The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
Comparison of approaches for rational siRNA design leading to a new efficient and transparent method
Open accessAbstract
Current literature describes several methods for the design of efficient siRNAs with 19 perfectly matched base pairs and 2 nt overhangs. Using four independent databases totaling 3336 experimentally verified siRNAs, we compared how well several of these methods predict siRNA cleavage efficiency. According to receiver operating characteristics (ROC) and correlation analyses, the best programs were BioPredsi, ThermoComposition and DSIR. We also studied individual parameters that significantly and consistently correlated with siRNA efficacy in different databases. As a result of this work we developed a new method which utilizes linear regression fitting with local duplex stability, nucleotide position-dependent preferences and total G/C content of siRNA duplexes as input parameters. The new method's discrimination ability of efficient and inefficient siRNAs is comparable with that of the best methods identified, but its parameters are more obviously related to the mechanisms of siRNA action in comparison with BioPredsi. This permits insight to the underlying physical features and relative importance of the parameters. The new method of predicting siRNA efficiency is faster than that of ThermoComposition because it does not employ time-consuming RNA secondary structure calculations and has much less parameters than DSIR. It is available as a web tool called 'siRNA scales'.
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Cites
Rational siRNA design for RNA interference
Reynolds, A., Leake, D., Boese, Q., Scaringe, S., Marshall, W. S., & Khvorova, A. (2004) · Nature Biotechnology · doi:10.1038/nbt936 · Cited by 2,094
Xia, T., SantaLucia, J., Burkard, M. E., Kierzek, R., Schroeder, S. J., Jiao, X., Cox, C., & Turner, D. H. (1998) · Biochemistry · doi:10.1021/bi9809425 · Cited by 1,140
Efficient Reduction of Target RNAs by Small Interfering RNA and RNase H-dependent Antisense Agents
Vickers, T. A., Koo, S., Bennett, C. F., Crooke, S. T., Dean, N. M., & Baker, B. F. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m210326200 · Cited by 461
Cited by
Bennett, C. F., & Swayze, E. E. (2010) · Annual Review of Pharmacology and Toxicology · doi:10.1146/annurev.pharmtox.010909.105654 · Cited by 1,374
Origins and evolution of eukaryotic RNA interference
SHABALINA, S., & KOONIN, E. (2008) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2008.06.005 · Cited by 561
Self-citationRNAi-based drug design: considerations and future directions
Tang, Q., & Khvorova, A. (2024) · Nature Reviews Drug Discovery · doi:10.1038/s41573-024-00912-9 · Cited by 282
Pulford, B., Reim, N., Bell, A., Veatch, J., Forster, G., Bender, H., Meyerett, C., Hafeman, S., Michel, B., Johnson, T., et al. (2010) · PLoS ONE · doi:10.1371/journal.pone.0011085 · Cited by 85
Titze-de-Almeida, R., Titze-de-Almeida, S. S., Ferreira, N. R., Fontanari, C., Faccioli, L. H., & Del Bel, E. (2019) · Neurotoxicity Research · doi:10.1007/s12640-019-00043-9 · Cited by 18
Metadata
- Authors
- Matveeva, O., Nechipurenko, Y., Rossi, L., Moore, B., Saetrom, P., Ogurtsov, A. Y., Atkins, J. F., & Shabalina, S. A.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2007-03-29
- Volume
- 35
- Issue
- 8
- Pages
- e63-e63
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W1986687961
- Cited by
- 179
- References
- 3
- FWCI
- 4.31
- Type
- journal article
- Language
- en
- Open access
- gold
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- Matveeva, O., Nechipurenko, Y., Rossi, L., Moore, B., Saetrom, P., Ogurtsov, A. Y., Atkins, J. F., & Shabalina, S. A. (2007). Comparison of approaches for rational siRNA design leading to a new efficient and transparent method. Nucleic Acids Research. https://doi.org/10.1093/nar/gkm088
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