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Kinetic stability of intermolecular DNA quadruplexes

Kinetic stability of intermolecular DNA quadruplexes
Kinetic stability of intermolecular DNA quadruplexes
Fluorescently labeled oligodeoxyribonucleotides containing a single tract of four successive guanines have been used to study the thermodynamic and kinetic properties of short intermolecular DNA quadruplexes. When these assemble to form intermolecular quadruplexes the fluorophores are in close proximity and the fluorescence is quenched. On raising the temperature these complexes dissociate and there is a large increase in fluorescence. These complexes are exceptionally stable in potassium-containing buffers, and possess Tm values that are too high to measure. Tm values were determined in sodium-containing buffers for which the rate of reannealing is extremely slow; the melting profiles are effectively irreversible, and the apparent melting temperatures are dependent on the rates of heating. The dissociation kinetics of these complexes was estimated by rapidly increasing the temperature and following the time-dependent changes in fluorescence. From these data we have estimated the half-lives of these quadruplexes at 37°C. Addition of a T to the unlabeled end of the oligonucleotide increases quadruplex stability. In contrast, addition of a T between the fluorophore and the oligonucleotide leads to a decrease in stability.
0006-3495
365-373
Merkina, Elena.E.
c2229d69-8a63-400d-9b61-025f380bb09d
Fox, Keith.R.
9da5debc-4e45-473e-ab8c-550d1104659f
Merkina, Elena.E.
c2229d69-8a63-400d-9b61-025f380bb09d
Fox, Keith.R.
9da5debc-4e45-473e-ab8c-550d1104659f

Merkina, Elena.E. and Fox, Keith.R. (2005) Kinetic stability of intermolecular DNA quadruplexes. Biophysical Journal, 89, 365-373. (doi:10.1529/biophysj.105.061259).

Record type: Article

Abstract

Fluorescently labeled oligodeoxyribonucleotides containing a single tract of four successive guanines have been used to study the thermodynamic and kinetic properties of short intermolecular DNA quadruplexes. When these assemble to form intermolecular quadruplexes the fluorophores are in close proximity and the fluorescence is quenched. On raising the temperature these complexes dissociate and there is a large increase in fluorescence. These complexes are exceptionally stable in potassium-containing buffers, and possess Tm values that are too high to measure. Tm values were determined in sodium-containing buffers for which the rate of reannealing is extremely slow; the melting profiles are effectively irreversible, and the apparent melting temperatures are dependent on the rates of heating. The dissociation kinetics of these complexes was estimated by rapidly increasing the temperature and following the time-dependent changes in fluorescence. From these data we have estimated the half-lives of these quadruplexes at 37°C. Addition of a T to the unlabeled end of the oligonucleotide increases quadruplex stability. In contrast, addition of a T between the fluorophore and the oligonucleotide leads to a decrease in stability.

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More information

Published date: 22 April 2005

Identifiers

Local EPrints ID: 56372
URI: https://eprints.soton.ac.uk/id/eprint/56372
ISSN: 0006-3495
PURE UUID: 195398fa-cf30-489a-ae84-2cc2aa0d060b
ORCID for Keith.R. Fox: ORCID iD orcid.org/0000-0002-2925-7315

Catalogue record

Date deposited: 07 Aug 2008
Last modified: 14 Mar 2019 01:56

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