1
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Monopoli KR, Korkin D, Khvorova A. Asymmetric trichotomous partitioning overcomes dataset limitations in building machine learning models for predicting siRNA efficacy. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:93-109. [PMID: 37456778 PMCID: PMC10338369 DOI: 10.1016/j.omtn.2023.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 06/09/2023] [Indexed: 07/18/2023]
Abstract
Chemically modified small interfering RNAs (siRNAs) are promising therapeutics guiding sequence-specific silencing of disease genes. Identifying chemically modified siRNA sequences that effectively silence target genes remains challenging. Such determinations necessitate computational algorithms. Machine learning is a powerful predictive approach for tackling biological problems but typically requires datasets significantly larger than most available siRNA datasets. Here, we describe a framework applying machine learning to a small dataset (356 modified sequences) for siRNA efficacy prediction. To overcome noise and biological limitations in siRNA datasets, we apply a trichotomous, two-threshold, partitioning approach, producing several combinations of classification threshold pairs. We then test the effects of different thresholds on random forest machine learning model performance using a novel evaluation metric accounting for class imbalances. We identify thresholds yielding a model with high predictive power, outperforming a linear model generated from the same data, that was predictive upon experimental evaluation. Using a novel model feature extraction method, we observe target site base importances and base preferences consistent with our current understanding of the siRNA-mediated silencing mechanism, with the random forest providing higher resolution than the linear model. This framework applies to any classification challenge involving small biological datasets, providing an opportunity to develop high-performing design algorithms for oligonucleotide therapies.
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Affiliation(s)
- Kathryn R. Monopoli
- Department of Bioinformatics & Computational Biology, Worcester Polytechnic Institute, Worcester, MA 01609, USA
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Dmitry Korkin
- Department of Bioinformatics & Computational Biology, Worcester Polytechnic Institute, Worcester, MA 01609, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
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2
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Fan Y, Yang Z. Inhaled siRNA Formulations for Respiratory Diseases: From Basic Research to Clinical Application. Pharmaceutics 2022; 14:1193. [PMID: 35745766 PMCID: PMC9227582 DOI: 10.3390/pharmaceutics14061193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 12/10/2022] Open
Abstract
The development of siRNA technology has provided new opportunities for gene-specific inhibition and knockdown, as well as new ideas for the treatment of disease. Four siRNA drugs have already been approved for marketing. However, the instability of siRNA in vivo makes systemic delivery ineffective. Inhaled siRNA formulations can deliver drugs directly to the lung, showing great potential for treating respiratory diseases. The clinical applications of inhaled siRNA formulations still face challenges because effective delivery of siRNA to the lung requires overcoming the pulmonary and cellular barriers. This paper reviews the research progress for siRNA inhalation formulations for the treatment of various respiratory diseases and summarizes the chemical structural modifications and the various delivery systems for siRNA. Finally, we conclude the latest clinical application research for inhaled siRNA formulations and discuss the potential difficulty in efficient clinical application.
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Affiliation(s)
| | - Zhijun Yang
- School of Chinese Medicine, Hong Kong Baptist University, 224 Waterloo Rd., Kowloon Tong, Hong Kong, China;
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3
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Fàbrega C, Aviñó A, Eritja R. Chemical Modifications in Nucleic Acids for Therapeutic and Diagnostic Applications. CHEM REC 2021; 22:e202100270. [DOI: 10.1002/tcr.202100270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/26/2021] [Accepted: 11/26/2021] [Indexed: 11/08/2022]
Affiliation(s)
- Carme Fàbrega
- Department of Surfactants and Nanobiotechnology Institute for Advanced Chemistry of Catalonia (IQAC) Spanish National Research Council (CSIC) Jordi Girona 18–26 E-08034 Barcelona Spain
- Networking Center on Bioengineering Biomaterials and Nanomedicine (CIBER-BBN) E-08034 Barcelona Spain
| | - Anna Aviñó
- Department of Surfactants and Nanobiotechnology Institute for Advanced Chemistry of Catalonia (IQAC) Spanish National Research Council (CSIC) Jordi Girona 18–26 E-08034 Barcelona Spain
- Networking Center on Bioengineering Biomaterials and Nanomedicine (CIBER-BBN) E-08034 Barcelona Spain
| | - Ramon Eritja
- Department of Surfactants and Nanobiotechnology Institute for Advanced Chemistry of Catalonia (IQAC) Spanish National Research Council (CSIC) Jordi Girona 18–26 E-08034 Barcelona Spain
- Networking Center on Bioengineering Biomaterials and Nanomedicine (CIBER-BBN) E-08034 Barcelona Spain
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4
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Aghamiri S, Raee P, Talaei S, Mohammadi-Yeganeh S, Bayat S, Rezaee D, Ghavidel AA, Teymouri A, Roshanzamiri S, Farhadi S, Ghanbarian H. Nonviral siRNA delivery systems for pancreatic cancer therapy. Biotechnol Bioeng 2021; 118:3669-3690. [PMID: 34170520 DOI: 10.1002/bit.27869] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 06/17/2021] [Accepted: 06/19/2021] [Indexed: 12/17/2022]
Abstract
The serious drawbacks of the conventional treatment of pancreatic ductal adenocarcinoma (PDAC) such as nonspecific toxicity and high resistance to chemo and radiation therapy, have prompted the development and application of countless small interfering RNA (siRNA)-based therapeutics. Recent advances in drug delivery systems hold great promise for improving siRNA-based therapeutics and developing a new class of drugs, known as nano-siRNA drugs. However, many fundamental questions, regarding toxicity, immunostimulation, and poor knowledge of nano-bio interactions, need to be addressed before clinical translation. In this review, we provide recent achievements in the design and development of various nonviral delivery vehicles for pancreatic cancer therapy. More importantly, codelivery of conventional anticancer drugs with siRNA as a new revolutionary pancreatic cancer combinational therapy is completely discussed.
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Affiliation(s)
- Shahin Aghamiri
- Student Research Committee, Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Pourya Raee
- Department of Biology and Anatomical Sciences, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sam Talaei
- Department of Clinical Pharmacy, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Samira Mohammadi-Yeganeh
- Medical Nanotechnology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shiva Bayat
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Delsuz Rezaee
- Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Afshin A Ghavidel
- Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Alireza Teymouri
- Department of Infectious Disease, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Soheil Roshanzamiri
- Department of Clinical Pharmacy, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shohreh Farhadi
- Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Ghanbarian
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Tissue Engineering and Applied Cell SciencesSchool of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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5
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Chernikov IV, Vlassov VV, Chernolovskaya EL. Current Development of siRNA Bioconjugates: From Research to the Clinic. Front Pharmacol 2019; 10:444. [PMID: 31105570 PMCID: PMC6498891 DOI: 10.3389/fphar.2019.00444] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 04/08/2019] [Indexed: 12/12/2022] Open
Abstract
Small interfering RNAs (siRNAs) acting via RNA interference mechanisms are able to recognize a homologous mRNA sequence in the cell and induce its degradation. The main problems in the development of siRNA-based drugs for therapeutic use are the low efficiency of siRNA delivery to target cells and the degradation of siRNAs by nucleases in biological fluids. Various approaches have been proposed to solve the problem of siRNA delivery in vivo (e.g., viruses, cationic lipids, polymers, nanoparticles), but all have limitations for therapeutic use. One of the most promising approaches to solve the problem of siRNA delivery to target cells is bioconjugation; i.e., the covalent connection of siRNAs with biogenic molecules (lipophilic molecules, antibodies, aptamers, ligands, peptides, or polymers). Bioconjugates are "ideal nanoparticles" since they do not need a positive charge to form complexes, are less toxic, and are less effectively recognized by components of the immune system because of their small size. This review is focused on strategies and principles for constructing siRNA bioconjugates for in vivo use.
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Affiliation(s)
- Ivan V Chernikov
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Valentin V Vlassov
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Elena L Chernolovskaya
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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6
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Guo F, Li Q, Zhou C. Synthesis and biological applications of fluoro-modified nucleic acids. Org Biomol Chem 2018; 15:9552-9565. [PMID: 29086791 DOI: 10.1039/c7ob02094e] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Owing to the unique physical properties of a fluorine atom, incorporating fluoro-modifications into nucleic acids offers striking biophysical and biochemical features, and thus significantly extends the breadth and depth of biological applications of nucleic acids. In this review, fluoro-modified nucleic acids that have been synthesized through either solid phase synthesis or the enzymatic approach are briefly summarised, followed by a section describing their biomedical applications in nucleic acid-based therapeutics, 18F PET imaging and mechanistic studies of DNA modifying enzymes. In the last part, the utility of 19F NMR and MRI for probing the structure, dynamics and molecular interactions of fluorinated nucleic acids is reviewed.
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Affiliation(s)
- Fengmin Guo
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China.
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7
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siRNAmod: A database of experimentally validated chemically modified siRNAs. Sci Rep 2016; 6:20031. [PMID: 26818131 PMCID: PMC4730238 DOI: 10.1038/srep20031] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 12/21/2015] [Indexed: 11/21/2022] Open
Abstract
Small interfering RNA (siRNA) technology has vast potential for functional genomics and development of therapeutics. However, it faces many obstacles predominantly instability of siRNAs due to nuclease digestion and subsequently biologically short half-life. Chemical modifications in siRNAs provide means to overcome these shortcomings and improve their stability and potency. Despite enormous utility bioinformatics resource of these chemically modified siRNAs (cm-siRNAs) is lacking. Therefore, we have developed siRNAmod, a specialized databank for chemically modified siRNAs. Currently, our repository contains a total of 4894 chemically modified-siRNA sequences, comprising 128 unique chemical modifications on different positions with various permutations and combinations. It incorporates important information on siRNA sequence, chemical modification, their number and respective position, structure, simplified molecular input line entry system canonical (SMILES), efficacy of modified siRNA, target gene, cell line, experimental methods, reference etc. It is developed and hosted using Linux Apache MySQL PHP (LAMP) software bundle. Standard user-friendly browse, search facility and analysis tools are also integrated. It would assist in understanding the effect of chemical modifications and further development of stable and efficacious siRNAs for research as well as therapeutics. siRNAmod is freely available at: http://crdd.osdd.net/servers/sirnamod.
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8
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Kokil GR, Veedu RN, Ramm GA, Prins JB, Parekh HS. Type 2 diabetes mellitus: limitations of conventional therapies and intervention with nucleic acid-based therapeutics. Chem Rev 2015; 115:4719-43. [PMID: 25918949 DOI: 10.1021/cr5002832] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Ganesh R Kokil
- †School of Pharmacy, Pharmacy Australia Centre of Excellence, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Rakesh N Veedu
- §Center for Comparative Genomics, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia.,∥Western Australian Neuroscience Research Institute, Perth, WA 6150, Australia.,‡School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane QLD 4072 Australia
| | - Grant A Ramm
- ⊥The Hepatic Fibrosis Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia.,#Faculty of Medicine and Biomedical Sciences, The University of Queensland, Brisbane, QLD 4006, Australia
| | - Johannes B Prins
- ∇Mater Research Institute, The University of Queensland, Brisbane, QLD 4101, Australia
| | - Harendra S Parekh
- †School of Pharmacy, Pharmacy Australia Centre of Excellence, The University of Queensland, Brisbane, QLD 4102, Australia
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9
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Ittig D, Luisier S, Weiler J, Schümperli D, Leumann CJ. Improving gene silencing of siRNAs via tricyclo-DNA modification. ARTIFICIAL DNA, PNA & XNA 2014; 1:9-16. [PMID: 21687522 DOI: 10.4161/adna.1.1.11385] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2010] [Revised: 01/22/2010] [Accepted: 02/03/2010] [Indexed: 12/16/2022]
Abstract
Small interfering RNAs (siRNAs) can be exploited for the selective silencing of disease-related genes via the RNA interference (RNAi) machinery and therefore raise hope for future therapeutic applications. Especially chemically modified siRNAs are of interest as they are expected to convert lead siRNA sequences into effective drugs. To study the potential of tricyclo-DNA (tc-DNA) in this context we systematically incorporated tc-DNA units at various positions in a siRNA duplex targeted to the EGFP gene that was expressed in HeLa cells. Silencing activity was measured by FACS, mRNA levels were determined by RT-PCR and the biostability of the modifed siRNAs was determined in human serum. We found that modifications in the 3'-overhangs in both the sense and antisense strands were compatible with the RNAi machinery leading to similar activities compared to wild-type (wt) siRNA. Additional modifications at the 3'-end, the 5'-end and in the center of the sense (passenger) strand were also well tolerated and did not compromise activity. Extensive modifications of the 3'- and the 5'-end in the antisense (guide) strand, however, abolished RNAi activity. Interestingly, modifications in the center of the duplex on both strands, corresponding to the position of the cleavage site by AGO2, increased efficacy relative to wt by a factor of 4 at the lowest concentrations (2 nM) investigated. In all cases, reduction of EGFP fluorescence was accompanied with a reduction of the EGFP mRNA level. Serum stability analysis further showed that 3'-overhang modifications only moderately increased stability while more extensive substitution by tc-DNA residues significantly enhanced biostability.
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Affiliation(s)
- Damian Ittig
- Department of Chemistry and Biochemistry; University of Bern; Bern, Switzerland
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10
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Design, synthesis, antiviral and cytostatic evaluation of novel isoxazolidine nucleotide analogues with a carbamoyl linker. Bioorg Med Chem 2013; 21:1097-108. [PMID: 23380474 PMCID: PMC7127400 DOI: 10.1016/j.bmc.2013.01.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 12/27/2012] [Accepted: 01/02/2013] [Indexed: 01/08/2023]
Abstract
5-Arylcarbamoyl-2-methylisoxazolidin-3-yl-3-phosphonates have been synthesised from N-methyl-C-diethoxyphosphorylnitrone and N-arylacrylamides in good yields. cis- and trans-isoxazolidine phosphonates obtained herein were evaluated for activity against a broad range of DNA and RNA viruses. None of the compounds were endowed with antiviral activity at subtoxic concentrations. Isoxazolidines having phenyl substituted with halogen (Ar = 2-F-C6H4; 3-Br-C6H4; and 4-Br-C6H4) have been found to inhibit proliferation of L1210, CEM as well as HeLa cells with IC50 in the 100–170 μM range.
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11
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Attwater J, Tagami S, Kimoto M, Butler K, Kool ET, Wengel J, Herdewijn P, Hirao I, Holliger P. Chemical fidelity of an RNA polymerase ribozyme. Chem Sci 2013. [DOI: 10.1039/c3sc50574j] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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12
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Deleavey GF, Damha MJ. Designing chemically modified oligonucleotides for targeted gene silencing. ACTA ACUST UNITED AC 2012; 19:937-54. [PMID: 22921062 DOI: 10.1016/j.chembiol.2012.07.011] [Citation(s) in RCA: 430] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2012] [Revised: 06/28/2012] [Accepted: 07/02/2012] [Indexed: 02/07/2023]
Abstract
Oligonucleotides (ONs), and their chemically modified mimics, are now routinely used in the laboratory as a means to control the expression of fundamentally interesting or therapeutically relevant genes. ONs are also under active investigation in the clinic, with many expressing cautious optimism that at least some ON-based therapies will succeed in the coming years. In this review, we will discuss several classes of ONs used for controlling gene expression, with an emphasis on antisense ONs (AONs), small interfering RNAs (siRNAs), and microRNA-targeting ONs (anti-miRNAs). This review provides a current and detailed account of ON chemical modification strategies for the optimization of biological activity and therapeutic application, while clarifying the biological pathways, chemical properties, benefits, and limitations of oligonucleotide analogs used in nucleic acids research.
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Affiliation(s)
- Glen F Deleavey
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, QC H3A 0B8, Canada.
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13
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Efthymiou TC, Peel B, Huynh V, Desaulniers JP. Evaluation of siRNAs that contain internal variable-length spacer linkages. Bioorg Med Chem Lett 2012; 22:5590-4. [DOI: 10.1016/j.bmcl.2012.07.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 07/02/2012] [Indexed: 12/30/2022]
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14
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Hernández AR, Peterson LW, Kool ET. Steric restrictions of RISC in RNA interference identified with size-expanded RNA nucleobases. ACS Chem Biol 2012; 7:1454-61. [PMID: 22646660 DOI: 10.1021/cb300174c] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Understanding the interactions between small interfering RNAs (siRNAs) and the RNA-induced silencing complex (RISC), the key protein complex of RNA interference (RNAi), is of great importance to the development of siRNAs with improved biological and potentially therapeutic function. Although various chemically modified siRNAs have been reported, relatively few studies with modified nucleobases exist. Here we describe the synthesis and hybridization properties of siRNAs bearing size-expanded RNA (xRNA) nucleobases and their use as a novel and systematic set of steric probes in RNAi. xRNA nucleobases are expanded by 2.4 Å using benzo-homologation and retain canonical Watson-Crick base-pairing groups. Our data show that the modified siRNA duplexes display small changes in melting temperature (+1.4 to -5.0 °C); substitutions near the center are somewhat destabilizing to the RNA duplex, while substitutions near the ends are stabilizing. RNAi studies in a dual-reporter luciferase assay in HeLa cells revealed that xRNA nucleobases in the antisense strand reduce activity at some central positions near the seed region but are generally well tolerated near the ends. Most importantly, we observed that xRNA substitutions near the 3'-end increased activity over that of wild-type siRNAs. The data are analyzed in terms of site-dependent steric effects in RISC. Circular dichroism experiments show that single xRNA substitutions do not significantly distort the native A-form helical structure of the siRNA duplex, and serum stability studies demonstrated that xRNA substitutions protect siRNAs against nuclease degradation.
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Affiliation(s)
- Armando R. Hernández
- Department
of Chemistry, Stanford University, Stanford,
California 94305, United States
| | - Larryn W. Peterson
- Department
of Chemistry, Stanford University, Stanford,
California 94305, United States
| | - Eric T. Kool
- Department
of Chemistry, Stanford University, Stanford,
California 94305, United States
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15
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Zhang J, Zheng J, Lu C, Du Q, Liang Z, Xi Z. Modification of the siRNA passenger strand by 5-nitroindole dramatically reduces its off-target effects. Chembiochem 2012; 13:1940-5. [PMID: 22887813 DOI: 10.1002/cbic.201200349] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Indexed: 12/16/2022]
Abstract
During the formation of RNA-induced silencing complex (RISC), the passenger and guide strand of an siRNA duplex separate from each other to generate an active RISC complex. Accumulating evidence shows that an siRNA passenger strand can also assemble into a RISC complex and mediate RNA interference, thereby causing undesired off-target effects. To reduce this effect, the so-called "universal base" 5-nitroindole nucleotides were incorporated into an siRNA passenger strand. Melting temperature and circular dichroism spectrum measurements showed no significant changes compared to the unmodified duplex, thus indicating the formation of normal A-form conformation. Using a dual luciferase reporter assay, we have further shown that 5-nitroindole modification at position 15 of the siRNA passenger strand drastically decreased the RNAi (RNA interfering) potency of this strand, whereas the potency of the RNA guide strand was not much affected. These results could provide a practical approach for reducing off-target effects mediated by the siRNA passenger strand.
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Affiliation(s)
- Junbin Zhang
- Department of Chemical Biology and State Key Laboratory of Elemento-organic Chemistry, Nankai University, Tianjin, China
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16
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Efthymiou TC, Huynh V, Oentoro J, Peel B, Desaulniers JP. Efficient synthesis and cell-based silencing activity of siRNAS that contain triazole backbone linkages. Bioorg Med Chem Lett 2011; 22:1722-6. [PMID: 22260772 DOI: 10.1016/j.bmcl.2011.12.104] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Revised: 12/16/2011] [Accepted: 12/20/2011] [Indexed: 10/14/2022]
Abstract
An efficient synthesis of siRNAs modified at the backbone with a triazole functionality is reported. Through the use of 4,4'-dimethoxytrityl (DMT) phosphoramidite chemistry, triazole backbone dimers were site-specifically incorporated throughout various siRNAs targeting both firefly luciferase and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene transcripts as representatives of an exogenous and endogenous gene, respectively. Following the successful silencing of the firefly luciferase reporter gene, triazole-modified siRNAs were also found to be capable of silencing GAPDH in a dose-dependent manner. Backbone modifications approaching the 3'-end on the sense strand were tolerated without compromising siRNA potency. This study highlights the compatibility of triazole-modified siRNAs within the RNAi pathway, and the modification's potential to impart favorable properties to siRNAs designed to target other endogenous genes.
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Affiliation(s)
- Tim C Efthymiou
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, Ontario, Canada
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17
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Wahba AS, Azizi F, Deleavey GF, Brown C, Robert F, Carrier M, Kalota A, Gewirtz AM, Pelletier J, Hudson RHE, Damha MJ. Phenylpyrrolocytosine as an unobtrusive base modification for monitoring activity and cellular trafficking of siRNA. ACS Chem Biol 2011; 6:912-9. [PMID: 21667942 DOI: 10.1021/cb200070k] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
6-Phenylpyrrolocytosine (PhpC) is a cytosine mimic with excellent base-pairing fidelity, thermal stability, and high fluorescence. In this work, PhpC-containing small interfering RNAs (siRNAs) are shown to possess thermal stability and gene silencing activity that is virtually identical to that of natural siRNA. The emissive properties of PhpC allow the cellular trafficking of PhpC-containing siRNAs to be monitored by fluorescence microscopy. Accumulation in the cytoplasm of HeLa cells was observed using real time imaging. These findings demonstrate that PhpC-modified siRNAs retain the properties of natural siRNAs while allowing for fluorescence-based detection and monitoring, providing an ideal system for probing siRNA uptake and trafficking.
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Affiliation(s)
- Alexander S. Wahba
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC, Canada H3A 2K6
| | - Fereshteh Azizi
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC, Canada H3A 2K6
| | - Glen F. Deleavey
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC, Canada H3A 2K6
| | - Claire Brown
- McGill University Life Sciences Complex Imaging Facility, Montreal, QC, Canada H3G 0B1
| | - Francis Robert
- Department of Biochemistry and Goodman Cancer Center, McGill University, Montreal, Quebec, Canada H3G 0B1
| | - Marilyn Carrier
- Department of Biochemistry and Goodman Cancer Center, McGill University, Montreal, Quebec, Canada H3G 0B1
| | - Anna Kalota
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Alan M. Gewirtz
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Jerry Pelletier
- Department of Biochemistry and Goodman Cancer Center, McGill University, Montreal, Quebec, Canada H3G 0B1
| | - Robert H. E. Hudson
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada N6A 5B7
| | - Masad J. Damha
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC, Canada H3A 2K6
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18
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Peacock H, Kannan A, Beal PA, Burrows CJ. Chemical modification of siRNA bases to probe and enhance RNA interference. J Org Chem 2011; 76:7295-300. [PMID: 21834582 DOI: 10.1021/jo2012225] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Considerable attention has focused on the use of alternatives to the native ribose and phosphate backbone of small interfering RNAs for therapeutic applications of the RNA interference pathway. In this synopsis, we highlight the less common chemical modifications, namely, those of the RNA nucleobases. Base modifications have the potential to lend insight into the mechanism of gene silencing and to lead to novel methods to overcome off-target effects that arise due to deleterious protein binding or mis-targeting of mRNA.
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Affiliation(s)
- Hayden Peacock
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, USA
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Hedman HK, Kirpekar F, Elmroth SKC. Platinum Interference with siRNA Non-seed Regions Fine-Tunes Silencing Capacity. J Am Chem Soc 2011; 133:11977-84. [DOI: 10.1021/ja111082e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Hanna K. Hedman
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Finn Kirpekar
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Sofi K. C. Elmroth
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
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20
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Kannan A, Fostvedt E, Beal PA, Burrows CJ. 8-Oxoguanosine switches modulate the activity of alkylated siRNAs by controlling steric effects in the major versus minor grooves. J Am Chem Soc 2011; 133:6343-51. [PMID: 21452817 DOI: 10.1021/ja2003878] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Small interfering double-stranded RNAs have been synthesized bearing one or more base modifications at nucleotide positions 4, 11, and/or 16 in the guide strand. The chemically modified base is an N(2)-alkyl-8-oxo-7,8-dihydroguanine (alkyl = propyl, benzyl) that can alternatively pair in a Watson-Crick sense opposite cytosine (C) or as a Hoogsteen pair opposite adenine (A). Cellular delivery with C opposite led to effective targeting of A-containing but not C-containing mRNA sequences in a dual luciferase assay with RNA interference levels that were generally as good as or better than unmodified sequences. The higher activity is ascribed to an inhibitory effect of the alkyl group projecting into the minor groove of double-stranded RNA preventing off-target binding to proteins such as PKR (RNA-activated protein kinase).
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Affiliation(s)
- Arunkumar Kannan
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, USA
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21
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Kannan A, Burrows CJ. Synthesis of N2-alkyl-8-oxo-7,8-dihydro-2'-deoxyguanosine derivatives and effects of these modifications on RNA duplex stability. J Org Chem 2010; 76:720-3. [PMID: 21192638 DOI: 10.1021/jo102187y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
N(2)-alkyl analogues of 8-oxo-7,8-dihydro-2'-deoxyguanosine (OG) were synthesized (alkyl = propyl, benzyl) via reductive amination of the protected OG nucleoside and incorporated into various positions of an RNA strand. Thermal stability studies of duplexes containing A or C opposite a single modified base revealed only moderate destabilization. Both OG as well as its N(2)-alkyl analogues can pair opposite A or C with nearly equal stability, potentially offering a new means of modulating RNA-protein interactions in the minor vs major grooves.
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Affiliation(s)
- Arunkumar Kannan
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
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22
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Peacock H, Fostvedt E, Beal PA. Minor-groove-modulating adenosine replacements control protein binding and RNAi activity in siRNAs. ACS Chem Biol 2010; 5:1115-24. [PMID: 20863128 DOI: 10.1021/cb100245u] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Short-interfering RNAs (siRNAs) are common tools in molecular biology; however, the development of RNAi-based therapeutics is limited by immunostimulatory and nonspecific effects mediated by off-target RNA-binding proteins. The RNA-dependent protein kinase (PKR) and adenosine deaminase that acts on RNA 1 (ADAR1) are two proteins implicated in RNAi off-target effects and share a common means of interaction with siRNAs through double-stranded RNA binding motifs (dsRBMs). Here we report the site-specific introduction of N²-propargyl 2-aminopurine into siRNAs and subsequent conversion to two bulky products via copper-catalyzed azide alkyne cycloaddition (CuAAC) with either N-azidoacetyl-mannosamine azide or N-ethylpiperidine azide. We observed position-specific effects on RNAi activity for modifications made to both the passenger and guide strands. These findings are rationalized in light of recent structural studies of components of the RNA-induced silencing complex (RISC) and RISC-loading complex (RLC). The most active siRNAs were assayed for binding affinity to PKR and ADAR1. PKR binding was significantly reduced by multiple modifications, regardless of size, and ADAR1 binding was reduced in a position- and size-sensitive manner. Our findings present a strategy for designing siRNAs that reduce off-target dsRBM-protein binding while retaining native RNAi activity.
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Affiliation(s)
- Hayden Peacock
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Erik Fostvedt
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Peter A. Beal
- Department of Chemistry, University of California, Davis, California 95616, United States
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23
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Terrazas M, Eritja R. Synthesis and properties of small interfering RNA duplexes carrying 5-ethyluridine residues. Mol Divers 2010; 15:677-86. [PMID: 21080069 DOI: 10.1007/s11030-010-9290-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Accepted: 10/22/2010] [Indexed: 11/30/2022]
Abstract
Oligoribonucleotides carrying 5-ethyluridine units were prepared using solid-phase phosphoramidite chemistry. The introduction of the tert-butyldimethylsilyl group at the 2'-OH position proceeded in good yield and very high 2'-regioselectivity. RNA duplexes carrying 5-ethyluridine either at the sense or the guide strands display RNAi activity comparable to or slightly better than that of unmodified RNA duplexes. Gene suppression experiments using luciferase targets in SH-SY5Y cells show that the ethyl group is generally well accepted at all positions although a small decrease in RNA interference activity is observed when one 5-ethylU residue is incorporated in the 3' overhangs.
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Affiliation(s)
- Montserrat Terrazas
- Institute for Research in Biomedicine (IRB Barcelona), Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Baldiri i Reixac 10, 08028 Barcelona, Spain
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24
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Abstract
During RNA-induced silencing complex (RISC) assembly the guide (or antisense) strand has to separate from its complementary passenger (or sense) strand to generate the active RISC complex. Although this process was found to be facilitated through sense strand cleavage, there is evidence for an alternate mechanism, in which the strands are dissociated without prior cleavage. Here we show that the potency of siRNA can be improved by modulating the internal thermodynamic stability profile with chemical modifications. Using a model siRNA targeting the firefly luciferase gene with subnanomolar IC50, we found that placement of thermally destabilizing modifications, such as non-canonical bases like 2,4-difluorotoluene or single base pair mismatches in the central region of the sense strand (9-12 nt), significantly improve the potency. For this particular siRNA, the strongest correlation between the decrease in thermal stability and the increase in potency was found at position 10. Controls with stabilized sugar-phosphate backbone indicate that enzymatic cleavage of the sense strand prior to strand dissociation is not required for silencing activity. Similar potency-enhancing effects were observed as this approach was applied to other functional siRNAs targeting a different site on the firefly luciferase transcript or endogenously expressed PTEN.
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25
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Shukla S, Sumaria CS, Pradeepkumar PI. Exploring chemical modifications for siRNA therapeutics: a structural and functional outlook. ChemMedChem 2010; 5:328-49. [PMID: 20043313 DOI: 10.1002/cmdc.200900444] [Citation(s) in RCA: 156] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
RNA interference (RNAi) is a post-transcriptional gene silencing mechanism induced by small interfering RNAs (siRNAs) and micro-RNAs (miRNAs), and has proved to be one of the most important scientific discoveries made in the last century. The robustness of RNAi has opened up new avenues in the development of siRNAs as therapeutic agents against various diseases including cancer and HIV. However, there had remained a lack of a clear mechanistic understanding of messenger RNA (mRNA) cleavage mediated by Argonaute2 of the RNA-induced silencing complex (RISC), due to inadequate structural data. The X-ray crystal structures of the Argonaute (Ago)-DNA-RNA complexes reported recently have proven to be a breakthrough in this field, and the structural details can provide guidelines for the design of the next generation of siRNA therapeutics. To harness siRNAs as therapeutic agents, the prudent use of various chemical modifications is warranted to enhance nuclease resistance, prevent immune activation, decrease off-target effects, and to improve pharmacokinetic and pharmacodynamic properties. The focus of this review is to interpret the tolerance of various chemical modifications employed in siRNAs toward RNAi by taking into account the crystal structures and biochemical studies of Ago-RNA complexes. Moreover, the challenges and recent progress in imparting druglike properties to siRNAs along with their delivery strategies are discussed.
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Affiliation(s)
- Siddharth Shukla
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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26
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Abstract
The ability to manipulate the RNA interference (RNAi) machinery to specifically silence the expression of target genes could be a powerful therapeutic strategy. Since the discovery that RNAi can be triggered in mammalian cells by short double-stranded RNAs (small interfering RNA, siRNA), there has been a tremendous push by researchers, from academia to big pharma, to move siRNAs into clinical application. The challenges facing siRNA therapeutics are significant. The inherent properties of siRNAs (polyanionic, vulnerable to nuclease cleavage) make clinical application difficult due to poor cellular uptake and rapid clearance. Side effects of siRNAs have also proven to be a further complication. Fortunately, numerous chemical modification strategies have been identified that allow many of these obstacles to be overcome. This unit will present an overview of (1) the chemical modifications available to the nucleic acid chemist for modifying siRNAs, (2) the application of chemical modifications to address specific therapeutic obstacles, and (3) the factors that must be considered when assessing the activity of modified siRNAs.
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Terrazas M, Kool ET. RNA major groove modifications improve siRNA stability and biological activity. Nucleic Acids Res 2009; 37:346-53. [PMID: 19042976 PMCID: PMC2632910 DOI: 10.1093/nar/gkn958] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2008] [Revised: 11/10/2008] [Accepted: 11/11/2008] [Indexed: 11/15/2022] Open
Abstract
RNA 5-methyl and 5-propynyl pyrimidine analogs were substituted into short interfering RNAs (siRNAs) to probe major groove steric effects in the active RNA-induced silencing complex (RISC). Synthetic RNA guide strands containing varied combinations of propynyl and methyl substitution revealed that all C-5 substitutions increased the thermal stability of siRNA duplexes containing them. Cellular gene suppression experiments using luciferase targets in HeLa cells showed that the bulky 5-propynyl modification was detrimental to RNA interference activity, despite its stabilization of the helix. Detrimental effects of this substitution were greatest at the 5'-half of the guide strand, suggesting close steric approach of proteins in the RISC complex with that end of the siRNA/mRNA duplex. However, substitutions with the smaller 5-methyl group resulted in gene silencing activities comparable to or better than that of wild-type siRNA. The major groove modifications also increased the serum stability of siRNAs.
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Affiliation(s)
| | - Eric T. Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA
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