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Tyagi A, Ahmed F, Thakur N, Sharma A, Raghava GPS, Kumar M. HIVsirDB: a database of HIV inhibiting siRNAs. PLoS One 2011; 6:e25917. [PMID: 22022467 PMCID: PMC3191155 DOI: 10.1371/journal.pone.0025917] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Accepted: 09/13/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Human immunodeficiency virus (HIV) is responsible for millions of deaths every year. The current treatment involves the use of multiple antiretroviral agents that may harm patients due to their toxic nature. RNA interference (RNAi) is a potent candidate for the future treatment of HIV, uses short interfering RNA (siRNA/shRNA) for silencing HIV genes. In this study, attempts have been made to create a database HIVsirDB of siRNAs responsible for silencing HIV genes. DESCRIPTIONS HIVsirDB is a manually curated database of HIV inhibiting siRNAs that provides comprehensive information about each siRNA or shRNA. Information was collected and compiled from literature and public resources. This database contains around 750 siRNAs that includes 75 partially complementary siRNAs differing by one or more bases with the target sites and over 100 escape mutant sequences. HIVsirDB structure contains sixteen fields including siRNA sequence, HIV strain, targeted genome region, efficacy and conservation of target sequences. In order to facilitate user, many tools have been integrated in this database that includes; i) siRNAmap for mapping siRNAs on target sequence, ii) HIVsirblast for BLAST search against database, iii) siRNAalign for aligning siRNAs. CONCLUSION HIVsirDB is a freely accessible database of siRNAs which can silence or degrade HIV genes. It covers 26 types of HIV strains and 28 cell types. This database will be very useful for developing models for predicting efficacy of HIV inhibiting siRNAs. In summary this is a useful resource for researchers working in the field of siRNA based HIV therapy. HIVsirDB database is accessible at http://crdd.osdd.net/raghava/hivsir/.
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Affiliation(s)
- Atul Tyagi
- Bioinformatics Centre, Institute of Microbial Technology (CSIR), Chandigarh, India
| | - Firoz Ahmed
- Bioinformatics Centre, Institute of Microbial Technology (CSIR), Chandigarh, India
| | - Nishant Thakur
- Bioinformatics Centre, Institute of Microbial Technology (CSIR), Chandigarh, India
| | - Arun Sharma
- Bioinformatics Centre, Institute of Microbial Technology (CSIR), Chandigarh, India
| | | | - Manoj Kumar
- Bioinformatics Centre, Institute of Microbial Technology (CSIR), Chandigarh, India
- * E-mail:
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Sugiyama R, Hayafune M, Habu Y, Yamamoto N, Takaku H. HIV-1 RT-dependent DNAzyme expression inhibits HIV-1 replication without the emergence of escape viruses. Nucleic Acids Res 2011; 39:589-98. [PMID: 20833635 PMCID: PMC3025543 DOI: 10.1093/nar/gkq794] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Revised: 08/18/2010] [Accepted: 08/23/2010] [Indexed: 12/12/2022] Open
Abstract
DNAzymes are easier to prepare and less sensitive to chemical and enzymatic degradation than ribozymes; however, a DNA enzyme expression system has not yet been developed. In this study, we exploited the mechanism of HIV-1 reverse transcription (RT) in a DNA enzyme expression system. We constructed HIV-1 RT-dependent lentiviral DNAzyme expression vectors including the HIV-1 primer binding site, the DNA enzyme, and either a native tRNA (Lys-3), tR(M)DtR(L), or one of two truncated tRNAs (Lys-3), tR(M)DΔARMtR(L) or tR(M)D3'-endtR(L). Lentiviral vector-mediated DNAzyme expression showed high levels of inhibition of HIV-1 replication in SupT1 cells. We also demonstrated the usefulness of this approach in a long-term assay, in which we found that the DNAzymes prevented escape from inhibition of HIV. These results suggest that HIV-1 RT-dependent lentiviral vector-derived DNAzymes prevent the emergence of escape mutations.
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Affiliation(s)
- Ryuichi Sugiyama
- Department of Life and Environmental Science, High Technology Research Center, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino-shi, Chiba 275-0016, Japan, Department of Microbiology, Immunology and Pathology 1619 Campus Delivery, Colorado State University, Fort Collins, CO 80523-161, USA and Influenza Virus Research Center, National Institute of Infectious Diseases, 4-7-1 Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Masaaki Hayafune
- Department of Life and Environmental Science, High Technology Research Center, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino-shi, Chiba 275-0016, Japan, Department of Microbiology, Immunology and Pathology 1619 Campus Delivery, Colorado State University, Fort Collins, CO 80523-161, USA and Influenza Virus Research Center, National Institute of Infectious Diseases, 4-7-1 Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Yuichiro Habu
- Department of Life and Environmental Science, High Technology Research Center, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino-shi, Chiba 275-0016, Japan, Department of Microbiology, Immunology and Pathology 1619 Campus Delivery, Colorado State University, Fort Collins, CO 80523-161, USA and Influenza Virus Research Center, National Institute of Infectious Diseases, 4-7-1 Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Norio Yamamoto
- Department of Life and Environmental Science, High Technology Research Center, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino-shi, Chiba 275-0016, Japan, Department of Microbiology, Immunology and Pathology 1619 Campus Delivery, Colorado State University, Fort Collins, CO 80523-161, USA and Influenza Virus Research Center, National Institute of Infectious Diseases, 4-7-1 Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Hiroshi Takaku
- Department of Life and Environmental Science, High Technology Research Center, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino-shi, Chiba 275-0016, Japan, Department of Microbiology, Immunology and Pathology 1619 Campus Delivery, Colorado State University, Fort Collins, CO 80523-161, USA and Influenza Virus Research Center, National Institute of Infectious Diseases, 4-7-1 Musashimurayama-shi, Tokyo 208-0011, Japan
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