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.
|Number of pages||6|
|Journal||Biochemical and Biophysical Research Communications|
|Publication status||Published - 2009 Jul 17|
Bibliographical noteFunding Information:
This work was supported by BK21 program from the Korean Ministry of Education, start-up research funds provided by Yonsei University and Seoul R&BD Programs (NT080612, KU080657).
All Science Journal Classification (ASJC) codes
- Molecular Biology
- Cell Biology