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Travagliante G, Gaeta M, Gangemi CMA, Alaimo S, Ferro A, Purrello R, D'Urso A. Interactions between achiral porphyrins and a mature miRNA. NANOSCALE 2024; 16:5137-5148. [PMID: 38305723 DOI: 10.1039/d3nr05504c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
Recent discoveries have revealed that mature miRNAs could form highly ordered structures similar to aptamers, suggesting diverse functions beyond mRNA recognition and degradation. This study focuses on understanding the secondary structures of human miR-26b-5p (UUCAAGUAAUUCAGGAUAGGU) using circular dichroism (CD) and chiroptical probes; in particular, four achiral porphyrins were utilized to both act as chiroptical probes and influence miRNA thermodynamic stability. Various spectroscopic techniques, including UV-Vis, fluorescence, resonance light scattering (RLS), electronic circular dichroism (ECD), and CD melting, were employed to study their interactions. UV-Vis titration revealed that meso-tetrakis(4-N-methylpyridyl) porphyrin (H2T4) and meso-tetrakis(4-carboxyphenylspermine) porphyrin (H2TCPPSpm4) formed complexes with distinct binding stoichiometries up to 6 : 1 and 3 : 1 ratios, respectively, and these results were supported by RLS and fluorescence, while the zinc(II) derivative porphyrin ZnT4 exhibited a weaker interaction. ZnTCPPSpm4 formed aggregates in PBS with higher organization in the presence of miRNA. CD titrations displayed an induced CD signal in the Soret region for every porphyrin investigated, indicating that they can be used as chiroptical probes for miR-26b-5p. Lastly, CD melting experiments revealed that at a 1 : 1 ratio, porphyrins did not significantly affect miRNA stability, except for H2TCPPSpm4. However, at a 3 : 1 ratio, all porphyrins, except ZnTCPPSpm4, exhibited a strong destabilizing effect on miRNA secondary structures. These findings shed light on the structural versatility of miR-26b-5p and highlight the potential of porphyrins as chiroptical probes and modulators of miRNA stability.
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Affiliation(s)
- Gabriele Travagliante
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, 95125, Catania, Italy.
| | - Massimiliano Gaeta
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, 95125, Catania, Italy.
| | - Chiara M A Gangemi
- Dipartimento di Scienze chimiche, biologiche, farmaceutiche e ambientali, Università degli Studi di Messina, V.le Ferdinando Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Salvatore Alaimo
- Dipartimento di Medicina Clinica e Sperimentale, c/o Dipartimento di Matematica e Informatica, Università degli Studi di Catania, Viale A. Doria 6, 95125, Catania, Italy
| | - Alfredo Ferro
- Dipartimento di Medicina Clinica e Sperimentale, c/o Dipartimento di Matematica e Informatica, Università degli Studi di Catania, Viale A. Doria 6, 95125, Catania, Italy
| | - Roberto Purrello
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, 95125, Catania, Italy.
| | - Alessandro D'Urso
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, 95125, Catania, Italy.
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2
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Chira S, Ciocan C, Bica C, Calin GA, Berindan-Neagoe I. Artificial miRNAs derived from miR-181 family members have potential in cancer therapy due to an altered spectrum of target mRNAs. FEBS Lett 2023; 597:1989-2005. [PMID: 37283340 DOI: 10.1002/1873-3468.14673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/08/2023] [Accepted: 05/22/2023] [Indexed: 06/08/2023]
Abstract
miRNAs are a class of noncoding RNAs with gene regulation properties, and they function as key factors in cell homeostasis. The interaction of miRNAs with their target mRNAs is largely considered to rely on sequence complementarity; however, some evidence indicates that mature miRNAs can adopt diverse conformations with implications for their function. Using the oncogenic miR-181 family as a study model, we suggest that a potential relationship between the primary sequence and secondary structure of miRNAs may have an impact on the number and spectrum of targeted cellular transcripts. We further emphasize that specific alterations in miR-181 primary sequences might impose certain constraints on target gene selection compared with the wild-type sequences, leading to the targeting of new transcripts with upregulated function in cancer.
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Affiliation(s)
- Sergiu Chira
- Research Center for Functional Genomics, Biomedicine, and Translational Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Cristina Ciocan
- Research Center for Functional Genomics, Biomedicine, and Translational Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Cecilia Bica
- Research Center for Functional Genomics, Biomedicine, and Translational Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - George A Calin
- Translational Molecular Pathology, MD Anderson Cancer Center, Texas State University, Houston, TX, USA
- The RNA Interference and Non-codingRNA Center, MD Anderson Cancer Center, Texas State University, Houston, TX, USA
| | - Ioana Berindan-Neagoe
- Research Center for Functional Genomics, Biomedicine, and Translational Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
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3
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Baumann V, Athanasiou AT, Faridani OR, Schwerdtfeger AR, Wallner B, Steinborn R. Identification of extremely GC-rich micro RNAs for RT-qPCR data normalization in human plasma. Front Genet 2023; 13:1058668. [PMID: 36685854 PMCID: PMC9846067 DOI: 10.3389/fgene.2022.1058668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 12/02/2022] [Indexed: 01/05/2023] Open
Abstract
We aimed at extending the repertoire of high-quality miRNA normalizers for reverse transcription-quantitative PCR (RT-qPCR) of human plasma with special emphasis on the extremely guanine-cytosine-rich portion of the miRNome. For high-throughput selection of stable candidates, microarray technology was preferred over small-RNA sequencing (sRNA-seq) since the latter underrepresented miRNAs with a guanine-cytosine (GC) content of at least 75% (p = 0.0002, n = 2). miRNA abundances measured on the microarray were ranked for consistency and uniformity using nine normalization approaches. The eleven most stable sequences included miRNAs of moderate, but also extreme GC content (45%-65%: miR-320d, miR-425-5p, miR-185-5p, miR-486-5p; 80%-95%: miR-1915-3p, miR-3656-5p, miR-3665-5p, miR-3960-5p, miR-4488-5p, miR-4497 and miR-4787-5p). In contrast, the seven extremely GC-rich miRNAs were not found in the two plasma miRNomes screened by sRNA-seq. Stem-loop RT-qPCR was employed for stability verification in 32 plasma samples of healthy male Caucasians (age range: 18-55 years). In general, inter-individual variance of miRNA abundance was low or very low as indicated by coefficient of variation (CV) values of 0.6%-8.2%. miR-3665 and miR-1915-3p outperformed in this analysis (CVs: 0.6 and 2.4%, respectively). The eight most stable sequences included four extremely GC-rich miRNAs (miR-1915-3p, miR-3665, miR-4787-5p and miR-4497). The best-performing duo normalization factor (NF) for the condition of human plasma, miR-320d and miR-4787-5p, also included a GC-extreme miRNA. In summary, the identification of extremely guanine-cytosine-rich plasma normalizers will help to increase accuracy of PCR-based miRNA quantification, thus raise the potential that miRNAs become markers for psychological stress reactions or early and precise diagnosis of clinical phenotypes. The novel miRNAs might also be useful for orthologous contexts considering their conservation in related animal genomes.
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Affiliation(s)
- Volker Baumann
- Genomics Core Facility, VetCore, University of Veterinary Medicine, Vienna, Austria
| | | | - Omid R. Faridani
- Garvan Institute of Medical Research, Sydney, NSW, Australia,Lowy Cancer Research Centre, School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia
| | | | - Bernard Wallner
- Department of Behavioral and Cognitive Biology, University of Vienna, Vienna, Austria
| | - Ralf Steinborn
- Genomics Core Facility, VetCore, University of Veterinary Medicine, Vienna, Austria,Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria,*Correspondence: Ralf Steinborn,
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Zada S, Lu H, Dai W, Tang S, Khan S, Yang F, Qiao Y, Fu P, Dong H, Zhang X. Multiple amplified microRNAs monitoring in living cells based on fluorescence quenching of Mo 2B and hybridization chain reaction. Biosens Bioelectron 2022; 197:113815. [PMID: 34814033 DOI: 10.1016/j.bios.2021.113815] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 10/10/2021] [Accepted: 11/15/2021] [Indexed: 02/07/2023]
Abstract
Imaging intracellular microRNAs (miRNAs) demonstrated an essential role in exposing their biological and pathological functions. However, the detection of sequence-specific miRNAs in living cells remains a key challenge. Herein, a facile amplified multiple intracellular miRNAs imaging platform was constructed based on Mo2B nanosheets (NSs) fluorescence (FL) quenching and hybridization chain reaction (HCR). The Mo2B NSs demonstrated strong interaction with the hairpin probes (HPs), ssDNA loop, and excellent multiple FL dyes quenching performance, achieving ultralow background signal. After transfection, the HPs recognized specific targets miRNAs, the corresponding HCR was triggered to produce tremendous DNA-miRNA duplex helixes, which dissociated from the surface of the Mo2B NSs to produce strong FL for miRNAs detection. It realized to image multiple miRNAs biomarkers in different cells to discriminate cancer cells from normal cells owing to the excellent sensitivity, and the regulated expression change of miRNAs in cancer cells was also successfully monitored. The facile and versatile Mo2B-based FL quenching platform open an avenue to profile miRNAs expression pattern in living cells, and has great applications in miRNAs based biological and biomedical research.
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Affiliation(s)
- Shah Zada
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Research Centre for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing, 100083, PR China
| | - Huiting Lu
- School of Chemistry and Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing, 100083, PR China
| | - Wenhao Dai
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Research Centre for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing, 100083, PR China
| | - Songsong Tang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Research Centre for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing, 100083, PR China
| | - Sikandar Khan
- Department of Biotechnology, Shaheed Benazir Bhutto University, Sheringal, KPK, Pakistan
| | - Fan Yang
- College of Basic Medical Sciences, Shanxi University, Taiyuan, 030001, PR China
| | - Yuchun Qiao
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Research Centre for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing, 100083, PR China
| | - Pengcheng Fu
- State Key Laboratory of Marine Resource Utilization in South China Sea Hainan University, 58 Renmin Avenue, Meilan District Haikou, Hainan Province, 570228, PR China
| | - Haifeng Dong
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Research Centre for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing, 100083, PR China; Marshall Laboratory of Biomedical Engineering Research Center for Biosensor and Nanotheranostic, School of Biomedical Engineering, Health Science Centre, Shenzhen University, Shenzhen, Guangdong, 518060, PR China.
| | - Xueji Zhang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Research Centre for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing, 100083, PR China; Marshall Laboratory of Biomedical Engineering Research Center for Biosensor and Nanotheranostic, School of Biomedical Engineering, Health Science Centre, Shenzhen University, Shenzhen, Guangdong, 518060, PR China.
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5
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Qu N, Ying Y, Qin J, Chen AK. Rational design of self-assembled RNA nanostructures for HIV-1 virus assembly blockade. Nucleic Acids Res 2021; 50:e44. [PMID: 34967412 PMCID: PMC9071489 DOI: 10.1093/nar/gkab1282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/16/2021] [Accepted: 12/15/2021] [Indexed: 11/14/2022] Open
Abstract
Many pathological processes are driven by RNA-protein interactions, making such interactions promising targets for molecular interventions. HIV-1 assembly is one such process, in which the viral genomic RNA interacts with the viral Gag protein and serves as a scaffold to drive Gag multimerization that ultimately leads to formation of a virus particle. Here, we develop self-assembled RNA nanostructures that can inhibit HIV-1 virus assembly, achieved through hybridization of multiple artificial small RNAs with a stem-loop structure (STL) that we identify as a prominent ligand of Gag that can inhibit virus particle production via STL-Gag interactions. The resulting STL-decorated nanostructures (double and triple stem-loop structures denoted as Dumbbell and Tribell, respectively) can elicit more pronounced viral blockade than their building blocks, with the inhibition arising as a result of nanostructures interfering with Gag multimerization. These findings could open up new avenues for RNA-based therapy.
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Affiliation(s)
- Na Qu
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing 100871, China
| | - Yachen Ying
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing 100871, China.,Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China.,National Biomedical Imaging Center, Peking University, Beijing 100871, China
| | - Jinshan Qin
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing 100871, China.,Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China.,National Biomedical Imaging Center, Peking University, Beijing 100871, China
| | - Antony K Chen
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing 100871, China.,National Biomedical Imaging Center, Peking University, Beijing 100871, China
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Das T, Das TK, Khodarkovskaya A, Dash S. Non-coding RNAs and their bioengineering applications for neurological diseases. Bioengineered 2021; 12:11675-11698. [PMID: 34756133 PMCID: PMC8810045 DOI: 10.1080/21655979.2021.2003667] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Engineering of cellular biomolecules is an emerging landscape presenting creative therapeutic opportunities. Recently, several strategies such as biomimetic materials, drug-releasing scaffolds, stem cells, and dynamic culture systems have been developed to improve specific biological functions, however, have been confounded with fundamental and technical roadblocks. Rapidly emerging investigations on the bioengineering prospects of mammalian ribonucleic acid (RNA) is expected to result in significant biomedical advances. More specifically, the current trend focuses on devising non-coding (nc) RNAs as therapeutic candidates for complex neurological diseases. Given the pleiotropic and regulatory role, ncRNAs such as microRNAs and long non-coding RNAs are deemed as attractive therapeutic candidates. Currently, the list of non-coding RNAs in mammals is evolving, which presents the plethora of hidden possibilities including their scope in biomedicine. Herein, we critically review on the emerging repertoire of ncRNAs in neurological diseases such as Alzheimer’s disease, Parkinson’s disease, neuroinflammation and drug abuse disorders. Importantly, we present the advances in engineering of ncRNAs to improve their biocompatibility and therapeutic feasibility as well as provide key insights into the applications of bioengineered non-coding RNAs that are investigated for neurological diseases.
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Affiliation(s)
- Tuhin Das
- Quanta Therapeutics, San Francisco, CA, 94158, USA.,RayBiotech, Inc, 3607 Parkway Lane, Peachtree Corners, GA, 30092, USA
| | - Tushar Kanti Das
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Anne Khodarkovskaya
- Department of Pathology, Weill Cornell Medicine, Medical College of Cornell University, New York, NY, 10065, USA
| | - Sabyasachi Dash
- Department of Pathology, Weill Cornell Medicine, Medical College of Cornell University, New York, NY, 10065, USA.,School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, Odisha, 751024 India
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Comegna M, Conte G, Falanga AP, Marzano M, Cernera G, Di Lullo AM, Amato F, Borbone N, D'Errico S, Ungaro F, d'Angelo I, Oliviero G, Castaldo G. Assisting PNA transport through cystic fibrosis human airway epithelia with biodegradable hybrid lipid-polymer nanoparticles. Sci Rep 2021; 11:6393. [PMID: 33737583 PMCID: PMC7973768 DOI: 10.1038/s41598-021-85549-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 03/01/2021] [Indexed: 12/11/2022] Open
Abstract
Cystic fibrosis (CF) is characterized by an airway obstruction caused by a thick mucus due to a malfunctioning Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) protein. The sticky mucus restricts drugs in reaching target cells limiting the efficiency of treatments. The development of new approaches to enhance drug delivery to the lungs represents CF treatment's main challenge. In this work, we report the production and characterization of hybrid core–shell nanoparticles (hNPs) comprising a PLGA core and a dipalmitoylphosphatidylcholine (DPPC) shell engineered for inhalation. We loaded hNPs with a 7-mer peptide nucleic acid (PNA) previously considered for its ability to modulate the post-transcriptional regulation of the CFTR gene. We also investigated the in vitro release kinetics of hNPs and their efficacy in PNA delivery across the human epithelial airway barrier using an ex vivo model based on human primary nasal epithelial cells (HNEC) from CF patients. Confocal analyses and hNPs transport assay demonstrated the ability of hNPs to overcome the mucus barrier and release their PNA cargo within the cytoplasm, where it can exert its biological function.
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Affiliation(s)
- Marika Comegna
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131, Naples, Italy.,CEINGE-Biotecnologie Avanzate S.c.a.r.l., 80145, Naples, Italy
| | - Gemma Conte
- Di.S.T.A.Bi.F., University of Campania Luigi Vanvitelli, 81100, Caserta, Italy
| | | | - Maria Marzano
- Institute of Crystallography, National Research Council, 70126, Bari, Italy
| | - Gustavo Cernera
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131, Naples, Italy.,CEINGE-Biotecnologie Avanzate S.c.a.r.l., 80145, Naples, Italy
| | - Antonella Miriam Di Lullo
- ENT Section, Department of Neuroscience, Reproductive and Odontostomatological Sciences, University of Naples Federico II, 80131, Naples, Italy
| | - Felice Amato
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131, Naples, Italy.,CEINGE-Biotecnologie Avanzate S.c.a.r.l., 80145, Naples, Italy
| | - Nicola Borbone
- Department of Pharmacy, University of Naples Federico II, 80131, Naples, Italy
| | - Stefano D'Errico
- Department of Pharmacy, University of Naples Federico II, 80131, Naples, Italy
| | - Francesca Ungaro
- Department of Pharmacy, University of Naples Federico II, 80131, Naples, Italy
| | - Ivana d'Angelo
- Di.S.T.A.Bi.F., University of Campania Luigi Vanvitelli, 81100, Caserta, Italy.
| | - Giorgia Oliviero
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131, Naples, Italy.
| | - Giuseppe Castaldo
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131, Naples, Italy.,CEINGE-Biotecnologie Avanzate S.c.a.r.l., 80145, Naples, Italy
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