Single-fluorophore monitoring of DNA hybridization for investigating the effect of secondary structure on the nucleation step |
| |
Authors: | Joon-Jung Jo |
| |
Institution: | Department of Biotechnology, Yonsei University, Shinchon-Dong 134, Seodaemun-Gu, Seoul 120-749, South Korea |
| |
Abstract: | Nucleic acid hybridization is one of the essential biological processes involved in storage and transmission of genetic information. Here we quantitatively determined the effect of secondary structure on the hybridization activation energy using structurally defined oligonucleotides. It turned out that activation energy is linearly proportional to the length of a single-stranded region flanking a nucleation site, generating a 0.18 kcal/mol energy barrier per nucleotide. Based on this result, we propose that the presence of single-stranded segments available for non-productive base pairing with a nucleation counterpart extends the searching process for nucleation sites to find a perfect match. This result may provide insights into rational selection of a target mRNA site for siRNA and antisense gene silencing. |
| |
Keywords: | DNA oligonucleotide Hybridization kinetics Single-fluorophore measurement Secondary structure Nucleation Activation energy Salt dependence |
本文献已被 ScienceDirect 等数据库收录! |
|