Computational models with thermodynamic and composition features improve siRNA design.

ABSTRACT:

Background

Small interfering RNAs (siRNAs) have become an important tool in cell and molecular biology. Reliable design of siRNA molecules is essential for the needs of large functional genomics projects.

Results

To improve the design of efficient siRNA molecules, we performed a comparative, thermodynamic and correlation analysis on a heterogeneous set of 653 siRNAs collected from the literature. We used this training set to select siRNA features and optimize computational models. We identified 18 parameters that correlate significantly with silencing efficiency. Some of these parameters characterize only the siRNA sequence, while others involve the whole mRNA. Most importantly, we derived an siRNA position-dependent consensus, and optimized the free-energy difference of the

SUBMITTER: Shabalina SA 

PROVIDER: S-EPMC1431570 | biostudies-literature | 2006 Feb

REPOSITORIES: biostudies-literature