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Cadoni E, Rosa-Gastaldo D, Manicardi A, Mancin F, Madder A. Exploiting Double Exchange Diels-Alder Cycloadditions for Immobilization of Peptide Nucleic Acids on Gold Nanoparticles. Front Chem 2020; 8:4. [PMID: 32039162 PMCID: PMC6989547 DOI: 10.3389/fchem.2020.00004] [Citation(s) in RCA: 8] [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: 11/15/2019] [Accepted: 01/06/2020] [Indexed: 12/22/2022] Open
Abstract
The generation of PNA-decorated gold nanoparticles (AuNPs) has revealed to be more difficult as compared to the generation of DNA-functionalized ones. The less polar nature of this artificial nucleic acid system and the associated tendency of the neutral poly-amidic backbone to aspecifically adsorb onto the gold surface rather than forming a covalent bond through gold-thiol interaction, combined with the low solubility of PNAs itself, form the main limiting factors in the functionalization of AuNP. Here, we provide a convenient methodology that allows to easily conjugate PNAs to AuNP. Positively charged PNAs containing a masked furan moiety were immobilized via a double exchange Diels-Alder cycloaddition onto masked maleimide-functionalized AuNPs in a one-pot fashion. Conjugated PNA strands retain their ability to selectively hybridize with target DNA strands. Moreover, the duplexes resulting from hybridization can be detached through a retro-Diels-Alder reaction, thus allowing straightforward catch-and-release of specific nucleic acid targets.
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Affiliation(s)
- Enrico Cadoni
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Ghent, Belgium.,Dipartimento di Scienze Chimiche, Università di Padova, Padova, Italy
| | | | - Alex Manicardi
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Ghent, Belgium
| | - Fabrizio Mancin
- Dipartimento di Scienze Chimiche, Università di Padova, Padova, Italy
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Ghent, Belgium
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52
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Cartwright IM, Haskins JS, Kato TA. PNA Telomere and Centromere FISH Staining for Accurate Analysis of Radiation-Induced Chromosomal Aberrations. Methods Mol Biol 2020; 1984:95-100. [PMID: 31267424 DOI: 10.1007/978-1-4939-9432-8_11] [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] [Indexed: 11/29/2022]
Abstract
Dicentric and centric ring chromosomes are used for radiation-induced damage analysis and biodosimetry after radiation exposure. However, Giemsa stain-based cytogenetic analysis is labor-intense and time-consuming. Moreover, the disadvantage of Giemsa based chromosome analysis is a potential poor reproducibility when researchers are not fully trained for analysis. These problems come from analysis of morphological abnormality of chromosomal aberrations. Locus-specific FISH probes were used to overcome this problem. Centromere probes can visualize centromere locations and help identify dicentric chromosomes and centric rings. Telomere probes help to identify terminal deletion and telomere fusions. Probes were originally designed with a DNA probe but Peptide nucleic acid (PNA) probes took the place of DNA probes. This chapter introduces PNA telomere and centromere FISH staining and accurate analysis of chromosomal aberrations.
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Affiliation(s)
- Ian M Cartwright
- Department of Medicine, University of Colorado Denver, Aurora, CO, USA.
| | - Jeremy S Haskins
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Takamitsu A Kato
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
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53
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Mercurio S, Cauteruccio S, Manenti R, Candiani S, Scarì G, Licandro E, Pennati R. miR-7 Knockdown by Peptide Nucleic Acids in the Ascidian Ciona intestinalis. Int J Mol Sci 2019; 20:ijms20205127. [PMID: 31623150 PMCID: PMC6829576 DOI: 10.3390/ijms20205127] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 09/18/2019] [Revised: 10/10/2019] [Accepted: 10/14/2019] [Indexed: 12/12/2022] Open
Abstract
Peptide Nucleic Acids (PNAs) are synthetic mimics of natural oligonucleotides, which bind complementary DNA/RNA strands with high sequence specificity. They display numerous advantages, but in vivo applications are still rare. One of the main drawbacks of PNAs application is the poor cellular uptake that could be overcome by using experimental models, in which microinjection techniques allow direct delivery of molecules into eggs. Thus, in this communication, we investigated PNAs efficiency in miR-7 downregulation and compared its effects with those obtained with the commercially available antisense molecule, Antagomir (Dharmacon) in the ascidian Ciona intestinalis. Ascidians are marine invertebrates closely related to vertebrates, in which PNA techniques have not been applied yet. Our results suggested that anti-miR-7 PNAs were able to reach their specific targets in the developing ascidian embryos with high efficiency, as the same effects were obtained with both PNA and Antagomir. To the best of our knowledge, this is the first evidence that unmodified PNAs can be applied in in vivo knockdown strategies when directly injected into eggs.
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Affiliation(s)
- Silvia Mercurio
- Department of Environmental Science and Policy, Università degli Studi di Milano, 20133 Milano, Italy.
| | - Silvia Cauteruccio
- Department of Chemistry, Università degli Studi di Milano, 20133 Milano, Italy.
| | - Raoul Manenti
- Department of Environmental Science and Policy, Università degli Studi di Milano, 20133 Milano, Italy.
| | - Simona Candiani
- Department of Earth Science, Environment and Life, Università degli Studi di Genova, 16126 Genova, Italy.
| | - 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.
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54
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Ong AAL, Tan J, Bhadra M, Dezanet C, Patil KM, Chong MS, Kierzek R, Decout JL, Roca X, Chen G. RNA Secondary Structure-Based Design of Antisense Peptide Nucleic Acids for Modulating Disease-Associated Aberrant Tau Pre-mRNA Alternative Splicing. Molecules 2019; 24:molecules24163020. [PMID: 31434312 PMCID: PMC6720520 DOI: 10.3390/molecules24163020] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 07/09/2019] [Revised: 08/14/2019] [Accepted: 08/19/2019] [Indexed: 12/18/2022] Open
Abstract
Alternative splicing of tau pre-mRNA is regulated by a 5' splice site (5'ss) hairpin present at the exon 10-intron 10 junction. Single mutations within the hairpin sequence alter hairpin structural stability and/or the binding of splicing factors, resulting in disease-causing aberrant splicing of exon 10. The hairpin structure contains about seven stably formed base pairs and thus may be suitable for targeting through antisense strands. Here, we used antisense peptide nucleic acids (asPNAs) to probe and target the tau pre-mRNA exon 10 5'ss hairpin structure through strand invasion. We characterized by electrophoretic mobility shift assay the binding of the designed asPNAs to model tau splice site hairpins. The relatively short (10-15 mer) asPNAs showed nanomolar binding to wild-type hairpins as well as a disease-causing mutant hairpin C+19G, albeit with reduced binding strength. Thus, the structural stabilizing effect of C+19G mutation could be revealed by asPNA binding. In addition, our cell culture minigene splicing assay data revealed that application of an asPNA targeting the 3' arm of the hairpin resulted in an increased exon 10 inclusion level for the disease-associated mutant C+19G, probably by exposing the 5'ss as well as inhibiting the binding of protein factors to the intronic spicing silencer. On the contrary, the application of asPNAs targeting the 5' arm of the hairpin caused an increased exon 10 exclusion for a disease-associated mutant C+14U, mainly by blocking the 5'ss. PNAs could enter cells through conjugation with amino sugar neamine or by cotransfection with minigene plasmids using a commercially available transfection reagent.
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Affiliation(s)
- Alan Ann Lerk Ong
- NTU Institute for Health Technologies (HeathTech NTU), Interdisciplinary Graduate School, Nanyang Technological University, 50 Nanyang Drive, Singapore 637553, Singapore
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
| | - Jiazi Tan
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
| | - Malini Bhadra
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Clément Dezanet
- University Grenoble Alpes/CNRS, Département de Pharmacochimie Moléculaire, ICMG FR 2607, UMR 5063, 470 Rue de la Chimie, F-38041 Grenoble, France
| | - Kiran M Patil
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
| | - Mei Sian Chong
- Geriatic Education & Research Institute, 2 Yishun Central 2, Singapore 768024, Singapore
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Jean-Luc Decout
- University Grenoble Alpes/CNRS, Département de Pharmacochimie Moléculaire, ICMG FR 2607, UMR 5063, 470 Rue de la Chimie, F-38041 Grenoble, France
| | - Xavier Roca
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Gang Chen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore.
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55
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Piacenti V, Langella E, Autiero I, Nolan JC, Piskareva O, Adamo MFA, Saviano M, Moccia M. A combined experimental and computational study on peptide nucleic acid ( PNA) analogues of tumor suppressive miRNA-34a. Bioorg Chem 2019; 91:103165. [PMID: 31419642 DOI: 10.1016/j.bioorg.2019.103165] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 07/19/2019] [Accepted: 07/29/2019] [Indexed: 12/12/2022]
Abstract
MicroRNAs are a ubiquitous class of non-coding RNAs able to regulate gene expression in diverse biological processes. Widespread miRNAs deregulation was reported in numerous diseases including cancer, with several miRNAs playing oncogenic and/or tumor suppressive role by targeting multiple mRNAs simultaneously. Based on these findings, miRNAs have emerged as promising therapeutic tools for cancer treatment. Herein, for the first time, peptide nucleic acids (PNAs) were studied to develop a new class of molecules able to target 3'UTR on MYCN mRNA without a fully complementary base pairing sequence (as miRNAs). For our proof of concept study we have selected as a model the miRNA-34a, which acts as a tumor suppressor in a number of cancers including neuroblastoma. In particular, miRNA-34a is a direct regulator of MYCN oncogene, whose overexpression is a prominent biomarker for the highly aggressive neuroblastoma phenotype. The design and synthesis of three PNA-based oligomers of different length was described, and their interaction with two binding sites on the target MYCN mRNA was investigated by molecular dynamics simulation, and spectroscopic techniques (CD, UV). Intake assay and confocal microscopy of PNA sequences were also carried out in vitro on neuroblastoma Kelly cells. Despite the presence of multiple mismatches, the PNA/RNA hetero duplexes retain very interesting features in terms of stability, affinity as well as of cellular uptake.
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Affiliation(s)
- Valerio Piacenti
- RCSI, Dept. of Pharmaceutical & Medicinal Chemistry, 123 St Stephen's Green, Dublin 2, Ireland
| | - Emma Langella
- National Research Council (CNR)-IBB, via Mezzocannone 16, 80134 Naples, Italy
| | - Ida Autiero
- National Research Council (CNR)-IBB, via Mezzocannone 16, 80134 Naples, Italy
| | - John C Nolan
- RCSI, Dept. of Cancer Genetics, York Street, Dublin 2, Ireland
| | - Olga Piskareva
- RCSI, Dept. of Cancer Genetics, York Street, Dublin 2, Ireland
| | - Mauro F A Adamo
- RCSI, Dept. of Pharmaceutical & Medicinal Chemistry, 123 St Stephen's Green, Dublin 2, Ireland
| | - Michele Saviano
- National Research Council (CNR)-IC, via G. Amendola 122/O, 70126 Bari, Italy
| | - Maria Moccia
- National Research Council (CNR)-IC, via G. Amendola 122/O, 70126 Bari, Italy.
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56
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Abstract
In this work, single-channel current recordings were used to selectively detect individual ssDNA strands in the vestibule of the α-hemolysin (α-HL) protein nanopore. The sensing mechanism was based on the detection of the intrinsic topological change of target ssDNA molecules after the hybridization with complementary PNA fragments. The readily distinguishable current signatures of PNA-DNA duplexes reversible association with the α-HL's vestibule, in terms of blockade amplitudes and kinetic features, allows specific detection of nucleic acid hybridization.
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Affiliation(s)
| | | | - Jonggwan Park
- Department of Bioinformatics, Kongju National University, Kongju, South Korea, 32588
| | - Chang Ho Seo
- Department of Bioinformatics, Kongju National University, Kongju, South Korea, 32588
| | - Yoonkyung Park
- Department of Department of Biomedical Science and Research Center for Proteinaceous Materials (RCPM), Chosun University, Gwangju, South Korea, 61452
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57
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Abstract
Peptide Nucleic Acids (PNAs) are oligonucleotide mimics that can be used to block the biological action of microRNA, thus affecting gene expression post-transcriptionally. PNAs are obtained with solid-phase peptide synthesis, and can be easily conjugated to other peptides. Conjugation with R8-Peptide or modification of the PNA backbone (at C5 or C2 carbon) with arginine side chains allows efficient cellular uptake. The present protocol describes the synthesis of cationic PNAs that can be used alone as drugs or for efficient co-delivery in suitable inorganic nanocarriers.
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Affiliation(s)
- Alex Manicardi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Roberto Gambari
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Luisa de Cola
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS) Université de Strasbourg, Strasbourg, France
| | - Roberto Corradini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.
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58
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Bertucci A, Silvestrini S, Corradini R, De Cola L. Loading of PNA and Other Molecular Payloads on Inorganic Nanostructures for Theranostics. Methods Mol Biol 2018; 1811:65-77. [PMID: 29926446 DOI: 10.1007/978-1-4939-8582-1_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Peptide Nucleic Acids (PNAs) are oligonucleotide mimics that can be used as drugs as they can interact with DNA and RNA targets in organisms. Loading PNAs into inorganic nanocarriers can improve their cellular uptake and co-delivering them together with drugs can improve the therapy efficacy by synergic effects. Furthermore, the functionalization of the carriers with labels allows theranostics, and the possibility to monitor the efficacy of the therapy in real time. The present protocol describes the synthesis of Zeolites-L nanocrystals and mesoporous silica nanoparticles and their loading with cationic PNAs and other smaller molecular weight payloads towards theranostics applications.
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59
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Fortunati S, Rozzi A, Curti F, Giannetto M, Corradini R, Careri M. Novel amperometric genosensor based on peptide nucleic acid ( PNA) probes immobilized on carbon nanotubes-screen printed electrodes for the determination of trace levels of non-amplified DNA in genetically modified (GM) soy. Biosens Bioelectron 2019; 129:7-14. [PMID: 30682690 DOI: 10.1016/j.bios.2019.01.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [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: 11/05/2018] [Revised: 01/07/2019] [Accepted: 01/11/2019] [Indexed: 02/09/2023]
Abstract
A novel amperometric genosensor based on PNA probes covalently bound on the surface of Single Walled Carbon Nanotubes - Screen Printed Electrodes (SWCNT-SPEs) was developed and validated in samples of non-amplified genomic DNA extracted from genetically modified (GM)-Soy. The sandwich assay is based on a first recognition of a 20-mer portion of the target DNA by a complementary PNA Capture Probe (CP) and a second hybridization with a PNA Signalling Probe (SP), with a complementary sequence to a different portion of the target DNA. The SP was labelled with biotin to measure current signal by means of a final incubation of an Alkaline Phosphatase-streptavidin conjugate (ALP-Strp). The electrochemical detection was carried out using hydroquinone diphosphate (HQDP) as enzymatic substrate. The genoassay provided a linear range from 250 pM to 2.5 nM, LOD of 64 pM and LOQ of 215 pM Excellent selectivity towards one base mismatch (1-MM) or scrambled (SCR) sequences was obtained. A simple protocol for extraction and analysis of non-amplified soybean genomic DNA without sample treatment was developed and validated. Our study provides insight into how the outstanding recognition efficiency of PNAs can be combined with the unique properties of CNTs in terms of signal response enhancement for direct detection of genomic DNA samples at the level of interest without previous amplification.
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Affiliation(s)
- Simone Fortunati
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Andrea Rozzi
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Federica Curti
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Marco Giannetto
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy.
| | - Roberto Corradini
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy.
| | - Maria Careri
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
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60
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Abstract
While <2% of DNA encodes for functional proteins, >70% is transcribed into RNA. Although the function of most RNA transcripts is unknown, such non-coding RNAs are attractive targets for molecular recognition because of the potentially important roles they play in regulation of gene expression and development of disease. In this chapter, we describe peptide nucleic acids (PNAs) that form sequence-specific triple helices with double-stranded RNA (dsRNA). We provide protocols for sequence design and biophysical characterization of PNAs and discuss first examples where such PNAs have been used for functional modulation of dsRNA. The triplex-forming PNAs represent a new approach for RNA recognition that may find future applications in fundamental science, biotechnology and medicine.
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61
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Giovannone N, Antonopoulos A, Liang J, Geddes Sweeney J, Kudelka MR, King SL, Lee GS, Cummings RD, Dell A, Barthel SR, Widlund HR, Haslam SM, Dimitroff CJ. Human B Cell Differentiation Is Characterized by Progressive Remodeling of O-Linked Glycans. Front Immunol 2018; 9:2857. [PMID: 30619255 PMCID: PMC6302748 DOI: 10.3389/fimmu.2018.02857] [Citation(s) in RCA: 26] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 11/20/2018] [Indexed: 12/16/2022] Open
Abstract
Germinal centers (GC) are microanatomical niches where B cells proliferate, undergo antibody affinity maturation, and differentiate to long-lived memory B cells and antibody-secreting plasma cells. For decades, GC B cells have been defined by their reactivity to the plant lectin peanut agglutinin (PNA), which binds serine/threonine (O-linked) glycans containing the asialylated disaccharide Gal-β1,3-GalNAc-Ser/Thr (also called T-antigen). In T cells, acquisition of PNA binding by activated T cells and thymocytes has been linked with altered tissue homing patterns, cell signaling, and survival. Yet, in GC B cells, the glycobiological basis and significance of PNA binding remains surprisingly unresolved. Here, we investigated the basis for PNA reactivity of GC B cells. We found that GC B cell binding to PNA is associated with downregulation of the α2,3 sialyltransferase, ST3GAL1 (ST3Gal1), and overexpression of ST3Gal1 was sufficient to reverse PNA binding in B cell lines. Moreover, we found that the primary scaffold for PNA-reactive O-glycans in B cells is the B cell receptor-associated receptor-type tyrosine phosphatase CD45, suggesting a role for altered O-glycosylation in antigen receptor signaling. Consistent with similar reports in T cells, ST3Gal1 overexpression in B cells in vitro induced drastic shortening in O-glycans, which we confirmed by both antibody staining and mass spectrometric O-glycomic analysis. Unexpectedly, ST3Gal1-induced changes in O-glycan length also correlated with altered binding of two glycosylation-sensitive CD45 antibodies, RA3-6B2 (more commonly called B220) and MEM55, which (in humans) have previously been reported to favor binding to naïve/GC subsets and memory/plasmablast subsets, respectively. Analysis of primary B cell binding to B220, MEM55, and several plant lectins suggested that B cell differentiation is accompanied by significant loss of O-glycan complexity, including loss of extended Core 2 O-glycans. To our surprise, decreased O-glycan length from naïve to post-GC fates best correlated not with ST3Gal1, but rather downregulation of the Core 2 branching enzyme GCNT1. Thus, our data suggest that O-glycan remodeling is a feature of B cell differentiation, dually regulated by ST3Gal1 and GCNT1, that ultimately results in expression of distinct O-glycosylation states/CD45 glycoforms at each stage of B cell differentiation.
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Affiliation(s)
- Nicholas Giovannone
- Department of Dermatology, Brigham and Women's Hospital, Boston MA, United States.,Harvard Medical School, Boston MA, United States
| | | | - Jennifer Liang
- Department of Dermatology, Brigham and Women's Hospital, Boston MA, United States
| | - Jenna Geddes Sweeney
- Department of Dermatology, Brigham and Women's Hospital, Boston MA, United States.,Harvard Medical School, Boston MA, United States
| | - Matthew R Kudelka
- Department of Surgery, Beth Israel Deaconess Medical Center, Boston, MA, United States.,Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, United States
| | - Sandra L King
- Department of Dermatology, Brigham and Women's Hospital, Boston MA, United States
| | - Gi Soo Lee
- Department of Otology and Laryngology, Harvard Medical School, Boston, MA, United States
| | - Richard D Cummings
- Harvard Medical School, Boston MA, United States.,Department of Surgery, Beth Israel Deaconess Medical Center, Boston, MA, United States
| | - Anne Dell
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Steven R Barthel
- Department of Dermatology, Brigham and Women's Hospital, Boston MA, United States
| | - Hans R Widlund
- Department of Dermatology, Brigham and Women's Hospital, Boston MA, United States.,Harvard Medical School, Boston MA, United States
| | - Stuart M Haslam
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Charles J Dimitroff
- Department of Dermatology, Brigham and Women's Hospital, Boston MA, United States.,Harvard Medical School, Boston MA, United States
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62
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Malik S, Oyaghire S, Bahal R. Applications of PNA-laden nanoparticles for hematological disorders. Cell Mol Life Sci 2018; 76:1057-1065. [PMID: 30498995 DOI: 10.1007/s00018-018-2979-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 11/07/2018] [Accepted: 11/23/2018] [Indexed: 12/26/2022]
Abstract
Safe and efficient genome editing has been an unmitigated goal for biomedical researchers since its inception. The most prevalent strategy for gene editing is the use of engineered nucleases that induce DNA damage and take advantage of cellular DNA repair machinery. This includes meganucleases, zinc-finger nucleases, transcription activator-like effector nucleases, and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR/Cas9) systems. However, the clinical viability of these nucleases is marred by their off-target cleavage activity (≥ 50% in RNA-guided endonucleases). In addition, in vivo applications of CRISPR require systemic administration of Cas9 protein, mRNA, or DNA, which presents a significant delivery challenge. The development of nucleic acid probes that can recognize specific double-stranded DNA (dsDNA) regions and activate endogenous DNA repair machinery holds great promise for gene editing applications. Triplex-forming oligonucleotides (TFOs), which were introduced more than 25 years ago, are among the most extensively studied oligomeric dsDNA-targeting agents. TFOs bind duplex DNA to create a distorted helical structure, which can stimulate DNA repair and the exchange of a nearby mutated region-otherwise leading to an undesired phenotype-for a short single-stranded donor DNA that contains the corrective nucleotide sequence. Recombination can be induced within several hundred base-pairs of the TFO binding site and has been shown to depend on triplex-induced initiation of the nucleotide excision repair pathway and engagement of the homology-dependent repair pathway. Since TFOs do not possess any direct nuclease activity, their off-target effects are minimal when compared to engineered nucleases. This review comprehensively covers the advances made in peptide nucleic acid-based TFOs for site-specific gene editing and their therapeutic applications.
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Affiliation(s)
- Shipra Malik
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, USA
| | - Stanley Oyaghire
- Department of Therapeutic Radiology, Yale University, New Haven, CT, USA
| | - Raman Bahal
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, USA.
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63
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Vonbrüll M, Riegel E, Halter C, Aigner M, Bock H, Werner B, Lindhorst T, Czerny T. A Dominant Negative Antisense Approach Targeting β-Catenin. Mol Biotechnol 2018; 60:339-49. [PMID: 29524201 DOI: 10.1007/s12033-018-0058-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
There have been many attempts to unveil the therapeutic potential of antisense molecules during the last decade. Due to its specific role in canonical Wnt signalling, β-catenin is a potential target for an antisense-based antitumour therapy. In order to establish such a strategy with peptide nucleic acids, we developed a reporter assay for quantification of antisense effects. The luciferase-based assay detects splice blocking with high sensitivity. Using this assay, we show that the splice donor of exon 13 of β-catenin is particularly suitable for an antisense strategy, as it results in a truncated protein which lacks transactivating functions. Since the truncated proteins retain the interactions with Tcf/Lef proteins, they act in a dominant negative fashion competing with wild-type proteins and thus blocking the transcriptional activity of β-catenin. Furthermore, we show that the truncation does not interfere with binding of cadherin and α-catenin, both essential for its function in cell adhesion. Therefore, the antisense strategy blocks Wnt signalling with high efficiency but retains other important functions of β-catenin.
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64
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Jolly P, Rainbow J, Regoutz A, Estrela P, Moschou D. A PNA-based Lab-on-PCB diagnostic platform for rapid and high sensitivity DNA quantification. Biosens Bioelectron 2018; 123:244-250. [PMID: 30243847 DOI: 10.1016/j.bios.2018.09.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/17/2018] [Accepted: 09/01/2018] [Indexed: 10/28/2022]
Abstract
We report the development of a Lab-on-PCB DNA diagnostic platform, exploiting peptide nucleic acid (PNA) sequences as probes. The study demonstrates the optimization and characterization of two commercial PCB manufacturing gold electroplating processes for biosensing applications. Using an optimized ratio of PNA with a spacer molecule (MCH), the lowest limit of detection (LoD) to date for PCB-based DNA biosensors of 57 fM is reported. The study also showcases a fully integrated Lab-on-PCB microsystem designed for rapid detection, which employs PCB-integrated sample delivery, achieving DNA quantification in the 0.1-100 pM range for 5 μL samples analyzed within 5 min under continuous flow. The demonstrated biosensor proves the capability of PCB-based DNA biosensors for high sensitivity and paves the way for their integration in Lab-on-PCB DNA diagnostic microsystems.
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Affiliation(s)
- Pawan Jolly
- Centre for Biosensors, Bioelectronics and Biodevices (C3Bio) and Department of Electronic and Electrical Engineering, University of Bath, Bath BA2 7AY, UK; DxOnBoard Ltd, Carpenter House, Broad Quay, Bath BA1 1UD, UK.
| | - Joshua Rainbow
- Centre for Biosensors, Bioelectronics and Biodevices (C3Bio) and Department of Electronic and Electrical Engineering, University of Bath, Bath BA2 7AY, UK
| | - Anna Regoutz
- Department of Materials, Imperial College London, London SW7 2AZ, UK
| | - Pedro Estrela
- Centre for Biosensors, Bioelectronics and Biodevices (C3Bio) and Department of Electronic and Electrical Engineering, University of Bath, Bath BA2 7AY, UK
| | - Despina Moschou
- Centre for Biosensors, Bioelectronics and Biodevices (C3Bio) and Department of Electronic and Electrical Engineering, University of Bath, Bath BA2 7AY, UK; DxOnBoard Ltd, Carpenter House, Broad Quay, Bath BA1 1UD, UK.
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65
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Becker WM, Petersen A, Jappe U. Peanut allergens: new consolidated findings on structure, characteristics, and allergome. Allergol Select 2018; 2:67-79. [PMID: 31826045 DOI: 10.5414/ALX01418E] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Accepted: 03/29/2011] [Indexed: 11/18/2022] Open
Abstract
Immunoglobulin E-mediated food allergy is the result of a complex pathomechanism. Factors contributing to the dysfunction of the immune system are the allergenic sources and the variable matrix effects arising from the processes involved in interaction with the gastrointestinal tract, the allergens themselves through their structural features, and the specific behavior of the individual immune system. The starting point for elucidating the pathomechanism of food allergy is the identification of allergens and the description of their structure. They are the basis for in vitro diagnostics as well as the development of immunotherapeutic drugs. With regard to Class I food allergy, peanut allergy affects by far the largest group of patients. 11 allergens have been identified in peanuts. Ara h 1, Ara h 3, and Ara h 4 belong to the cupin superfamily, Ara h 2, Ara h 6, and Ara h 7 to the prolamin superfamily; Ara h 5 (profilins) and Ara h 8 (superfamily of Bet v 1-homologous proteins) are associated with aeroallergens. Peanut lipid transfer proteins (LTP) and two peanut oleosins are listed as Ara h 9, Ara h 10, and Ara h 11 by the IUIS Allergen Nomenclature Subcommittee. Peanut agglutinin (PNA) and a third oleosin have been shown to possess allergenic properties. The effect of the above specified allergens has to be considered in the context of their matrix, which is influenced by processing factors.
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Jin W, Jain A, Liu H, Zhao Z, Cheng K. Noncovalent Attachment of Chemical Moieties to siRNAs Using Peptide Nucleic Acid as a Complementary Linker. ACS Appl Bio Mater 2018; 1:643-651. [PMID: 31179438 DOI: 10.1021/acsabm.8b00141] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bioconjugation of siRNAs with chemical moieties is an effective strategy to improve the stability and cellular uptake of siRNAs. However, chemical conjugations of siRNAs are always challenging because of siRNAs' extremely poor stability. Therefore, a new strategy to attach a chemical moiety to siRNA without chemical reaction is highly needed. Peptide nucleic acids (PNAs) are DNA analogues in which the phosphate ribose ring in the backbone is replaced with a polyamide. Compared to DNA, PNA has a higher affinity for complementary DNA and better chemical stability. We, therefore, employed PNAs as a complementary linker to attach chemical moieties to siRNAs by annealing. The objective of this study is to develop an easy but efficient strategy to noncovalently attach chemical moieties to siRNAs without chemical modification of the siRNAs. We identified a PNA complementary sequence for hybridizing with siRNAs. Also, we compared the stability and silencing effects of different siRNA-PNA chimeras, which were annealed at different termini of the siRNA. siRNAs with a PNA annealed to the 3' end of the sense strand exhibited enhanced stability in the serum and maintained a good silencing effect. The siRNA-PNA chimera was then employed in two delivery systems to deliver the PCBP2 siRNA, a potential antifibrotic siRNA, to hepatic stellate cells. In both systems, the chimera demonstrated high cellular uptake and silencing activity. The results suggested that the siRNA-PNA chimera is an easy and efficient approach to attach targeting ligands or chemical moieties to siRNAs without chemical modification of the siRNA. This new technology will greatly reduce the difficulty and cost in conjugating chemical moieties to siRNAs.
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Affiliation(s)
- Wei Jin
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, 2464 Charlotte Street, Kansas City, Missouri 64108, United States
| | - Akshay Jain
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, 2464 Charlotte Street, Kansas City, Missouri 64108, United States
| | - Hao Liu
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, 2464 Charlotte Street, Kansas City, Missouri 64108, United States
| | - Zhen Zhao
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, 2464 Charlotte Street, Kansas City, Missouri 64108, United States
| | - Kun Cheng
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, 2464 Charlotte Street, Kansas City, Missouri 64108, United States
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Tian K, Shi R, Gu A, Pennella M, Gu LQ. Polycationic Probe-Guided Nanopore Single-Molecule Counter for Selective miRNA Detection. Methods Mol Biol 2018; 1632:255-268. [PMID: 28730445 DOI: 10.1007/978-1-4939-7138-1_17] [Citation(s) in RCA: 3] [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] [Indexed: 12/30/2022]
Abstract
MicroRNAs (miRNAs) are a class of noncoding RNAs that are being explored as a new type of disease biomarkers. The nanopore single-molecule sensor offers a potential noninvasive tool to detect miRNAs for diagnostics and prognosis applications. However, one of the challenges that limits its clinical applications is the presence of a large variety of nontarget nucleic acids in the biofluid extracts. Upon interacting with the nanopore, nontarget nucleic acids produce "contaminative" nanopore signals that interfere with target miRNA discrimination, thus severely lowering the accuracy in target miRNA detection. We have reported a novel method that utilizes a designed polycationic peptide-PNA probe to specifically guide the target miRNA migration toward the nanopore, whereas any nontarget nucleic acids without the probe bound is rejected by the nanopore. Consequently, nontarget species are driven away from the nanopore and only the target miRNA can be detected at low concentration. This method is also able to discriminate miRNAs with single-nucleotide difference by using PNA to capture miRNA. Considering the significance and impact of this substantial advance for the future miRNA detection in biofluid samples, we prepared this detailed protocol, by which the readers can view the experimental procedure, data analysis, and resulting explanation.
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Affiliation(s)
- Kai Tian
- Department of Bioengineering, University of Missouri, 134 Research Park, Columbia, MO, 65211, USA.,Dalton Cardiovascular Research Center, University of Missouri, 134 Research Park, Columbia, MO, 65211, USA
| | - Ruicheng Shi
- Department of Bioengineering, University of Missouri, 134 Research Park, Columbia, MO, 65211, USA.,Dalton Cardiovascular Research Center, University of Missouri, 134 Research Park, Columbia, MO, 65211, USA
| | - Amy Gu
- Department of Bioengineering, University of Missouri, 134 Research Park, Columbia, MO, 65211, USA.,Dalton Cardiovascular Research Center, University of Missouri, 134 Research Park, Columbia, MO, 65211, USA
| | - Michael Pennella
- Department of Bioengineering, University of Missouri, 134 Research Park, Columbia, MO, 65211, USA.,Dalton Cardiovascular Research Center, University of Missouri, 134 Research Park, Columbia, MO, 65211, USA
| | - Li-Qun Gu
- Department of Bioengineering, University of Missouri, 134 Research Park, Columbia, MO, 65211, USA. .,Dalton Cardiovascular Research Center, University of Missouri, 134 Research Park, Columbia, MO, 65211, USA.
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Abstract
Peptide nucleic acids (PNAs) can bind duplex DNA in a sequence-targeted manner, forming a triplex structure capable of inducing DNA repair and producing specific genome modifications. Since the first description of PNA-mediated gene editing in cell free extracts, PNAs have been used to successfully correct human disease-causing mutations in cell culture and in vivo in preclinical mouse models. Gene correction via PNAs has resulted in clinically-relevant functional protein restoration and disease improvement, with low off-target genome effects, indicating a strong therapeutic potential for PNAs in the treatment or cure of genetic disorders. This review discusses the progress that has been made in developing PNAs as an effective, targeted agent for gene editing, with an emphasis on recent in vivo, nanoparticle-based strategies.
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Rosso V, Petiti J, Bracco E, Pedrola R, Carnuccio F, Signorino E, Carturan S, Calabrese C, Bot-Sartor G, Ronconi M, Serra A, Saglio G, Frassoni F, Cilloni D. A novel assay to detect calreticulin mutations in myeloproliferative neoplasms. Oncotarget 2018; 8:6399-6405. [PMID: 28031530 PMCID: PMC5351640 DOI: 10.18632/oncotarget.14113] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 09/14/2016] [Accepted: 12/15/2016] [Indexed: 11/27/2022] Open
Abstract
The myeloproliferative neoplasms are chronic myeloid cancers divided in Philadelphia positive (Ph+), chronic myeloid leukemia, or negative: polycythemia vera (PV) essential thrombocythemia (ET), and primary myelofibrosis (PMF). Most Ph negative cases have an activating JAK2 or MPL mutation. Recently, somatic mutations in the calreticulin gene (CALR) were detected in 56–88% of JAK2/MPL-negative patients affected by ET or PMF. The most frequent mutations in CARL gene are type-1 and 2. Currently, CALR mutations are evaluated by sanger sequencing. The evaluation of CARL mutations increases the diagnostic accuracy in patients without other molecular markers and could represent a new therapeutic target for molecular drugs. We developed a novel detection assay in order to identify type-1 and 2 CALR mutations by PNA directed PCR clamping. Seventy-five patients affected by myeloproliferative neoplasms and seven controls were examined by direct DNA sequencing and by PNA directed PCR clamping. The assay resulted to be more sensitive, specific and cheaper than sanger sequencing and it could be applied even in laboratory not equipped for more sophisticated analysis. Interestingly, we report here a case carrying both type 1 and type2 mutations in CALR gene.
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Affiliation(s)
- Valentina Rosso
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Jessica Petiti
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Enrico Bracco
- Department of Oncology, University of Turin, Turin, Italy
| | - Roberto Pedrola
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Francesca Carnuccio
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Elisabetta Signorino
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Sonia Carturan
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Chiara Calabrese
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Giada Bot-Sartor
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Michela Ronconi
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Anna Serra
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Giuseppe Saglio
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Francesco Frassoni
- Department of Pediatric Hemato-Oncology and Stem Cell, Cellular Therapy Laboratory, Institute G. Gaslini, Genova, Italy
| | - Daniela Cilloni
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
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Westerlund K, Altai M, Mitran B, Konijnenberg M, Oroujeni M, Atterby C, de Jong M, Orlova A, Mattsson J, Micke P, Karlström AE, Tolmachev V. Radionuclide Therapy of HER2-Expressing Human Xenografts Using Affibody-Based Peptide Nucleic Acid-Mediated Pretargeting: In Vivo Proof of Principle. J Nucl Med 2018; 59:1092-1098. [PMID: 29439013 DOI: 10.2967/jnumed.118.208348] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 01/23/2018] [Indexed: 12/25/2022] Open
Abstract
Affibody molecules are small proteins engineered using a nonantibody scaffold. Radiolabeled Affibody molecules are excellent imaging probes, but their application to radionuclide therapy has been prevented by high renal reabsorption. The aim of this study was to test the hypothesis that Affibody-based peptide nucleic acid (PNA)-mediated pretargeted therapy of human epidermal growth factor receptor 2 (HER2)-expressing cancer extends survival without accompanying renal toxicity. Methods: A HER2-targeting Affibody molecule ligated with an AGTCGTGATGTAGTC PNA hybridization probe (ZHER2:342-SR-HP1) was used as the primary pretargeting agent. A complementary AGTCGTGATGTAGTC PNA conjugated to the chelator DOTA and labeled with the radionuclide 177Lu (177Lu-HP2) was used as the secondary agent. The influence of different factors on pretargeting was investigated. Experimental radionuclide therapy in mice bearing SKOV-3 xenografts was performed in 6 cycles separated by 7 d. Results: Optimal tumor targeting was achieved when 16 MBq/3.5 μg (0.65 nmol) of 177Lu-HP2 was injected 16 h after injection of 100 μg (7.7 nmol) of ZHER2:342-SR-HP1. The calculated absorbed dose to tumors was 1,075 mGy/MBq, whereas the absorbed dose to kidneys was 206 mGy/MBq and the absorbed dose to blood (surrogate of bone marrow) was 4 mGy/MBq. Survival of mice was significantly longer (P < 0.05) in the treatment group (66 d) than in the control groups treated with the same amount of ZHER2:342-SR-HP1 only (37 d), the same amount and activity of 177Lu-HP2 only (32 d), or phosphate-buffered saline (37 d). Conclusion: The studied pretargeting system can deliver an absorbed dose to tumors appreciably exceeding absorbed doses to critical organs, making Affibody-based PNA-mediated pretargeted radionuclide therapy highly attractive.
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Affiliation(s)
- Kristina Westerlund
- Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Mohamed Altai
- Department of Immunology, Genetics, and Pathology, Uppsala University, Uppsala, Sweden
| | - Bogdan Mitran
- Division of Molecular Imaging, Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden; and
| | - Mark Konijnenberg
- Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Maryam Oroujeni
- Department of Immunology, Genetics, and Pathology, Uppsala University, Uppsala, Sweden
| | - Christina Atterby
- Department of Immunology, Genetics, and Pathology, Uppsala University, Uppsala, Sweden
| | - Marion de Jong
- Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Anna Orlova
- Division of Molecular Imaging, Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden; and
| | - Johanna Mattsson
- Department of Immunology, Genetics, and Pathology, Uppsala University, Uppsala, Sweden
| | - Patrick Micke
- Department of Immunology, Genetics, and Pathology, Uppsala University, Uppsala, Sweden
| | | | - Vladimir Tolmachev
- Department of Immunology, Genetics, and Pathology, Uppsala University, Uppsala, Sweden
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Abstract
The implementation of quantitative approaches in telomere chromosome-oriented FISH (telomeric CO-FISH) allows the assessment of the relative efficiency of lagging versus leading strand telomere replication and thus provides information on the implicated mechanisms. Here we describe a simple method for telomere strand-specific analyses and discuss its potential applications.
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Petiti J, Rosso V, Lo Iacono M, Calabrese C, Signorino E, Gaidano V, Berger M, Saglio G, Cilloni D. Prognostic significance of The Wilms' Tumor-1 (WT1) rs16754 polymorphism in acute myeloid leukemia. Leuk Res 2018; 67:6-11. [PMID: 29407184 DOI: 10.1016/j.leukres.2018.01.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 12/28/2017] [Accepted: 01/22/2018] [Indexed: 11/29/2022]
Abstract
Acute myeloid leukemia is a genetically heterogeneous disease characterized by the accumulation of mutations in hematopoietic progenitor cells. For its heterogeneity, prognostic markers are very useful for therapeutic choice. The most important prognostic markers are age, white blood cell count, chromosomal alterations and gene mutations. Recent works have studied the prognostic significance of WT1 polymorphisms and mutations, highlighting the role of SNP rs16754 as a positive prognostic factor in AML patients. Nevertheless, the data are still unclear. To investigate the role of WT1 rs16754 polymorphism in AML, we designed a new tool for the detection using PNA directed PCR Clamping technology. Our data were able to establish a correlation between SNP rs16754 and the clinical outcome. Our results support the hypothesis that rs16754 polymorphism is an independent positive prognostic molecular marker that could be useful for therapeutic choice. In view of this, we described a novel assay faster, more sensitive and cheaper than DNA sequencing. The assay allows evaluating WT1 rs16754 polymorphism in diagnostic routine to improve prognostic information faster and without over-costing for diagnostic laboratories.
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Affiliation(s)
- Jessica Petiti
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy.
| | - Valentina Rosso
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy.
| | - Marco Lo Iacono
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy.
| | - Chiara Calabrese
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy.
| | - Elisabetta Signorino
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy.
| | - Valentina Gaidano
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy.
| | - Massimo Berger
- Pediatric Onco-Hematology, Stem Cell Transplantation and Cellular Therapy Divisions, Regina Margherita Children Hospital, Turin, Italy.
| | - Giuseppe Saglio
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy.
| | - Daniela Cilloni
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy.
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Berg T, Silveira MA, Moenter SM. Prepubertal Development of GABAergic Transmission to Gonadotropin-Releasing Hormone (GnRH) Neurons and Postsynaptic Response Are Altered by Prenatal Androgenization. J Neurosci 2018; 38:2283-93. [PMID: 29374136 DOI: 10.1523/JNEUROSCI.2304-17.2018] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 12/29/2017] [Accepted: 01/20/2018] [Indexed: 11/21/2022] Open
Abstract
Gonadotropin-releasing hormone (GnRH) neurons regulate reproduction through pulsatile GnRH release. Women with polycystic ovary syndrome (PCOS) have persistently elevated luteinizing hormone release frequency, reflecting GnRH release; this exacerbates hyperandrogenemia and disrupted reproductive cycles that are characteristic of this disorder. Clinical evidence suggests that neuroendocrine features of PCOS may manifest peripubertally. Adult mice prenatally exposed to androgens (PNA) mimic several reproductive features of PCOS. GnRH neurons from these mice have increased firing activity and receive increased GABAergic transmission, which is excitatory. When changes emerge during development is unknown. To study the typical postnatal development of GABAergic transmission and the effects of PNA treatment and sex, whole-cell voltage-clamp recordings were made of GABAergic postsynaptic currents (PSCs) in GnRH neurons in brain slices from prepubertal through adult control and PNA female and male mice. GABAergic transmission was present by 1 week of age in females and males and increased in frequency, reaching adult levels at 3 and 4 weeks, respectively. GABAergic PSC frequency was elevated in 3-week-old PNA versus control females. PSC frequency in both controls and PNA mice was activity independent, suggesting that PNA induces changes in synapse organization. PNA also alters the functional response of GnRH neurons to GABA. GABA induced firing in fewer neurons from 3-week-old PNA than control females; membrane potential depolarization induced by GABA was also reduced in cells from PNA mice at this age. PNA thus induces changes during development in the presynaptic organization of the GABAergic network afferent to GnRH neurons as well as the postsynaptic GnRH neuron response, both of which may contribute to adult reproductive dysfunction.SIGNIFICANCE STATEMENT The central neuronal network that regulates reproduction is overactive in polycystic ovary syndrome (PCOS), a leading cause of infertility. Recent evidence of neuroendocrine dysfunction in midpubertal girls suggests that the pathophysiological mechanisms underlying PCOS may arise before pubertal maturation. Prenatal exposure to androgens (PNA) in mice mimics several neuroendocrine features of PCOS. GABAergic transmission to gonadotropin-releasing hormone (GnRH) neurons is important for reproduction and is increased in adult PNA mice. The typical development of this network and when changes with PNA and sex arise relative to puberty are unknown. These studies provide evidence that PNA alters prepubertal development of the GABAergic network afferent to GnRH neurons, including both the presynaptic organization and postsynaptic response. These changes may contribute to reproductive dysfunction in adults.
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Doenz G, Dorn S, Aghaallaei N, Bajoghli B, Riegel E, Aigner M, Bock H, Werner B, Lindhorst T, Czerny T. The function of tcf3 in medaka embryos: efficient knockdown with pe PNAs. BMC Biotechnol 2018; 18:1. [PMID: 29316906 PMCID: PMC5759164 DOI: 10.1186/s12896-017-0411-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 12/11/2017] [Indexed: 12/16/2022] Open
Abstract
Background The application of antisense molecules, such as morpholino oligonucleotides, is an efficient method of gene inactivation in vivo. We recently introduced phosphonic ester modified peptide nucleic acids (PNA) for in vivo loss-of-function experiments in medaka embryos. Here we tested novel modifications of the PNA backbone to knockdown the medaka tcf3 gene. Results A single tcf3 gene exists in the medaka genome and its inactivation strongly affected eye development of the embryos, leading to size reduction and anophthalmia in severe cases. The function of Tcf3 strongly depends on co-repressor interactions. We found interactions with Groucho/Tle proteins to be most important for eye development. Using a dominant negative approach for combined inactivation of all groucho/tle genes also resulted in eye phenotypes, as did interference with three individual tle genes. Conclusions Our results show that side chain modified PNAs come close to the knockdown efficiency of morpholino oligonucleotides in vivo. A single medaka tcf3 gene combines the function of the two zebrafish paralogs hdl and tcf3b. In combination with Groucho/Tle corepressor proteins Tcf3 acts in anterior development and is critical for eye formation. Electronic supplementary material The online version of this article (10.1186/s12896-017-0411-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gerlinde Doenz
- Department for Applied Life Sciences, University of Applied Sciences, FH Campus Wien, Helmut-Qualtinger-Gasse 2, A-1030, Vienna, Austria
| | - Sebastian Dorn
- Department for Applied Life Sciences, University of Applied Sciences, FH Campus Wien, Helmut-Qualtinger-Gasse 2, A-1030, Vienna, Austria
| | - Narges Aghaallaei
- Centre for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany.,Department of Hematology, Oncology, Immunology, Rheumatology and Pulmonology, University Hospital Tübingen, Otfried-Mueller-Strasse 10, 72076, Tübingen, Germany
| | - Baubak Bajoghli
- Department of Hematology, Oncology, Immunology, Rheumatology and Pulmonology, University Hospital Tübingen, Otfried-Mueller-Strasse 10, 72076, Tübingen, Germany
| | - Elisabeth Riegel
- Department for Applied Life Sciences, University of Applied Sciences, FH Campus Wien, Helmut-Qualtinger-Gasse 2, A-1030, Vienna, Austria
| | | | - Holger Bock
- CAST Gründungszentrum GmbH, Wilhelm-Greil-Straße 15, A-6020, Innsbruck, Austria
| | - Birgit Werner
- UGISense AG, c/o Nordwind Capital GmbH, Residenzstrasse 18, 80333, München, Germany
| | - Thomas Lindhorst
- UGISense AG, c/o Nordwind Capital GmbH, Residenzstrasse 18, 80333, München, Germany
| | - Thomas Czerny
- Department for Applied Life Sciences, University of Applied Sciences, FH Campus Wien, Helmut-Qualtinger-Gasse 2, A-1030, Vienna, Austria.
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Elskens J, Manicardi A, Costi V, Madder A, Corradini R. Synthesis and Improved Cross-Linking Properties of C5-Modified Furan Bearing PNAs. Molecules 2017; 22:molecules22112010. [PMID: 29156637 PMCID: PMC6150320 DOI: 10.3390/molecules22112010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [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: 10/21/2017] [Revised: 11/07/2017] [Accepted: 11/09/2017] [Indexed: 12/21/2022] Open
Abstract
Over the past decades, peptide nucleic acid/DNA (PNA:DNA) duplex stability has been improved via backbone modification, often achieved via introducing an amino acid side chain at the α- or γ-position in the PNA sequence. It was previously shown that interstrand cross-linking can further enhance the binding event. In this work, we combined both strategies to fine-tune PNA crosslinking towards single stranded DNA sequences using a furan oxidation-based crosslinking method; for this purpose, γ-l-lysine and γ-l-arginine furan-PNA monomers were synthesized and incorporated in PNA sequences via solid phase synthesis. It was shown that the l-lysine γ-modification had a beneficial effect on crosslink efficiency due to pre-organization of the PNA helix and a favorable electrostatic interaction between the positively-charged lysine and the negatively-charged DNA backbone. Moreover, the crosslink yield could be optimized by carefully choosing the type of furan PNA monomer. This work is the first to describe a selective and biocompatible furan crosslinking strategy for crosslinking of γ-modified PNA sequences towards single-stranded DNA.
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Affiliation(s)
- Joke Elskens
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, 9000 Gent, Belgium.
| | - Alex Manicardi
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, 9000 Gent, Belgium.
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy.
| | - Valentina Costi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy.
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, 9000 Gent, Belgium.
| | - Roberto Corradini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy.
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Usui K, Okada A, Sakashita S, Shimooka M, Tsuruoka T, Nakano SI, Miyoshi D, Mashima T, Katahira M, Hamada Y. DNA G-Wire Formation Using an Artificial Peptide is Controlled by Protease Activity. Molecules 2017; 22:E1991. [PMID: 29144399 PMCID: PMC6150327 DOI: 10.3390/molecules22111991] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 10/27/2017] [Accepted: 11/03/2017] [Indexed: 01/23/2023] Open
Abstract
The development of a switching system for guanine nanowire (G-wire) formation by external signals is important for nanobiotechnological applications. Here, we demonstrate a DNA nanostructural switch (G-wire <--> particles) using a designed peptide and a protease. The peptide consists of a PNA sequence for inducing DNA to form DNA-PNA hybrid G-quadruplex structures, and a protease substrate sequence acting as a switching module that is dependent on the activity of a particular protease. Micro-scale analyses via TEM and AFM showed that G-rich DNA alone forms G-wires in the presence of Ca2+, and that the peptide disrupted this formation, resulting in the formation of particles. The addition of the protease and digestion of the peptide regenerated the G-wires. Macro-scale analyses by DLS, zeta potential, CD, and gel filtration were in agreement with the microscopic observations. These results imply that the secondary structure change (DNA G-quadruplex <--> DNA/PNA hybrid structure) induces a change in the well-formed nanostructure (G-wire <--> particles). Our findings demonstrate a control system for forming DNA G-wire structures dependent on protease activity using designed peptides. Such systems hold promise for regulating the formation of nanowire for various applications, including electronic circuits for use in nanobiotechnologies.
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Affiliation(s)
- Kenji Usui
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan.
| | - Arisa Okada
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan.
| | - Shungo Sakashita
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan.
| | - Masayuki Shimooka
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan.
| | - Takaaki Tsuruoka
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan.
| | - Shu-Ichi Nakano
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan.
| | - Daisuke Miyoshi
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan.
| | - Tsukasa Mashima
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.
- Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.
| | - Masato Katahira
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.
- Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.
| | - Yoshio Hamada
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan.
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Murtola M, Ghidini A, Virta P, Strömberg R. Zinc Ion-Dependent Peptide Nucleic Acid-Based Artificial Enzyme that Cleaves RNA-Bulge Size and Sequence Dependence. Molecules 2017; 22:molecules22111856. [PMID: 29109368 PMCID: PMC6150328 DOI: 10.3390/molecules22111856] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [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: 10/05/2017] [Revised: 10/25/2017] [Accepted: 10/27/2017] [Indexed: 11/17/2022] Open
Abstract
In this report, we investigate the efficiency and selectivity of a Zn2+-dependent peptide nucleic acid-based artificial ribonuclease (PNAzyme) that cleaves RNA target sequences. The target RNAs are varied to form different sizes (3 and 4 nucleotides, nt) and sequences in the bulge formed upon binding to the PNAzyme. PNAzyme-promoted cleavage of the target RNAs was observed and variation of the substrate showed a clear dependence on the sequence and size of the bulge. For targets that form 4-nt bulges, we identified systems with an improved efficacy (an estimated half-life of ca 7–8 h as compared to 11–12 h for sequences studied earlier) as well as systems with an improved site selectivity (up to over 70% cleavage at a single site as compared to 50–60% with previous targets sequences). For targets forming 3-nt bulges, the enhancement compared to previous systems was even more pronounced. Compared to a starting point of targets forming 3-nt AAA bulges (half-lives of ca 21–24 h), we could identify target sequences that were cleaved with half-lives three times lower (ca 7–8 h), i.e., at rates similar to those found for the fastest 4-nt bulge system. In addition, with the 3-nt bulge RNA target site selectivity was improved even further to reach well over 80% cleavage at a specific site.
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Affiliation(s)
- Merita Murtola
- Department of Chemistry, University of Turku, 20014 Turku, Finland.
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, 141 83 Huddinge, Stockholm, Sweden.
| | - Alice Ghidini
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, 141 83 Huddinge, Stockholm, Sweden.
| | - Pasi Virta
- Department of Chemistry, University of Turku, 20014 Turku, Finland.
| | - Roger Strömberg
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, 141 83 Huddinge, Stockholm, Sweden.
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Nim-Anussornkul D, Vilaivan T. Synthesis and optical properties of pyrrolidinyl peptide nucleic acid bearing a base discriminating fluorescence nucleobase 8-(pyrene-1-yl)-ethynyladenine. Bioorg Med Chem 2017; 25:6388-6397. [PMID: 29111370 DOI: 10.1016/j.bmc.2017.10.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Revised: 10/06/2017] [Accepted: 10/12/2017] [Indexed: 12/29/2022]
Abstract
A combination of fluorophore and nucleobase through a π-conjugated rigid linker integrates the base pairing and the fluorescence change into a single event. Such base discriminating fluorophore can change its fluorescence as a direct response to the base pairing event and therefore have advantages over tethered labels or base surrogates lacking the hydrogen-bonding ability. 8-(Pyrene-1-yl)ethynyl-adenine (APyE) has been extensively used as fluorescence labels in DNA and LNA, but it showed little discrimination between different nucleobases. Herein we investigated the synthesis, base pairing ability and optical properties of APyE in pyrrolidinyl peptide nucleic acid - a DNA mimic that shows much stronger affinity and specificity towards DNA than natural oligonucleotides. The APyE in PNA pairs specifically with thymine in the DNA strand, and resulted in 1.5-5.2-fold enhanced and blue-shifted fluorescence emission. Fluorescence quenching was observed in the presence of mismatched base or abasic site directly opposite to the APyE. The behavior of APyE in acpcPNA is distinctively different from DNA whereby a fluorescence was increased selectively upon duplex formation with complementary DNA and therefore emphasizing the unique advantages of using PNA as alternative oligonucleotide probes. Applications as color-shifting probe for detection of trinucleotide repeats in DNA were demonstrated, and the performance of the probe was further improved by combination with reduced graphene oxide as an external nanoquencher.
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Affiliation(s)
- Duangrat Nim-Anussornkul
- 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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79
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Ndeboko B, Ramamurthy N, Lemamy GJ, Jamard C, Nielsen PE, Cova L. Role of Cell-Penetrating Peptides in Intracellular Delivery of Peptide Nucleic Acids Targeting Hepadnaviral Replication. Mol Ther Nucleic Acids 2017; 9:162-9. [PMID: 29246295 DOI: 10.1016/j.omtn.2017.09.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 09/07/2017] [Accepted: 09/07/2017] [Indexed: 02/08/2023]
Abstract
Peptide nucleic acids (PNAs) are potentially attractive antisense agents against hepatitis B virus (HBV), although poor cellular uptake limits their therapeutic application. In the duck HBV (DHBV) model, we evaluated different cell-penetrating peptides (CPPs) for delivery to hepatocytes of a PNA-targeting hepadnaviral encapsidation signal (ε). This anti-ε PNA exhibited sequence-specific inhibition of DHBV RT in a cell-free system. Investigation of the best in vivo route of delivery of PNA conjugated to (D-Arg)8 (P1) showed that intraperitoneal injection to ducklings was ineffective, whereas intravenously (i.v.) injected fluorescein-P1-PNA reached the hepatocytes. Treatment of virus carriers with i.v.-administered P1-PNA resulted in a decrease in viral DNA compared to untreated controls. Surprisingly, a similar inhibition of viral replication was observed in vivo as well as in vitro in primary hepatocyte cultures for a control 2 nt mismatched PNA conjugated to P1. By contrast, the same PNA coupled to (D-Lys)4 (P2) inhibited DHBV replication in a sequence-specific manner. Interestingly, only P1, but not P2, displayed anti-DHBV activity in the absence of PNA cargo. Hence, we provide new evidence that CPP-PNA conjugates inhibit DHBV replication following low-dose administration. Importantly, our results demonstrate the key role of CPPs used as vehicles in antiviral specificity of CPP-PNA conjugates.
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80
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Gupta A, Quijano E, Liu Y, Bahal R, Scanlon SE, Song E, Hsieh WC, Braddock DE, Ly DH, Saltzman WM, Glazer PM. Anti-tumor Activity of miniPEG-γ-Modified PNAs to Inhibit MicroRNA-210 for Cancer Therapy. Mol Ther Nucleic Acids 2017; 9:111-119. [PMID: 29246289 PMCID: PMC5633812 DOI: 10.1016/j.omtn.2017.09.001] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [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] [Received: 01/28/2017] [Revised: 09/05/2017] [Accepted: 09/06/2017] [Indexed: 11/30/2022]
Abstract
MicroRNAs (miRs) are frequently overexpressed in human cancers. In particular, miR-210 is induced in hypoxic cells and acts to orchestrate the adaptation of tumor cells to hypoxia. Silencing oncogenic miRs such as miR-210 may therefore offer a promising approach to anticancer therapy. We have developed a miR-210 inhibition strategy based on a new class of conformationally preorganized antisense γ peptide nucleic acids (γPNAs) that possess vastly superior RNA-binding affinity, improved solubility, and favorable biocompatibility. For cellular delivery, we encapsulated the γPNAs in poly(lactic-co-glycolic acid) (PLGA) nanoparticles (NPs). Our results show that γPNAs targeting miR-210 cause significant delay in growth of a human tumor xenograft in mice compared to conventional PNAs. Further, histopathological analyses show considerable necrosis, fibrosis, and reduced cell proliferation in γPNA-treated tumors compared to controls. Overall, our work provides a chemical framework for a novel anti-miR therapeutic approach using γPNAs that should facilitate rational design of agents to potently inhibit oncogenic microRNAs.
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Affiliation(s)
- Anisha Gupta
- Department of Therapeutic Radiology, Yale University, New Haven, CT 06510, USA
| | - Elias Quijano
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Yanfeng Liu
- Department of Therapeutic Radiology, Yale University, New Haven, CT 06510, USA
| | - Raman Bahal
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, USA
| | - Susan E Scanlon
- Department of Therapeutic Radiology, Yale University, New Haven, CT 06510, USA
| | - Eric Song
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Wei-Che Hsieh
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | | | - Danith H Ly
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - W Mark Saltzman
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Peter M Glazer
- Department of Therapeutic Radiology, Yale University, New Haven, CT 06510, USA; Department of Genetics, Yale University, New Haven, CT 06510, USA.
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81
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Gupta A, Mishra A, Puri N. Peptide nucleic acids: Advanced tools for biomedical applications. J Biotechnol 2017; 259:148-159. [PMID: 28764969 PMCID: PMC7114329 DOI: 10.1016/j.jbiotec.2017.07.026] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Revised: 05/23/2017] [Accepted: 07/23/2017] [Indexed: 02/01/2023]
Abstract
Peptide Nucleic Acids − DNA/RNA analogues. Different Modifications on PNA backbone and their effects. Neutral backbone − remarkable hybridization properties. PNA based biosensors and their diverse biomedical applications. Potential antigene and antisense agents.
Peptide Nucleic Acids (PNAs) are the DNA/RNA analogues in which sugar-phosphate backbone is replaced by N-2-aminoethylglycine repeating units. PNA contains neutral backbone hence due to the absence of electrostatic repulsion, its hybridization shows remarkable stability towards complementary oligonucleotides. PNAs are highly resistant to cleavage by chemicals and enzymes due to the substrate specific nature of enzymes and therefore not degraded inside the cells. PNAs are emerging as new tools in the market due to their applications in antisense and antigene therapies by inhibiting translation and transcription respectively. Hence, several methods based on PNAs have been developed for designing various anticancer and antigene drugs, detection of mutations or modulation of PCR reactions. The duplex homopurine sequence of DNA may also be recognized by PNA, forming firm PNA/DNA/PNA triplex through strand invasion with a looped-out DNA strand. PNAs have also been found to replace DNA probes in varied investigative purposes. There are several disadvantages regarding cellular uptake of PNA, so modifications in PNA backbone or covalent coupling with cell penetrating peptides is necessary to improve its delivery inside the cells. In this review, hybridization properties along with potential applications of PNA in the field of diagnostics and pharmaceuticals are elaborated.
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Affiliation(s)
- Anjali Gupta
- Department of Chemistry, School of Basic and Applied Sciences, Galgotias University, Greater Noida, U.P., India.
| | - Anuradha Mishra
- School of Vocational Studies & Applied Sciences, Gautam Buddha University, Greater Noida, U.P., India
| | - Nidhi Puri
- Department of Applied Science & Humanities, I.T.S Engineering College, Greater Noida, U.P., India
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82
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Abstract
This study demonstrates efficient electrostatic control of surface hybridization through use of morpholinos, a charge-neutral DNA mimic, as the immobilized "probes". In addition to being compatible with low ionic strengths, use of uncharged probes renders the field interaction specific to the nucleic acid analyte. In contrast to DNA probes, morpholino probes enable facile cycling between hybridized and dehybridized states within minutes. Impact of ionic strength and temperature on the effectiveness of electrostatics to direct progress of hybridization is evaluated. Optimal electrostatic control is found when stability of probe-analyte duplexes is set so that electrostatics can efficiently switch between the forward (hybridization) and reverse (dehybridization) directions.
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Affiliation(s)
- Sade Ruffin
- Department of Chemical and
Biomolecular Engineering, New York University Tandon School of Engineering, 6 MetroTech Center, Brooklyn, New York 11201, United States
| | - Isabella A. Hung
- Department of Chemical and
Biomolecular Engineering, New York University Tandon School of Engineering, 6 MetroTech Center, Brooklyn, New York 11201, United States
| | - Ursula M. Koniges
- Department of Chemical and
Biomolecular Engineering, New York University Tandon School of Engineering, 6 MetroTech Center, Brooklyn, New York 11201, United States
| | - Rastislav Levicky
- Department of Chemical and
Biomolecular Engineering, New York University Tandon School of Engineering, 6 MetroTech Center, Brooklyn, New York 11201, United States
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83
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Altai M, Westerlund K, Velletta J, Mitran B, Honarvar H, Karlström AE. Evaluation of affibody molecule-based PNA-mediated radionuclide pretargeting: Development of an optimized conjugation protocol and 177Lu labeling. Nucl Med Biol 2017; 54:1-9. [PMID: 28810153 DOI: 10.1016/j.nucmedbio.2017.07.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 06/30/2017] [Accepted: 07/04/2017] [Indexed: 12/20/2022]
Abstract
INTRODUCTION We have previously developed a pretargeting approach for affibody-mediated cancer therapy based on PNA-PNA hybridization. In this article we have further developed this approach by optimizing the production of the primary agent, ZHER2:342-SR-HP1, and labeling the secondary agent, HP2, with the therapeutic radionuclide 177Lu. We also studied the biodistribution profile of 177Lu-HP2 in mice, and evaluated pretargeting with 177Lu-HP2 in vitro and in vivo. METHODS The biodistribution profile of 177Lu-HP2 was evaluated in NMRI mice and compared to the previously studied 111In-HP2. Pretargeting using 177Lu-HP2 was studied in vitro using the HER2-expressing cell lines BT-474 and SKOV-3, and in vivo in mice bearing SKOV-3 xenografts. RESULTS AND CONCLUSION Using an optimized production protocol for ZHER2:342-SR-HP1 the ligation time was reduced from 15h to 30min, and the yield increased from 45% to 70%. 177Lu-labeled HP2 binds specifically in vitro to BT474 and SKOV-3 cells pre-treated with ZHER2:342-SR-HP1. 177Lu-HP2 was shown to have a more rapid blood clearance compared to 111In-HP2 in NMRI mice, and the measured radioactivity in blood was 0.22±0.1 and 0.68±0.07%ID/g for 177Lu- and 111In-HP2, respectively, at 1h p.i. In contrast, no significant difference in kidney uptake was observed (4.47±1.17 and 3.94±0.58%ID/g for 177Lu- and 111In-HP2, respectively, at 1h p.i.). Co-injection with either Gelofusine or lysine significantly reduced the kidney uptake for 177Lu-HP2 (1.0±0.1 and 1.6±0.2, respectively, vs. 2.97±0.87%ID/g in controls at 4h p.i.). 177Lu-HP2 accumulated in SKOV-3 xenografts in BALB/C nu/nu mice when administered after injection of ZHER2:342-SR-HP1. Without pre-injection of ZHER2:342-SR-HP1, the uptake of 177Lu-HP2 was about 90-fold lower in tumor (0.23±0.08 vs. 20.7±3.5%ID/g). The tumor-to-kidney radioactivity accumulation ratio was almost 5-fold higher in the group of mice pre-injected with ZHER2:342-SR-HP1. In conclusion, 177Lu-HP2 was shown to be a promising secondary agent for affibody-mediated tumor pretargeting in vivo.
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Affiliation(s)
- Mohamed Altai
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Kristina Westerlund
- Division of Protein Technology, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Justin Velletta
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Bogdan Mitran
- Division of Molecular Imaging, Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | - Hadis Honarvar
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Amelie Eriksson Karlström
- Division of Protein Technology, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden.
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Zarrilli F, Amato F, Morgillo CM, Pinto B, Santarpia G, Borbone N, D'Errico S, Catalanotti B, Piccialli G, Castaldo G, Oliviero G. Peptide Nucleic Acids as miRNA Target Protectors for the Treatment of Cystic Fibrosis. Molecules 2017; 22:E1144. [PMID: 28698463 DOI: 10.3390/molecules22071144] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/03/2017] [Accepted: 07/04/2017] [Indexed: 12/12/2022] Open
Abstract
Cystic Fibrosis (CF) is one of the most common life shortening conditions in Caucasians. CF is caused by mutations in the CF Transmembrane Conductance Regulator (CFTR) gene which result in reduced or altered CFTR functionality. Several microRNAs (miRNAs) downregulate the expression of CFTR, thus causing or exacerbating the symptoms of CF. In this context, the design of anti-miRNA agents represents a valid functional tool, but its translation to the clinic might lead to unpredictable side effects because of the interference with the expression of other genes regulated by the same miRNAs. Herein, for the first time, is proposed the use of peptide nucleic acids (PNAs) to protect specific sequences in the 3’UTR (untranslated region) of the CFTR messenger RNA (mRNA) by action of miRNAs. Two PNAs (7 and 13 bases long) carrying the tetrapeptide Gly-SerP-SerP-Gly at their C-end, fully complementary to the 3’UTR sequence recognized by miR-509-3p, have been synthesized and the structural features of target PNA/RNA heteroduplexes have been investigated by spectroscopic and molecular dynamics studies. The co-transfection of the pLuc-CFTR-3´UTR vector with different combinations of PNAs, miR-509-3p, and controls in A549 cells demonstrated the ability of the longer PNA to rescue the luciferase activity by up to 70% of the control, thus supporting the use of suitable PNAs to counteract the reduction in the CFTR expression.
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85
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Tian Q, Rogness J, Meng M, Li Z. Quantitative determination of a siRNA (AD00370) in rat plasma using peptide nucleic acid probe and HPLC with fluorescence detection. Bioanalysis 2017; 9:861-72. [PMID: 28617037 DOI: 10.4155/bio-2017-0017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
AIM Toxicokinetic and pharmacokinetic studies of therapeutic oligonucleotides require validated bioanalytical methods for sensitive and specific quantification of oligonucleotide drug candidates in biological samples. RESULTS A peptide nucleic acid (PNA) hybridization-based HPLC-fluorescence assay was developed and validated for quantification of Arrowhead Pharmaceuticals' proprietary siRNA in rat plasma samples via hybridization and anion-exchange-HPLC (AEX-HPLC) with fluorescence detection. CONCLUSION The validated method provided a sensitive and selective approach for quantification of siRNA in biological samples at a linear quantitation range of 1-1000 ng/ml. The assay requires only 25 μl of plasma sample and shows excellent accuracy and precision even without using an internal standard, providing a useful quantification method for siRNA determination in biological matrix with limited sample volume.
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86
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Sharma P, Teymournejad O, Rikihisa Y. Peptide Nucleic Acid Knockdown and Intra-host Cell Complementation of Ehrlichia Type IV Secretion System Effector. Front Cell Infect Microbiol 2017. [PMID: 28638803 PMCID: PMC5461285 DOI: 10.3389/fcimb.2017.00228] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Survival of Ehrlichia chaffeensis depends on obligatory intracellular infection. One of the barriers to E. chaffeensis research progress has been the inability, using conventional techniques, to generate knock-out mutants for genes essential for intracellular infection. This study examined the use of Peptide Nucleic Acids (PNAs) technology to interrupt type IV secretion system (T4SS) effector protein expression in E. chaffeensis followed by intracellular complementation of the effector to determine its requirement for infection. Successful E. chaffeensis infection depends on the E. chaffeensis-specific T4SS protein effector, ehrlichial translocated factor-1 (Etf-1), which induces Rab5-regulated autophagy to provide host cytosolic nutrients required for E. chaffeensis proliferation. Etf-1 is also imported by host cell mitochondria where it inhibits host cell apoptosis to prolong its infection. We designed a PNA specific to Etf-1 and showed that the PNA bound to the target region of single-stranded Etf-1 RNA using a competitive binding assay. Electroporation of E. chaffeensis with this PNA significantly reduced Etf-1 mRNA and protein, and the bacteria's ability to induce host cell autophagy and infect host cells. Etf-1 PNA-mediated inhibition of ehrlichial Etf-1 expression and E. chaffeensis infection could be intracellularly trans-complemented by ectopic expression of Etf-1-GFP in host cells. These data affirmed the critical role of bacterial T4SS effector in host cell autophagy and E. chaffeensis infection, and demonstrated the use of PNA to analyze the gene functions of obligate intracellular bacteria.
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Affiliation(s)
- Pratibha Sharma
- Department of Veterinary Biosciences, Ohio State UniversityColumbus, OH, United States
| | - Omid Teymournejad
- Department of Veterinary Biosciences, Ohio State UniversityColumbus, OH, United States
| | - Yasuko Rikihisa
- Department of Veterinary Biosciences, Ohio State UniversityColumbus, OH, United States
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87
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Machida T, Novoa A, Gillon É, Zheng S, Claudinon J, Eierhoff T, Imberty A, Römer W, Winssinger N. Dynamic Cooperative Glycan Assembly Blocks the Binding of Bacterial Lectins to Epithelial Cells. Angew Chem Int Ed Engl 2017; 56:6762-6766. [PMID: 28504473 DOI: 10.1002/anie.201700813] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 03/20/2017] [Indexed: 11/06/2022]
Abstract
Pathogens frequently rely on lectins for adhesion and cellular entry into the host. Since these interactions typically result from multimeric binding of lectins to cell-surface glycans, novel therapeutic strategies are being developed with the use of glycomimetics as competitors of such interactions. Herein we study the benefit of nucleic acid based oligomeric assemblies with PNA-fucose conjugates. We demonstrate that the interactions of a lectin with epithelial cells can be inhibited with conjugates that do not form stable assemblies in solution but benefit from cooperativity between ligand-protein interactions and PNA hybridization to achieve high affinity. A dynamic dimeric assembly fully blocked the binding of the fucose-binding lectin BambL of Burkholderia ambifaria, a pathogenic bacterium, to epithelial cells with an efficiency of more than 700-fold compared to l-fucose.
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Affiliation(s)
- Takuya Machida
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Quai Ernest Ansermet 30, 1211, Geneva, Switzerland
| | - Alexandre Novoa
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Quai Ernest Ansermet 30, 1211, Geneva, Switzerland
| | - Émilie Gillon
- CERMAV UPR5301, CNRS, Université Grenoble Alpes, BP 53, 38041, Grenoble cedex 9, France
| | - Shuangshuang Zheng
- Faculty of Biology, Centre for Biological Signalling Studies (BIOSS), Albert-Ludwigs-University Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany
| | - Julie Claudinon
- Faculty of Biology, Centre for Biological Signalling Studies (BIOSS), Albert-Ludwigs-University Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany
| | - Thorsten Eierhoff
- Faculty of Biology, Centre for Biological Signalling Studies (BIOSS), Albert-Ludwigs-University Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany.,Present address: Institute of Biochemistry, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Anne Imberty
- CERMAV UPR5301, CNRS, Université Grenoble Alpes, BP 53, 38041, Grenoble cedex 9, France
| | - Winfried Römer
- Faculty of Biology, Centre for Biological Signalling Studies (BIOSS), Albert-Ludwigs-University Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Quai Ernest Ansermet 30, 1211, Geneva, Switzerland
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88
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Widaningrum T, Widyastuti E, Pratiwi FW, Faidoh Fatimah AI, Rijiravanich P, Somasundrum M, Surareungchai W. Sub-attomolar electrochemical measurement of DNA hybridization based on the detection of high coverage biobarcode latex labels at PNA-modified screen printed electrodes. Talanta 2017; 167:14-20. [PMID: 28340704 DOI: 10.1016/j.talanta.2017.01.094] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 01/31/2017] [Accepted: 01/31/2017] [Indexed: 11/21/2022]
Abstract
We have constructed biobarcode labels based on 468nm diameter latex spheres. Modification with polyallylamine and then glutaraldehyde was used to attach a high DNA loading, consisting of aminated probe DNA (approx. 1.01×102 molecules per sphere) and biobarcode DNA (approx. 1.66×104 molecules per sphere). Detection of the biobarcodes was performed by application of a Ag enhancer solution, causing association of the Ag+ ions with the phosphate groups of the DNA. The deposited Ag was detected by differential pulse voltammetry. A 30 mer sequence from the BL21 strain of E. coli was detected with an LOD of 2.6fM (calibration range 10 aM to 0.1pM, r2=0.91, n=45). The LOD was lowered to 0.56aM (calibration range 100zM to 0.1nM, r2=0.991, n=50) by utilizing a sandwich assay with PNA-modified screen printed electrodes, which lowered the Ag background current. The sandwich assay platform was used to calibrate E. coli strain BL2(DE3) with an LOD of 17.0 CFU mL-1 (calibration range 10 to 106 CFU mL-1, r2=0.99, n=33) with good discrimination against Salmonella.
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89
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Readman JB, Dickson G, Coldham NG. Tetrahedral DNA Nanoparticle Vector for Intracellular Delivery of Targeted Peptide Nucleic Acid Antisense Agents to Restore Antibiotic Sensitivity in Cefotaxime-Resistant Escherichia coli. Nucleic Acid Ther 2017; 27:176-181. [PMID: 28080251 DOI: 10.1089/nat.2016.0644] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The bacterial cell wall presents a barrier to the uptake of unmodified synthetic antisense oligonucleotides, such as peptide nucleic acids, and so is one of the greatest obstacles to the development of their use as therapeutic anti-bacterial agents. Cell-penetrating peptides have been covalently attached to antisense agents, to facilitate penetration of the bacterial cell wall and deliver their cargo into the cytoplasm. Although they are an effective vector for antisense oligonucleotides, they are not specific for bacterial cells and can exhibit growth inhibitory properties at higher doses. Using a bacterial cell growth assay in the presence of cefotaxime (CTX 16 mg/L), we have developed and evaluated a self-assembling non-toxic DNA tetrahedron nanoparticle vector incorporating a targeted anti-blaCTX-M-group 1 antisense peptide nucleic acid (PNA4) in its structure for penetration of the bacterial cell wall. A dose-dependent CTX potentiating effect was observed when PNA4 (0-40 μM) was incorporated into the structure of a DNA tetrahedron vector. The minimum inhibitory concentration (to CTX) of an Escherichia coli field isolate harboring a plasmid carrying blaCTX-M-3 was reduced from 35 to 16 mg/L in the presence of PNA4 carried by the DNA tetrahedron vector (40 μM), contrasting with no reduction in MIC in the presence of PNA4 alone. No growth inhibitory effects of the DNA tetrahedron vector alone were observed.
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Affiliation(s)
- John Benedict Readman
- 1 Bacteriology Department, Animal and Plant Health Agency , Addlestone, Surrey, United Kingdom .,2 Centre for Biomedical Sciences, School of Biological Sciences, Royal Holloway-University of London , Surrey, United Kingdom
| | - George Dickson
- 2 Centre for Biomedical Sciences, School of Biological Sciences, Royal Holloway-University of London , Surrey, United Kingdom
| | - Nick G Coldham
- 1 Bacteriology Department, Animal and Plant Health Agency , Addlestone, Surrey, United Kingdom
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90
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Valadbeigi H, Sadeghifard N, Salehi MB. Assessment of biofilm formation in Pseudomonas aeruginosa by antisense mazE- PNA. Microb Pathog 2017; 104:28-31. [PMID: 28062294 DOI: 10.1016/j.micpath.2017.01.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [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: 11/26/2016] [Revised: 12/28/2016] [Accepted: 01/02/2017] [Indexed: 01/22/2023]
Abstract
The hallmark patogenicity in Pseudomonas aeruginosa (P. aeruginosa) is biofilm formation that is not easy to eradicate, because it has variety mechanisms for antibiotic resistance. In addition, toxin-antitoxin (TA) system may play role in biofilm formation. The current study aimed to evaluate the role of TA loci in biofilm formation. Therefore, 18 P. aeruginosa clinical isolates were collected and evaluated for specific biofilm and TA genes. The analysis by RT-qPCR demonstrated that expression of mazE antitoxin in biofilm formation was increase. On the other hand, mazE antitoxin TA system was used as target for antisense PNA. mazE-PNA was able to influence in biofilm formation and was inhibit at 5,10 and 15 μM concentrations biofilm formation in P. aeruginosa. Therefore, it could be highlighted target for anti-biofilm target to eradicate P. aeruginosa biofilm producer.
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Affiliation(s)
- Hassan Valadbeigi
- Department of Microbiology, Science and Research Branch, Islamic Azad University, Fars, Iran; Department of Microbiology, Shiraz Branch, Islamic Azad University, Shiraz, Iran.
| | - Nourkhoda Sadeghifard
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran.
| | - Majid Baseri Salehi
- Department of Microbiology, Kazeroun Branch, Islamic Azad University, Kazeroun, Iran.
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91
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Abstract
Length is a functional parameter of telomeres, the nucleoprotein structures that protect chromosome ends. The availability of highly specific, high affinity probes for telomeric repeat sequences allowed the development of quantitative approaches aimed at measuring telomere length directly on chromosomes or in interphase nuclei. Here, we describe a general method for telomere quantitative FISH on metaphase chromosomes and discuss its most common applications in research.
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Affiliation(s)
- Isabelle Ourliac-Garnier
- Telomeres & Cancer laboratory, CNRS-UMR3244, Institut Curie, 26 rue d'Ulm, 75248, Paris, France
- UPMC Univ. Paris 06, F-75005, Paris, France
| | - Arturo Londoño-Vallejo
- Telomeres & Cancer laboratory, CNRS-UMR3244, Institut Curie, 26 rue d'Ulm, 75248, Paris, France.
- UPMC Univ. Paris 06, F-75005, Paris, France.
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92
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Abstract
Dysfunctional telomeres arising either through natural attrition due to telomerase deficiency or by the removal of telomere-binding proteins are recognized as double-stranded breaks (DSBs). Repair of DSBs is crucial for the maintenance of genome stability. In mammals, DSBs are repaired by either error-prone nonhomologous end joining (NHEJ) or error-free homologous recombination (HR) and can be visualized as chromosomal fusions.
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Affiliation(s)
- Rekha Rai
- Department of Laboratory Medicine, Yale University School of Medicine, 330 Cedar St., New Haven, CT, 06520, USA
| | - Asha S Multani
- Department of Laboratory Medicine, Yale University School of Medicine, 330 Cedar St., New Haven, CT, 06520, USA
| | - Sandy Chang
- Department of Laboratory Medicine, Yale University School of Medicine, 330 Cedar St., New Haven, CT, 06520, USA.
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93
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Pinto B, Rusciano G, D'Errico S, Borbone N, Sasso A, Piccialli V, Mayol L, Oliviero G, Piccialli G. Synthesis and label free characterization of a bimolecular PNA homo quadruplex. Biochim Biophys Acta Gen Subj 2016; 1861:1222-1228. [PMID: 27913190 DOI: 10.1016/j.bbagen.2016.11.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 11/25/2016] [Accepted: 11/26/2016] [Indexed: 12/31/2022]
Abstract
BACKGROUND G-quadruplex DNA is involved in many physiological and pathological processes. Both clinical and experimental studies on DNA G-quadruplexes are slowed down by their enzymatic instability. In this frame, more stable chemically modified analogs are needed. METHODS The bis-end-linked-(gggt)2 PNA molecule (BEL-PNA) was synthesized using in solution and solid phase synthetic approaches. Quadruplex formation was assessed by circular dichroism (CD) and surface enhanced Raman scattering (SERS). RESULTS An unprecedented bimolecular PNA homo quadruplex is here reported. To achieve this goal, we developed a bifunctional linker that once functionalized with gggt PNA strands and annealed in K+ buffer allowed the obtainment of a PNA homo quadruplex. The identification of the strong SERS band at ~1481cm-1, attributable to vibrations involving the quadruplex diagnostic Hoogsteen type hydrogen bonds, confirmed the formation of the PNA homo quadruplex. CONCLUSIONS By tethering two G-rich PNA strands to the two ends of a suitable bifunctional linker it is possible to obtain bimolecular PNA homo quadruplexes after annealing in K+-containing buffers. The formation of such CD-unfriendly complexes can be monitored, even at low concentrations, by using the SERS technique. GENERAL SIGNIFICANCE Given the importance of DNA G-quadruplexes in medicine and nanotechnology, the obtainment of G-quadruplex analogs provided with enhanced enzymatic stability, and their monitoring by highly sensitive label-free techniques are of the highest importance. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.
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Affiliation(s)
- Brunella Pinto
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy
| | - Giulia Rusciano
- Dipartimento di Scienze Fisiche, Università degli Studi di Napoli Federico II, 80126 Napoli, Italy
| | - Stefano D'Errico
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy
| | - Nicola Borbone
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy
| | - Antonio Sasso
- Dipartimento di Scienze Fisiche, Università degli Studi di Napoli Federico II, 80126 Napoli, Italy
| | - Vincenzo Piccialli
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, 80126 Napoli, Italy
| | - Luciano Mayol
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy
| | - Giorgia Oliviero
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy.
| | - Gennaro Piccialli
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy; CNR, Institute of Protein Biochemistry, 80131 Napoli, Italy.
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94
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Abstract
The discovery of an ever-expanding plethora of coding and non-coding RNAs with nodal and causal roles in the regulation of lung physiology and disease is reinvigorating interest in the clinical utility of the oligonucleotide therapeutic class. This is strongly supported through recent advances in nucleic acids chemistry, synthetic oligonucleotide delivery and viral gene therapy that have succeeded in bringing to market at least three nucleic acid-based drugs. As a consequence, multiple new candidates such as RNA interference modulators, antisense, and splice switching compounds are now progressing through clinical evaluation. Here, manipulation of RNA for the treatment of lung disease is explored, with emphasis on robust pharmacological evidence aligned to the five pillars of drug development: exposure to the appropriate tissue, binding to the desired molecular target, evidence of the expected mode of action, activity in the relevant patient population and commercially viable value proposition.
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95
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Beavers KR, Werfel TA, Shen T, Kavanaugh TE, Kilchrist KV, Mares JW, Fain JS, Wiese CB, Vickers KC, Weiss SM, Duvall CL. Porous Silicon and Polymer Nanocomposites for Delivery of Peptide Nucleic Acids as Anti-MicroRNA Therapies. Adv Mater 2016; 28:7984-7992. [PMID: 27383910 PMCID: PMC5152671 DOI: 10.1002/adma.201601646] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [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: 03/25/2016] [Revised: 06/01/2016] [Indexed: 05/10/2023]
Abstract
Self-assembled polymer/porous silicon nanocomposites overcome intracellular and systemic barriers for in vivo application of peptide nucleic acid (PNA) anti-microRNA therapeutics. Porous silicon (PSi) is leveraged as a biodegradable scaffold with high drug-cargo-loading capacity. Functionalization with a diblock polymer improves PSi nanoparticle colloidal stability, in vivo pharmacokinetics, and intracellular bioavailability through endosomal escape, enabling PNA to inhibit miR-122 in vivo.
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Affiliation(s)
- Kelsey R Beavers
- Interdisciplinary Graduate Program in Materials Science, Vanderbilt University, Nashville, TN, 37235, USA
| | - Thomas A Werfel
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37235, USA
| | - Tianwei Shen
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37235, USA
| | - Taylor E Kavanaugh
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37235, USA
| | - Kameron V Kilchrist
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37235, USA
| | - Jeremy W Mares
- Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, TN, 37235, USA
| | - Joshua S Fain
- Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, TN, 37235, USA
| | - Carrie B Wiese
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN, 37235, USA
| | - Kasey C Vickers
- Department of Medicine/Division of Cardiovascular Medicine, Vanderbilt University, Nashville, TN, 37235, USA
| | - Sharon M Weiss
- Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, TN, 37235, USA
| | - Craig L Duvall
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37235, USA.
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96
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Barbero N, Cauteruccio S, Thakare P, Licandro E, Viscardi G, Visentin S. Is it possible to study the kinetic parameters of interaction between PNA and parallel and antiparallel DNA by stopped-flow fluorescence? J Photochem Photobiol B 2016; 163:296-302. [PMID: 27611452 DOI: 10.1016/j.jphotobiol.2016.08.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 08/03/2016] [Accepted: 08/04/2016] [Indexed: 11/26/2022]
Abstract
Peptide nucleic acids (PNAs) are among the most interesting and versatile artificial structural mimics of nucleic acids and exhibit peculiar and important properties (i.e. high chemical stability, and a high resistance to cellular enzymes and nucleases). Despite their unnatural structure, they are able to recognize and bind DNA and RNA in a very high, specific and selective manner. One of the most popular, easy and reliable method to measure the stability of PNA-DNA hybrid systems is the melting temperature but the thermodynamic data are obtained using a big quantity of materials failing to provide information on the kinetics of the interaction. In the present work, the PNA decamer 6, with the TCACTAGATG sequence of nucleobases, and the corresponding fluorescent PNA-FITU (fluorescein isothiourea) decamer 8 were synthesized with standard manual Boc-based chemistry. The interaction of the PNA-FITU with parallel and antiparallel DNA has been studied by stopped-flow fluorescence, which is proposed as an alternative technique to obtain the kinetic parameters of the binding. The great advantage of using the stopped-flow technique is the possibility of studying the kinetics of the PNA-DNA duplex formation in a physiological environment. In particular, fluorescence stopped-flow technique has been exploited to compare the affinity of two PNA-DNA duplexes since it can discriminate between parallel and antiparallel DNA binding.
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Affiliation(s)
- N Barbero
- Department of Chemistry and NIS Interdepartmental Centre, University of Torino, Via P. Giuria 7, I-10125 Torino, Italy.
| | - S Cauteruccio
- Department of Chemistry, University of Milano, Via C. Golgi 19, I-20133 Milano, Italy.
| | - P Thakare
- Department of Chemistry, University of Milano, Via C. Golgi 19, I-20133 Milano, Italy
| | - E Licandro
- Department of Chemistry, University of Milano, Via C. Golgi 19, I-20133 Milano, Italy
| | - G Viscardi
- Department of Chemistry and NIS Interdepartmental Centre, University of Torino, Via P. Giuria 7, I-10125 Torino, Italy
| | - S Visentin
- Molecular Biotechnology and Health Sciences Department, University of Torino, Via Quarello 15, 10135 Torino, Italy
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97
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Yang LH, Ahn DJ, Koo E. Ultrasensitive FRET-based DNA sensor using PNA/DNA hybridization. Mater Sci Eng C Mater Biol Appl 2016; 69:625-30. [PMID: 27612755 DOI: 10.1016/j.msec.2016.07.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 07/06/2016] [Accepted: 07/08/2016] [Indexed: 10/21/2022]
Abstract
In the diagnosis of genetic diseases, rapid and highly sensitive DNA detection is crucial. Therefore, many strategies for detecting target DNA have been developed, including electrical, optical, and mechanical methods. Herein, a highly sensitive FRET based sensor was developed by using PNA (Peptide Nucleic Acid) probe and QD, in which red color QDs are hybridized with capture probes, reporter probes and target DNAs by EDC-NHS coupling. The hybridized probe with target DNA gives off fluorescent signal due to the energy transfer from QD to Cy5 dye in the reporter probe. Compared to the conventional DNA sensor using DNA probes, the DNA sensor using PNA probes shows higher FRET factor and efficiency due to the higher reactivity between PNA and target DNA. In addition, to elicit the effect of the distance between the donor and the acceptor, we have investigated two types of the reporter probes having Cy5 dyes attached at the different positions of the reporter probes. Results show that the shorter the distance between QDs and Cy5s, the stronger the signal intensity. Furthermore, based on the fluorescence microscopy images using microcapillary chips, the FRET signal is enhanced to be up to 276% times stronger than the signal obtained using the cuvette by the fluorescence spectrometer. These results suggest that the PNA probe system conjugated with QDs can be used as ultrasensitive DNA nanosensors.
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Affiliation(s)
- Lan-Hee Yang
- Advanced Materials Convergence Division, Korea Institute of Ceramic Engineering and Technology (KICET), Jinju-si, Gyeongsangnam-do 660-031, Republic of Korea; Department of Biomicrosystem Technology, Korea University, Seoul 136-701, Republic of Korea
| | - Dong June Ahn
- Department of Biomicrosystem Technology, Korea University, Seoul 136-701, Republic of Korea; Department of Chemical & Biological Engineering, KU-KIST Graduate School, Korea University, Seoul 136-701, Republic of Korea
| | - Eunhae Koo
- Advanced Materials Convergence Division, Korea Institute of Ceramic Engineering and Technology (KICET), Jinju-si, Gyeongsangnam-do 660-031, Republic of Korea.
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98
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Wiberg R, Kingham PJ, Novikova LN. A Morphological and Molecular Characterization of the Spinal Cord after Ventral Root Avulsion or Distal Peripheral Nerve Axotomy Injuries in Adult Rats. J Neurotrauma 2016; 34:652-660. [PMID: 27297543 DOI: 10.1089/neu.2015.4378] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Retrograde cell death in sensory dorsal root ganglion cells following peripheral nerve injury is well established. However, available data regarding the underlying mechanism behind injury induced motoneuron death are conflicting. By comparing morphological and molecular changes in spinal motoneurons after L4-L5 ventral root avulsion (VRA) and distal peripheral nerve axotomy (PNA) 7 and 14 days postoperatively, we aimed to gain more insight about the mechanism behind injury-induced motoneuron degeneration. Morphological changes in spinal cord were assessed by using quantitative immunohistochemistry. Neuronal degeneration was revealed by decreased immunostaining for microtubule-associated protein-2 in dendrites and synaptophysin in presynaptic boutons after both VRA and PNA. Significant motoneuron atrophy was already observed at 7 days post-injury, independently of injury type. Immunostaining for ED1 reactive microglia was significantly elevated in all experimental groups, as well as the astroglial marker glial fibrillary acidic protein (GFAP). Quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis of the ventral horn from L4-L5 spinal cord segments revealed a significant upregulation of genes involved in programmed cell death including caspase-3, caspase-8, and related death receptors TRAIL-R, tumor necrosis factor (TNF)-R, and Fas following VRA. In contrast, following PNA, caspase-3 and the death receptor gene expression levels did not differ from the control, and there was only a modest increased expression of caspase-8. Moreover, the altered gene expression correlated with protein changes. These results show that the spinal motoneurons reacted in a similar fashion with respect to morphological changes after both proximal and distal injury. However, the increased expression of caspase-3, caspase-8, and related death receptors after VRA suggest that injury- induced motoneuron degeneration is mediated through an apoptotic mechanism, which might involve both the intrinsic and the extrinsic pathways.
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Affiliation(s)
- Rebecca Wiberg
- 1 Department of Integrative Medical Biology, Section of Anatomy, Umeå University , Umeå, Sweden .,2 Department of Surgical and Perioperative Sciences, Section of Hand and Plastic Surgery, Umeå University , Umeå, Sweden
| | - Paul J Kingham
- 1 Department of Integrative Medical Biology, Section of Anatomy, Umeå University , Umeå, Sweden
| | - Liudmila N Novikova
- 1 Department of Integrative Medical Biology, Section of Anatomy, Umeå University , Umeå, Sweden
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99
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Asanuma H, Niwa R, Akahane M, Murayama K, Kashida H, Kamiya Y. Strand-invading linear probe combined with unmodified PNA. Bioorg Med Chem 2016; 24:4129-4137. [PMID: 27394693 DOI: 10.1016/j.bmc.2016.06.055] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 06/23/2016] [Accepted: 06/29/2016] [Indexed: 11/19/2022]
Abstract
Efficient strand invasion by a linear probe to fluorescently label double-stranded DNA has been implemented by employing a probe and unmodified PNA. As a fluorophore, we utilized ethynylperylene. Multiple ethynylperylene residues were incorporated into the DNA probe via a d-threoninol scaffold. The ethynylperylene did not significantly disrupt hybridization with complementary DNA. The linear probe self-quenched in the absence of target DNA and did not hybridize with PNA. A gel-shift assay revealed that linear probe and PNA combination invaded the central region of double-stranded DNA upon heat-shock treatment to form a double duplex. To further suppress the background emission and increase the stability of the probe/DNA duplex, a probe containing anthraquinones as well as ethynylperylene was synthesized. This probe and PNA invader pair detected an internal sequence in a double-stranded DNA with high sensitivity when heat shock treatment was used. The probe and PNA pair was able to invade at the terminus of a long double-stranded DNA at 40°C at 100mM NaCl concentration.
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Affiliation(s)
- Hiroyuki Asanuma
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan.
| | - Rie Niwa
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Mariko Akahane
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Keiji Murayama
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Hiromu Kashida
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Yukiko Kamiya
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
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100
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Machida T, Dutt S, Winssinger N. Allosterically Regulated Phosphatase Activity from Peptide- PNA Conjugates Folded Through Hybridization. Angew Chem Int Ed Engl 2016; 55:8595-8. [PMID: 27320214 DOI: 10.1002/anie.201602751] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 05/10/2016] [Indexed: 01/17/2023]
Abstract
The importance of spatial organization in short peptide catalysts is well recognized. We synthesized and screened a library of peptides flanked by peptide nucleic acids (PNAs) such that the peptide would be constrained in a hairpin loop upon hybridization. A screen for phosphatase activity led to the discovery of a catalyst with >25-fold rate acceleration over the linear peptide. We demonstrated that the hybridization-enforced folding of the peptide is necessary for activity, and designed a catalyst that is allosterically controlled using a complementary PNA sequence.
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Affiliation(s)
- Takuya Machida
- Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva, Quai Ernest Ansermet 30, 1211, Geneva, Switzerland
| | - Som Dutt
- Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva, Quai Ernest Ansermet 30, 1211, Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva, Quai Ernest Ansermet 30, 1211, Geneva, Switzerland.
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