Iowa State University is awarded a grant to develop small interference RNA (siRNA) design software. RNA interference (RNAi) is a natural phenomenon in cells where siRNAs guide the recognition, inhibition and potential degradation of target messenger RNAs (mRNA), resulting in the lost of their gene functions. RNAi is an important molecular biology technology that can be used to perform functional genomic studies. It is also suggested that siRNAs can be used as drugs to stop oncogenes in cancer cells or to fight off viruses. The RNAi technology depends on the quality of the artificially designed siRNAs - the most critical task is to discover siRNAs that are efficient in knocking down their target genes but produce no disturbance to the other tens of thousands of genes coexisting in cells. Reducing or eliminating side-effects can dramatically enhance the precision of RNAi technology. In fact, eliminating side-effects will be the basic requirement of any RNAi uses in medicine.
The two main goals of this project are 1) to create novel siRNA design software that can select high quality, gene-specific siRNAs based on the comprehensive thermodynamic analysis of an entire genome and 2) to validate the quality of the designed siRNAs with RNAi experiments. The intellectual merit of this project is the use of thermodynamic calculation in a whole-genome scale to perform optimal siRNA selection. The RNAi experiments will not only test the siRNAs but also guide the refinements to the project software algorithms and parameters. The broader impact that is expected from this project will be the most precise siRNA design software tool for biologists to use in their research. In addition, this project will provide an ideal interdisciplinary training environment for both computer science and biology graduate students to work together and advance in computational biology research. The software developed under this project will be made available from the Complex Computation Lab website at Iowa State University <www.complex.iastate.edu>.
