11646

Genetic regulation by non-coding RNA elements such as microRNA and small interfering RNA (siRNA) involves hybridization of a short single-stranded RNA with a complementary segment in a target mRNA. The physical basis of the hybridization process between the structured nucleic acids is not well understood primarily owing to the lack of information on the transition state structure. Here we use transition-state theory, inspired by Phi-value analysis in protein folding studies, to provide quantitative analysis of the relationship between changes in the secondary structure stability and the activation free energy. Time-course monitoring of the hybridization reaction was performed under pseudo-steady-state conditions using a single fluorophore. The Phi-value analysis indicates that the native secondary structure remains intact in the transition state. The native-like transition state was confirmed by examining salt dependence of the hybridization kinetics, indicating that the number of sodium ions associated with the transition state was not substantially affected by changes in the native secondary structure. These results propose that hybridization between structured nucleic acids undergoes a transition state leading to formation of a nucleation complex and then is followed by sequential displacement of pre-existing base pairings involving successive small energy barriers. The proposed mechanism might provide a new insight into physical processes during small RNA-mediated gene silencing, which is essential to selection of a target mRNA segment for siRNA design.
PMID: 20210364 [PubMed - as supplied by publisher]