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Intramolecular DNA quadruplexes with different arrangements of short and long loops

Record type: Article

We have examined the folding, stability and kinetics of intramolecular quadruplexes formed by DNA sequences containing four G3 tracts separated by either single T or T4 loops. All these sequences fold to form intramolecular quadruplexes and 1D-NMR spectra suggest that they each adopt unique structures (with the exception of the sequence with all three loops containing T4, which is polymorphic). The stability increases with the number of single T loops, though the arrangement of different length loops has little effect. In the presence of potassium ions, the oligonucleotides that contain at least one single T loop exhibit similar CD spectra, which are indicative of a parallel topology. In contrast, when all three loops are substituted with T4 the CD spectrum is typical of an antiparallel arrangement. In the presence of sodium ions, the sequences with two and three single T loops also adopt a parallel folded structure. Kinetic studies on the complexes with one or two T4 loops in the presence of potassium ions reveal that sequences with longer loops display slower folding rates.

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Citation

Rachwal, P.A., Findlow, I.S., Werner, J.M., Brown, T. and Fox, K.R. (2007) Intramolecular DNA quadruplexes with different arrangements of short and long loops Nucleic Acids Research, 35, (12), pp. 4214-4222. (doi:10.1093/nar/gkm316).

More information

Published date: 1 June 2007
Keywords: forming region, tract length, c-myc promoter, tetrahelical structure, kinetic stability, parallel quadruplexes, anti-hiv oligonucleotide, human telomeric sequence, melting curves, small-molecule

Identifiers

Local EPrints ID: 55859
URI: http://eprints.soton.ac.uk/id/eprint/55859
ISSN: 0305-1048
PURE UUID: 9ed67930-6d31-4bd4-9824-e2499c7de10d
ORCID for J.M. Werner: ORCID iD orcid.org/0000-0002-4712-1833
ORCID for K.R. Fox: ORCID iD orcid.org/0000-0002-2925-7315

Catalogue record

Date deposited: 06 Aug 2008
Last modified: 17 Jul 2017 14:31

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Contributors

Author: P.A. Rachwal
Author: I.S. Findlow
Author: J.M. Werner ORCID iD
Author: T. Brown
Author: K.R. Fox ORCID iD

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