Direct measurement of the rates and barriers on forward and reverse diffusions of intramolecular collision in overhang oligonucleotides

Peng Qu, Xinxing Yang, Xun Li, Xiaoxue Zhou, Xin Sheng Zhao

Research output: Contribution to journalArticle

Abstract

The dynamics of end-to-interior (Type I) and end-to-end (Type II) collisions in a dangling overhang anchored on a double-stranded DNA (dsDNA) was studied by monitoring the fluorescence quenching of tetramethylrhodamine (TMR) by guanosine residues through combining photoinduced electron transfer (PET) with fluorescence correlation spectroscopy (FCS) at different temperatures. TMR and guanosine residues are separated by a double helix with dangling bases ranging from 2 to 16. By analyzing the FCS data, we obtained the forward and reverse intrachain diffusion rate constants and respective barriers. For both Type I and Type II collisions, the intrachain diffusion rates followed the scaling law of the Gaussian chain model. Especially, the reverse intrachain diffusion rate was insensitive to the base length of separation. Both the activation enthalpy and activation entropy of the forward and reverse diffusions were length independent. The comparison between Type I and Type II collisions shows that the collision rate of end-to-interior is slower than that of end-to-end. The phenomenon is further checked in detail by a series of dangling DNA with the same separation length but different tail lengths (Type III).

Original languageEnglish (US)
Pages (from-to)8235-8243
Number of pages9
JournalJournal of Physical Chemistry B
Volume114
Issue number24
DOIs
StatePublished - Jun 24 2010
Externally publishedYes

Fingerprint

oligonucleotides
Oligonucleotides
electron transitions
Fluorescence spectroscopy
Biomolecules
Electron transitions
genes
guanosines
Quenching
Rate constants
DNA
deoxyribonucleic acid
Genes
Fluorescence
quenching
fluorescence
collisions
Guanosine
activation
collision rates

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Surfaces, Coatings and Films
  • Materials Chemistry

Cite this

Direct measurement of the rates and barriers on forward and reverse diffusions of intramolecular collision in overhang oligonucleotides. / Qu, Peng; Yang, Xinxing; Li, Xun; Zhou, Xiaoxue; Zhao, Xin Sheng.

In: Journal of Physical Chemistry B, Vol. 114, No. 24, 24.06.2010, p. 8235-8243.

Research output: Contribution to journalArticle

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