Single-fluorophore monitoring of DNA hybridization for investigating the effect of secondary structure on the nucleation step

Joon Jung Jo, Min Ji Kim, Jung Tae Son, Jandi Kim, Jong Shik Shin

Research output: Contribution to journalArticle

6 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)88-93
Number of pages6
JournalBiochemical and Biophysical Research Communications
Volume385
Issue number1
DOIs
Publication statusPublished - 2009 Jul 17

Fingerprint

Nucleic Acid Hybridization
Biological Phenomena
Fluorophores
Gene Silencing
Oligonucleotides
Base Pairing
Small Interfering RNA
Nucleation
Nucleotides
Messenger RNA
Monitoring
DNA
Activation energy
Energy barriers
Nucleic Acids
Genes

All Science Journal Classification (ASJC) codes

  • Biophysics
  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

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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.",
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Single-fluorophore monitoring of DNA hybridization for investigating the effect of secondary structure on the nucleation step. / Jo, Joon Jung; Kim, Min Ji; Son, Jung Tae; Kim, Jandi; Shin, Jong Shik.

In: Biochemical and Biophysical Research Communications, Vol. 385, No. 1, 17.07.2009, p. 88-93.

Research output: Contribution to journalArticle

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