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Habibian M, Yahyaee-Anzahaee M, Lucic M, Moroz E, Martín-Pintado N, Di Giovanni LD, Leroux JC, Hall J, González C, Damha MJ. Structural properties and gene-silencing activity of chemically modified DNA-RNA hybrids with parallel orientation. Nucleic Acids Res 2019; 46:1614-1623. [PMID: 29373740 PMCID: PMC5829573 DOI: 10.1093/nar/gky024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 01/12/2018] [Indexed: 01/24/2023] Open
Abstract
We report, herein, a new class of RNAi trigger molecules based on the unconventional parallel hybridization of two oligonucleotide chains. We have prepared and studied several parallel stranded (ps) duplexes, in which the parallel orientation is achieved through incorporation of isoguanine and isocytosine to form reverse Watson-Crick base pairs in ps-DNA:DNA, ps-DNA:RNA, ps-(DNA-2'F-ANA):RNA, and ps-DNA:2'F-RNA duplexes. The formation of these duplexes was confirmed by UV melting experiments, FRET and CD studies. In addition, NMR structural studies were conducted on a ps-DNA:RNA hybrid for the first time. Finally, we provide evidence for the unprecedented finding that ps-DNA:RNA and ps-DNA:2'F-RNA hybrids can engage the RNAi pathway to silence gene expression in vitro.
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Affiliation(s)
- Maryam Habibian
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 0B8, Canada
| | - Maryam Yahyaee-Anzahaee
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 0B8, Canada
| | - Matije Lucic
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Vladimir-Prelog-Weg 1-5, 8093 Zurich, Switzerland
| | - Elena Moroz
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Vladimir-Prelog-Weg 1-5, 8093 Zurich, Switzerland
| | - Nerea Martín-Pintado
- Instituto de Química Física 'Rocasolano', CSIC, Serrano 119, 28006 Madrid, Spain
| | - Logan Dante Di Giovanni
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 0B8, Canada
| | - Jean-Christophe Leroux
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Vladimir-Prelog-Weg 1-5, 8093 Zurich, Switzerland
| | - Jonathan Hall
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Vladimir-Prelog-Weg 1-5, 8093 Zurich, Switzerland
| | - Carlos González
- Instituto de Química Física 'Rocasolano', CSIC, Serrano 119, 28006 Madrid, Spain
| | - Masad J Damha
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 0B8, Canada
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Gene-specific silencing induced by parallel complementary RNA in Pseudomonas aeruginosa. Biotechnol Lett 2009; 31:1571-5. [DOI: 10.1007/s10529-009-0046-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Revised: 05/22/2009] [Accepted: 05/27/2009] [Indexed: 11/26/2022]
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Tchurikov NA, Chistyakova LG, Zavilgelsky GB, Manukhov IV, Chernov BK, Golova YB. Gene-specific silencing by expression of parallel complementary RNA in Escherichia coli. J Biol Chem 2000; 275:26523-9. [PMID: 10849423 DOI: 10.1074/jbc.m002833200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Gene-specific silencing refers to a phenomenon in which expression of an individual gene can be specifically repressed by different mechanisms on the levels of transcription, RNA splicing, transport, degradation in nuclei or cytoplasm, or blocking of translation. In different species gene-specific silencing was observed by expression or injections of antiparallel double-stranded RNA formed by a fragment of mRNA and antisense RNA. Here we show a potent and specific gene silencing in bacteria by expression of RNA, that is complementary in a parallel orientation to Escherichia coli lon mRNA. Moreover, the expression of parallel RNA is more effective at producing interference than expression of antisense RNA corresponding to the same mRNA region. Both effects of interference mediated either by parallel RNA or antiparallel RNA gradually decrease up to the 40th generation. Together with in vitro nuclease protection studies these results indicate that a parallel RNA duplex might be formed in vivo and both types of duplexes, antiparallel or parallel, can induce gene-specific silencing by similar mechanisms.
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Affiliation(s)
- N A Tchurikov
- Department of Genome Organization and Group of Genes Chemical Synthesis, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Vavilov str. 32, Moscow 117984, Russia.
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