Probing the transition state for nucleic acid hybridization using φ-value analysis

Jandi Kim, Jong Shik Shin

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

Genetic regulation by noncoding 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 because of the lack of information about the transition-state structure. Here we use transition-state theory, inspired by I-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 I-value analysis indicates that the native secondary structure remains intact in the transition state. The nativelike transition state was confirmed via examination of the 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 preexisting base pairings involving successive small energy barriers. The proposed mechanism might provide new insight into physical processes during small RNA-mediated gene silencing, which is essential to selection of a target mRNA segment for siRNA design.

Original languageEnglish
Pages (from-to)3420-3426
Number of pages7
JournalBiochemistry
Volume49
Issue number16
DOIs
Publication statusPublished - 2010 Apr 27

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Nucleic Acid Hybridization
Value engineering
Nucleic Acids
Small Interfering RNA
RNA
Physical Phenomena
Protein folding
Untranslated RNA
Messenger RNA
Fluorophores
Energy barriers
Protein Folding
Gene Silencing
MicroRNAs
Base Pairing
Free energy
Nucleation
Salts
Genes
Sodium

All Science Journal Classification (ASJC) codes

  • Biochemistry

Cite this

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Probing the transition state for nucleic acid hybridization using φ-value analysis. / Kim, Jandi; Shin, Jong Shik.

In: Biochemistry, Vol. 49, No. 16, 27.04.2010, p. 3420-3426.

Research output: Contribution to journalArticle

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