispecies biofilm formation using NAM-FISH and CSLM.
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Affiliation(s)
- Jontana Allkja
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Andreia S Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal.
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.
- IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, University of Porto, Porto, Portugal.
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal.
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Abstract
Fluorescence in situ hybridization (FISH) is a well-established technique that allows the detection of microorganisms in diverse types of samples (e.g., clinical, food, environmental samples, and biofilm communities). The FISH probe design is an essential step in this technique. For this, two strategies can be used, the manual form based on multiple sequence alignment to identify conserved regions and programs/software specifically developed for the selection of the sequence of the probe. Additionally, databases/software for the theoretical evaluation of the probes in terms of specificity, sensitivity, and thermodynamic parameters (melting temperature and Gibbs free energy change) are used. The purpose of this chapter is to describe the essential steps and guidelines for the design of FISH probes (e.g., DNA and Nucleic Acid Mimic (NAM) probes), and its theoretical evaluation through the application of diverse bioinformatic tools.
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Affiliation(s)
- Helena Teixeira
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Ana L Sousa
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal.,INIAV - National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, Lugar da Madalena, Vairão, Vila do Conde, Portugal
| | - Andreia S Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal. .,i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal. .,IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal. .,CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal.
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Moccia M, Mercurio FA, Langella E, Piacenti V, Leone M, Adamo MFA, Saviano M. Structural Insights on Tiny Peptide Nucleic Acid ( PNA) Analogues of miRNA-34a: An in silico and Experimental Integrated Approach. Front Chem 2020; 8:568575. [PMID: 33330358 PMCID: PMC7719796 DOI: 10.3389/fchem.2020.568575] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 11/02/2020] [Indexed: 11/17/2022] Open
Abstract
In the present work, structural features of the interaction between peptide nucleic acid (PNA)-based analogs of the tumor-suppressor microRNA-34a with both its binding sites on MYCN mRNA were investigated. In particular, the region from base 1 to 8 ("seed" region) of miR-34a was reproduced in the form of an 8-mer PNA fragment (tiny PNA), and binding to target 3'UTR MYCN mRNA, was studied by a seldom reported and detailed NMR characterization, providing evidence for the formation of anti-parallel duplexes with a well-organized structural core. The formation of PNA-3'UTR duplexes was also confirmed by Circular Dichroism, and their melting curves were measured by UV spectroscopy. Nevertheless, this study offered a valuable comparison between molecular dynamics predictions and experimental evidence, which showed great correlation. Preliminary uptake assays were carried out in Neuroblastoma Kelly cells, using short peptide conjugates as carriers and FITC fluorescent tag for subcellular localization. Moderate internalization was observed without the use of transfecting agents. The reported results corroborate the interest toward the design and development of chimeric PNA/RNA sequences as effective RNA-targeting agents.
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Affiliation(s)
- Maria Moccia
- Institute of Crystallography, National Research Council, Department of Chemical Sciences and Materials Technologies, Bari, Italy
| | - Flavia Anna Mercurio
- Institute of Biostructures and Bioimaging, National Research Council, Naples, Italy
| | - Emma Langella
- Institute of Biostructures and Bioimaging, National Research Council, Naples, Italy
| | - Valerio Piacenti
- Royal College of Surgeons in Ireland, Department of Pharmaceutical and Medicinal Chemistry, Dublin, Ireland
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging, National Research Council, Naples, Italy
| | - Mauro F. A. Adamo
- Royal College of Surgeons in Ireland, Department of Pharmaceutical and Medicinal Chemistry, Dublin, Ireland
| | - Michele Saviano
- Institute of Crystallography, National Research Council, Department of Chemical Sciences and Materials Technologies, Bari, Italy
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Muangkaew P, Vilaivan T. Pyrrolidinyl Peptide Nucleic Acid Probes Capable of Crosslinking with DNA: Effects of Terminal and Internal Modifications on Crosslink Efficiency. Chembiochem 2020; 22:241-252. [PMID: 32889765 DOI: 10.1002/cbic.202000589] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/03/2020] [Indexed: 12/27/2022]
Abstract
In this study, we describe a furan-modified acpcPNA as a probe that can form an interstrand crosslink (ICL) with its DNA target upon activation with N-bromosuccinimide (NBS). To overcome the problem of furan instability under acidic conditions, a simple and versatile post-synthetic methodology for the attachment of the furan group to the PNA probe was developed. Unlike in other designs, the furan was placed at the end of the PNA molecule or tethered to the PNA backbone with all the base pairs in the PNA ⋅ DNA duplexes fully preserved. Hence, the true reactivity of each nucleobase towards the crosslinking could be compared. We show that all DNA bases except T could participate in the crosslinking reaction when the furan was placed at the end of the PNA strand. The crosslinking process was sensitive to mispairing, and lower crosslinking efficiency was observed in the presence of a base-mismatch in the PNA ⋅ DNA duplex. In contrast, when the furan was placed at internal positions of the acpcPNA ⋅ DNA duplex, no ICL was observed; this was explained by the inability of a hydrogen-bonded nucleobase to participate in the crosslinking reaction. The crosslinking efficiency was considerably improved, despite lower duplex stability, when an unpaired base (in the form of C-insertion) was present in the complementary DNA strand close to the furan modification site.
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Affiliation(s)
- Penthip Muangkaew
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok, 10330, Thailand
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok, 10330, Thailand
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40
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Choi WS, Jeong JH, Nicolas HDG, Oh S, Antigua KJC, Park JH, Kim B, Yoon SW, Shin KS, Choi YK, Baek YH, Song MS. Peptide Nucleic Acid ( PNA)-Enhanced Specificity of a Dual-Target Real-Time Quantitative Polymerase Chain Reaction (RT-qPCR) Assay for the Detection and Differentiation of SARS-CoV-2 from Related Viruses. Diagnostics (Basel) 2020; 10:diagnostics10100775. [PMID: 33007999 PMCID: PMC7601008 DOI: 10.3390/diagnostics10100775] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/24/2020] [Accepted: 09/29/2020] [Indexed: 12/02/2022] Open
Abstract
The threat posed by coronaviruses to human health has necessitated the development of a highly specific and sensitive viral detection method that could differentiate between the currently circulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other SARS-related coronaviruses (SARSr-CoVs). In this study, we developed a peptide nucleic acid (PNA)-based real-time quantitative polymerase chain reaction (RT-qPCR) assay targeting the N gene to efficiently discriminate SARS-CoV-2 from other SARSr-CoVs in human clinical samples. Without compromising the sensitivity, this method significantly enhanced the specificity of SARS-CoV-2 detection by 100-fold as compared to conventional RT-qPCR. In addition, we designed an RT-qPCR method for the sensitive and universal detection of ORF3ab-E genes of SARSr-CoV with a limit of detection (LOD) of 3.3 RNA copies per microliter. Thus, the developed assay serves as a confirmative dual-target detection method. Our PNA-mediated dual-target RT-qPCR assay can detect clinical SARS-CoV-2 samples in the range of 18.10–35.19 Ct values with an 82.6–100% detection rate. Furthermore, our assay showed no cross-reactions with other coronaviruses such as human coronaviruses (229E, NL63, and OC43) and Middle East respiratory syndrome coronavirus, influenza viruses (Type B, H1N1, H3N2, HPAI H5Nx, and H7N9), and other respiratory disease-causing viruses (MPV, RSV A, RSV B, PIV, AdV, and HRV). We, thus, developed a PNA-based RT-qPCR assay that differentiates emerging pathogens such as SARS-CoV-2 from closely related viruses such as SARSr-CoV and allows diagnosis of infections related to already identified or new coronavirus strains.
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Affiliation(s)
- Won-Suk Choi
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju 28644, Korea; (W.-S.C.); (J.H.J.); (H.D.G.N.); (S.O.); (K.J.C.A.); (J.-H.P.); (B.K.); (Y.K.C.)
| | - Ju Hwan Jeong
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju 28644, Korea; (W.-S.C.); (J.H.J.); (H.D.G.N.); (S.O.); (K.J.C.A.); (J.-H.P.); (B.K.); (Y.K.C.)
| | - Halcyon Dawn G. Nicolas
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju 28644, Korea; (W.-S.C.); (J.H.J.); (H.D.G.N.); (S.O.); (K.J.C.A.); (J.-H.P.); (B.K.); (Y.K.C.)
| | - Sol Oh
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju 28644, Korea; (W.-S.C.); (J.H.J.); (H.D.G.N.); (S.O.); (K.J.C.A.); (J.-H.P.); (B.K.); (Y.K.C.)
| | - Khristine Joy C. Antigua
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju 28644, Korea; (W.-S.C.); (J.H.J.); (H.D.G.N.); (S.O.); (K.J.C.A.); (J.-H.P.); (B.K.); (Y.K.C.)
| | - Ji-Hyun Park
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju 28644, Korea; (W.-S.C.); (J.H.J.); (H.D.G.N.); (S.O.); (K.J.C.A.); (J.-H.P.); (B.K.); (Y.K.C.)
| | - Beomkyu Kim
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju 28644, Korea; (W.-S.C.); (J.H.J.); (H.D.G.N.); (S.O.); (K.J.C.A.); (J.-H.P.); (B.K.); (Y.K.C.)
| | - Sun-Woo Yoon
- Infectious Diseases Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea;
| | - Kyeong Seob Shin
- Department of Laboratory Medicine, Chungbuk National University College of Medicine, Cheongju 28644, Korea;
| | - Young Ki Choi
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju 28644, Korea; (W.-S.C.); (J.H.J.); (H.D.G.N.); (S.O.); (K.J.C.A.); (J.-H.P.); (B.K.); (Y.K.C.)
| | - Yun Hee Baek
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju 28644, Korea; (W.-S.C.); (J.H.J.); (H.D.G.N.); (S.O.); (K.J.C.A.); (J.-H.P.); (B.K.); (Y.K.C.)
- Correspondence: (Y.H.B.); (M.-S.S.)
| | - Min-Suk Song
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju 28644, Korea; (W.-S.C.); (J.H.J.); (H.D.G.N.); (S.O.); (K.J.C.A.); (J.-H.P.); (B.K.); (Y.K.C.)
- Correspondence: (Y.H.B.); (M.-S.S.)
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41
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Singh KRB, Sridevi P, Singh RP. Potential applications of peptide nucleic acid in biomedical domain. Eng Rep 2020; 2:e12238. [PMID: 32838227 PMCID: PMC7404446 DOI: 10.1002/eng2.12238] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 06/19/2020] [Accepted: 06/19/2020] [Indexed: 05/03/2023]
Abstract
Peptide Nucleic Acid (PNA) are DNA/RNA synthetic analogs with 2-([2-aminoethyl] amino) acetic acid backbone. They partake unique antisense and antigene properties, just due to its inhibitory effect on transcription and translation; they also undergo complementary binding to RNA/DNA with high affinity and specificity. Hence, to date, many methods utilizing PNA for diagnosis and treatment of various diseases namely cancer, AIDS, human papillomavirus, and so on, have been designed and developed. They are being used widely in polymerase chain reaction modulation/mutation, fluorescent in-situ hybridization, and in microarray as a probe; they are also utilized in many in-vitro and in-vivo assays and for developing micro and nano-sized biosensor/chip/array technologies. Earlier reviews, focused only on PNA properties, structure, and modifications related to diagnostics and therapeutics; our review emphasizes on PNA properties and synthesis along with its potential applications in diagnosis and therapeutics. Furthermore, prospects in biomedical applications of PNAs are being discussed in depth.
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Affiliation(s)
- Kshitij RB Singh
- Department of Biotechnology, Faculty of ScienceIndira Gandhi National Tribal UniversityAmarkantakMadhya Pradesh484887India
| | - Parikipandla Sridevi
- Department of Biotechnology, Faculty of ScienceIndira Gandhi National Tribal UniversityAmarkantakMadhya Pradesh484887India
| | - Ravindra Pratap Singh
- Department of Biotechnology, Faculty of ScienceIndira Gandhi National Tribal UniversityAmarkantakMadhya Pradesh484887India
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Malik S, Lim J, Slack FJ, Braddock DT, Bahal R. Next generation miRNA inhibition using short anti-seed PNAs encapsulated in PLGA nanoparticles. J Control Release 2020; 327:406-419. [PMID: 32835710 DOI: 10.1016/j.jconrel.2020.08.026] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 02/07/2023]
Abstract
Selective inhibition of microRNAs (miRNAs) offers a new avenue for cancer therapeutics. While most of the current anti-miRNA (antimiR) reagents target full length miRNAs, here we investigate novel nanoparticle-delivered short PNA probes containing cationic domains targeting the seed region of the miRNA for effective antimiR therapy. For proof of concept, we tested PNAs targeting miRNA-155 and employed poly(lactic-co-glycolic acid) (PLGA)-based nanoparticle formulation for delivery. A comprehensive evaluation of PLGA nanoparticles (NPs) containing short PNA probes showed significantly superior loading, release profile, and uniform size distribution, compared to conventional non-cationic PNA probes. Confocal microscopy and flow cytometry analyses showed efficient transfection efficiency and uniform distribution of PLGA NPs containing short PNA probes in the cytoplasm. Functional analysis also confirmed efficient miRNA-155 inhibition including an effect on its downstream target proteins. Further, reduced tumor growth was observed after systemic delivery of PLGA nanoparticles containing short PNA probes in vivo in a xenograft mouse model following inhibition of miR-155. There was no evidence of acute or chronic toxicity associated with systemic delivery of PLGA NPs containing short PNA probes in the mice. Overall, in this paper we present a novel antimiR strategy based on PLGA nanoparticle delivered short PNA probes for potential cancer therapy.
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Affiliation(s)
- Shipra Malik
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, USA
| | - Jihoon Lim
- Department of Pathology, BIDMC Cancer Center, Harvard Medical School, 330, Brookline Ave, Boston, MA 02215, USA
| | - Frank J Slack
- Department of Pathology, BIDMC Cancer Center, Harvard Medical School, 330, Brookline Ave, Boston, MA 02215, USA
| | - Demetrios T Braddock
- Department of Pathology, Yale University School of Medicine, 310 Cedar Street, New Haven, CT 06510, USA
| | - Raman Bahal
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, USA.
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Nekrasov MD, Lukyanenko ER, Kurkin AV. Synthesis of N-substituted morpholine nucleoside derivatives. Nucleosides Nucleotides Nucleic Acids 2020; 39:1223-1244. [PMID: 32744921 DOI: 10.1080/15257770.2020.1788078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Herein, we report the synthesis of substituted morpholino nucleoside derivatives starting from ribonucleosides. The present protocol shows high functional group tolerance, uses mild reaction conditions, and gives moderate to good yields. This transformation is based on two sequential pathways: (i) the oxidation of the ribonucleosides to the corresponding dialdehyde using sodium periodate and (ii) the reductive amination of the in situ generated dialdehydes with the hydrochloride salts of various the alkylamines.
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Affiliation(s)
- Mikhail D Nekrasov
- Lomonosov Moscow State University, Department of Chemistry, Moscow, Russia.,Marlin Biotech LLC, Research Department, Moscow, Russia
| | | | - Alexander V Kurkin
- Lomonosov Moscow State University, Department of Chemistry, Moscow, Russia
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Billaud A, Verriele V, Dauvé J, Chevalier LM, Morel A. Non-Small-Cell Lung Cancer-Sensitive Detection of the p.Thr790Met EGFR Alteration by Preamplification before PNA-Mediated PCR Clamping and Pyrosequencing. Diagnostics (Basel) 2020; 10:diagnostics10080527. [PMID: 32751202 PMCID: PMC7460542 DOI: 10.3390/diagnostics10080527] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/19/2020] [Accepted: 07/27/2020] [Indexed: 12/24/2022] Open
Abstract
Targeted therapies and, more precisely, EGFR tyrosine kinase inhibitors (TKIs) have been a major improvement in the therapeutic management of EGFR-mutated non-small-cell lung cancers (NSCLCs). Earlier administration of these TKIs throughout tumor progression is imperative to improve patient outcomes. Consequently, studies have focused on refining the characterization of biomarkers, especially concerning the resistance mutation p.Thr790Met of EGFR. Herein, we developed peptide nucleic acid (PNA)-mediated PCR clamping followed by pyrosequencing, favoring enrichment of the mutated fraction. A preamplification step was first added to increase the amplifiable DNA fraction. Throughout the application of our method on DNA extracted from FFPE samples of 46 patients with NSCLC who had relapsed under first-generation EGFR TKI, we evaluated a sensitivity of 93.3% and a specificity of 100%. All 19 patients who were positive for the p.Thr790Met mutation with NGS were also found to be positive with our protocol. The only discordant case was a sample with no mutation detected with NGS, but which was positive with PNA. This protocol allows for the detection of the p.Thr790Met mutation with a sensitivity of 0.5% which will permit earlier detection and an improvement of therapeutic management.
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Affiliation(s)
- Amandine Billaud
- Université d’Angers, Inserm, CRCINA, F-49000 Angers, France; (A.B.); (L.-M.C.)
- Institut de Cancérologie de l’Ouest Nantes-Angers, 49000 Angers, France; (V.V.); (J.D.)
| | - Veronique Verriele
- Institut de Cancérologie de l’Ouest Nantes-Angers, 49000 Angers, France; (V.V.); (J.D.)
| | - Jonathan Dauvé
- Institut de Cancérologie de l’Ouest Nantes-Angers, 49000 Angers, France; (V.V.); (J.D.)
| | - Louise-Marie Chevalier
- Université d’Angers, Inserm, CRCINA, F-49000 Angers, France; (A.B.); (L.-M.C.)
- Institut de Cancérologie de l’Ouest Nantes-Angers, 49000 Angers, France; (V.V.); (J.D.)
| | - Alain Morel
- Université d’Angers, Inserm, CRCINA, F-49000 Angers, France; (A.B.); (L.-M.C.)
- Institut de Cancérologie de l’Ouest Nantes-Angers, 49000 Angers, France; (V.V.); (J.D.)
- Correspondence: ; Tel.: +33-241-352-717
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Miguel V, Rey C, Aceña JL, Maqueda F, Fernández-Hernando C, Rodríguez-Puyol D, Vaquero JJ, Lamas S. The pHLIP system as a vehicle for microRNAs in the kidney. Nefrologia 2020; 40:491-8. [PMID: 32693933 DOI: 10.1016/j.nefro.2020.05.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/11/2020] [Accepted: 05/20/2020] [Indexed: 11/23/2022] Open
Abstract
MicroRNAs (miRNAs) are small endogenous RNAs that regulate gene expression through post-transcriptional repression of their target messenger RNAs. A study of changes in expression of certain miRNAs in the kidney has supplied evidence on their pathogenic role and therapeutic potential in nephrology. This review proposes a nanotechnology approach based on the binding of analogs or inhibitors of miRNAs formed by peptide nucleic acids (PNAs) to peptides with a transmembrane structure sensitive to a low pH, called pHLIPs (pH [low] insertion peptides). The review draws on the concept that an acidic pH in the microenvironment of the renal tubule may facilitate concentration and distribution of the pHLIP-PNA complex in this organ. In this context, we have demonstrated for the first time that targeted administration of miR-33 inhibitors with the pHLIP system effectively prevents the development of renal fibrosis, thus opening up this technology to new strategies for diagnosis and treatment of kidney diseases.
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Dhar A, Ahmed I, Mallick S, Roy S. A Peptide- PNA Hybrid Beacon for Sensitive Detection of Protein Biomarkers in Biological Fluids. Chembiochem 2020; 21:2121-2125. [PMID: 32187425 DOI: 10.1002/cbic.202000097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/14/2020] [Indexed: 01/03/2023]
Abstract
Specific and rapid detection of proteins in biological fluids poses a challenging problem. In biological fluids, many proteins are present at low concentrations, requiring high affinity and specificity of the beacon-protein interaction. We report the design of a peptide-PNA hybrid beacon that exploits the dimeric nature of a target protein, S100B, a biomarker for brain trauma, to enhance binding affinity and specificity. The complementary base-pairing of the PNA bases brings the two arms of the beacon, one carrying an Alexa tag and the other carrying a Dabcyl moiety, into proximity, thus quenching Alexa fluorescence. Each of the arms carries a sequence that binds to one of the subunits. Binding to the target separates the quencher from the probe lifting the quenching of fluorescence. Enhanced affinity and specificity resulting from simultaneously binding to two sites allowed specific detection of S100B at low-nanomolar concentrations in the presence of serum. The design can be easily adapted for the detection of proteins containing multiple binding sites and could prove useful for rapid and sensitive biomarker detection.
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Affiliation(s)
- Amlanjyoti Dhar
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII M, Kolkata, 700054, India
| | - Israr Ahmed
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata, 700 032, India
| | - Shampa Mallick
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata, 700 032, India
| | - Siddhartha Roy
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII M, Kolkata, 700054, India
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Abstract
The growing interest in G-quadruplex (G4) structure and function is motivating intense efforts to develop G4-binding ligands. This chapter describes the design and testing of peptide nucleic acid (PNA) oligomers, which can bind to G4 DNA or RNA in two distinct ways, leading to formation of heteroduplexes or heteroquadruplexes. Guidelines for designing G4-targeting PNAs and step-by-step protocols for characterizing their binding through biophysical or biochemical methods are provided.
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Abstract
Detection of specific oligonucleotide sequences is central to numerous applications, and technologies amenable to point-of-care diagnostics or end users are needed. Here, we report a technology making use of a bioluminescent readout and smartphone quantification. The sensor is a semisynthetic luciferase (H-Luc-PNA conjugate) that is turned on by a strand-displacement reaction. We demonstrated sensing of three different microRNAs (miRs), as representative cancer biomarkers, and demonstrate the possibility to integrate an AND gate to sense two sequences simultaneously.
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Affiliation(s)
- Dalu Chang
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest Ansermet, 1211 Geneva, Switzerland
| | - Ki Tae Kim
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest Ansermet, 1211 Geneva, Switzerland
| | - Eric Lindberg
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest Ansermet, 1211 Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest Ansermet, 1211 Geneva, Switzerland
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Mercurio S, Cauteruccio S, Manenti R, Candiani S, Scarì G, Licandro E, Pennati R. Exploring miR-9 Involvement in Ciona intestinalis Neural Development Using Peptide Nucleic Acids. Int J Mol Sci 2020; 21:ijms21062001. [PMID: 32183450 PMCID: PMC7139483 DOI: 10.3390/ijms21062001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/12/2020] [Accepted: 03/13/2020] [Indexed: 12/16/2022] Open
Abstract
The microRNAs are small RNAs that regulate gene expression at the post-transcriptional level and can be involved in the onset of neurodegenerative diseases and cancer. They are emerging as possible targets for antisense-based therapy, even though the in vivo stability of miRNA analogues is still questioned. We tested the ability of peptide nucleic acids, a novel class of nucleic acid mimics, to downregulate miR-9 in vivo in an invertebrate model organism, the ascidian Ciona intestinalis, by microinjection of antisense molecules in the eggs. It is known that miR-9 is a well-conserved microRNA in bilaterians and we found that it is expressed in epidermal sensory neurons of the tail in the larva of C. intestinalis. Larvae developed from injected eggs showed a reduced differentiation of tail neurons, confirming the possibility to use peptide nucleic acid PNA to downregulate miRNA in a whole organism. By identifying putative targets of miR-9, we discuss the role of this miRNA in the development of the peripheral nervous system of ascidians.
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Affiliation(s)
- Silvia Mercurio
- Department of Environmental Science and Policy, Università degli Studi di Milano, 20133 Milano, Italy; (S.M.); (R.M.); (R.P.)
| | - Silvia Cauteruccio
- Department of Chemistry, Università degli Studi di Milano, 20133 Milano, Italy;
- Correspondence: (S.C.); (S.C.); Tel.: +39-0250314147 (S.C.); +39-0103538051 (S.C.)
| | - Raoul Manenti
- Department of Environmental Science and Policy, Università degli Studi di Milano, 20133 Milano, Italy; (S.M.); (R.M.); (R.P.)
| | - Simona Candiani
- Department of Earth Science, Environment and Life, Università degli Studi di Genova, 16132 Genova, Italy
- Correspondence: (S.C.); (S.C.); Tel.: +39-0250314147 (S.C.); +39-0103538051 (S.C.)
| | - Giorgio Scarì
- Department of Biosciences, Università degli Studi di Milano, 20133 Milano, Italy;
| | - Emanuela Licandro
- Department of Chemistry, Università degli Studi di Milano, 20133 Milano, Italy;
| | - Roberta Pennati
- Department of Environmental Science and Policy, Università degli Studi di Milano, 20133 Milano, Italy; (S.M.); (R.M.); (R.P.)
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Economos NG, Oyaghire S, Quijano E, Ricciardi AS, Saltzman WM, Glazer PM. Peptide Nucleic Acids and Gene Editing: Perspectives on Structure and Repair. Molecules 2020; 25:E735. [PMID: 32046275 DOI: 10.3390/molecules25030735] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 02/05/2020] [Accepted: 02/06/2020] [Indexed: 12/14/2022] Open
Abstract
Unusual nucleic acid structures are salient triggers of endogenous repair and can occur in sequence-specific contexts. Peptide nucleic acids (PNAs) rely on these principles to achieve non-enzymatic gene editing. By forming high-affinity heterotriplex structures within the genome, PNAs have been used to correct multiple human disease-relevant mutations with low off-target effects. Advances in molecular design, chemical modification, and delivery have enabled systemic in vivo application of PNAs resulting in detectable editing in preclinical mouse models. In a model of β-thalassemia, treated animals demonstrated clinically relevant protein restoration and disease phenotype amelioration, suggesting a potential for curative therapeutic application of PNAs to monogenic disorders. This review discusses the rationale and advances of PNA technologies and their application to gene editing with an emphasis on structural biochemistry and repair.
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