Short report
Optimal design and validation of antiviral siRNA for targeting HIV-1
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* Corresponding authors: Yuki Naito y-naito@RNAi.jp - Yutaka Takebe takebe@nih.go.jp
1 Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
2 Laboratory of Molecular Virology and Epidemiology, AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
Retrovirology 2007, 4:80 doi:10.1186/1742-4690-4-80
Published: 8 November 2007Additional files
Additional file 1:
The list of 495 near full-length genome sequences of HIV-1 group M.
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Additional file 2:
The list of published siRNA/shRNAs targeting HIV-1.
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Additional file 3:
The list of highly conserved siRNA targets identified in this study.
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Additional file 4:
The siRNA sequences and their target sites. The sequences of 41 siRNAs and their target sites are shown. The siRNA numbers indicate the nucleotide position in HXB2 (GenBank K03455). The conservation level of each siRNA in HIV-1 group M sequence is depicted in color chart at the rightmost column. BMH (branched multiple hairpin) and LDI (long distance interaction) conformations of the HIV-1 leader RNA and siRNAs targeting them are shown.
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Additional file 5:
Supplementary materials and methods.
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Additional file 6:
Target sites of the 41 siRNAs used in this study. Sequence alignment of the target site from the four HIV-1 infectious molecular clones: pNL4-2 (subtype B); 95MM-yIDU106 (subtype B'); 93IN101 (subtype C); or 93JP-NH1 (CRF01_AE).
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Additional file 7:
Coverage of HIV-1 group M by single siRNA or two siRNAs. (A) Coverage of HIV-1 group M by 41 siRNAs used in this study. (B) Coverage of HIV-1 group M by combining two siRNAs from above. Coverage was calculated by considering only the HIV-1 sequences which contain the corresponding regions.
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