Single-fluorophore monitoring of DNA hybridization for investigating the effect of secondary structure on the nucleation step.
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.
Jo
Joon-Jung
JJ
Department of Biotechnology, Yonsei University, Shinchon-Dong 134, Seodaemun-Gu, Seoul 120-749, South Korea.
Kim
Min-Ji
MJ
Son
Jung-Tae
JT
Kim
Jandi
J
Shin
Jong-Shik
JS
D001483:Base Sequence; D002264:Carboxylic Acids / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D005456:Fluorescent Dyes / Q000737:chemistry; D006824:Hybridization, Genetic; D009690:Nucleic Acid Conformation; D009693:Nucleic Acid Hybridization / Q000379:methods*; D009838:Oligodeoxyribonucleotides / Q000737:chemistry / Q000235:genetics
D002264:Carboxylic Acids; D005456:Fluorescent Dyes; D009838:Oligodeoxyribonucleotides; C436864:Oregon Green 488 carboxylic acid; D004247:DNA