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Effect of G-tract length on the topology and stability of intramolecular DNA quadruplexes

Record type: Article

G-Rich sequences are known to form four-stranded structures that are based on stacks of G-quartets, and sequences with the potential to adopt these structures are common in eukaryotic genomes. However, there are few rules for predicting the relative stability of folded complexes that are adopted by sequences with different-length G-tracts or variable-length linkers between them. We have used thermal melting, circular dichroism, and gel electrophoresis to examine the topology and stability of intramolecular G-quadruplexes that are formed by sequences of the type d(GnT)4 and d(GnT2)4 (n = 3-7) in the presence of varying concentrations of sodium and potassium. In the presence of potassium or sodium, d(GnT)4 sequences form intramolecular parallel complexes with the following order of stability: n = 3 > n = 7 > n = 6 > n = 5 > n = 4. d(G3T)4 is anomalously stable. In contrast, the stability of d(GnT2)4 increases with the length of the G-tract (n = 7 > n = 6 > n = 5 > n = 4 > n = 3). The CD spectra for d(GnT)4 in the presence of potassium exhibit positive peaks around 260 nm, consistent with the formation of parallel topologies. These peaks are retained in sodium-containing buffers, but when n = 4, 5, or 6, CD maxima are observed around 290 nm, suggesting that these sequences [especially d(G5T)4] have some antiparallel characteristics. d(G3T2)4 adopts a parallel conformation in the presence of both sodium and potassium, while all the other d(GnT2)4 complexes exhibit predominantly antiparallel features. The properties of these complexes are also affected by the rate of annealing, and faster rates favor parallel complexes.

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Citation

Rachwal, Philip A., Brown, Tom and Fox, Keith R. (2007) Effect of G-tract length on the topology and stability of intramolecular DNA quadruplexes Biochemistry, 46, (11), pp. 3036-3044. (doi:10.1021/bi062118j).

More information

Submitted date: 11 October 2006
Published date: 20 March 2007

Identifiers

Local EPrints ID: 56823
URI: http://eprints.soton.ac.uk/id/eprint/56823
ISSN: 0006-2960
PURE UUID: 814085fd-fc91-43c3-bd1b-708b41e56254
ORCID for Keith R. Fox: ORCID iD orcid.org/0000-0002-2925-7315

Catalogue record

Date deposited: 07 Aug 2008
Last modified: 11 Jul 2017 09:46

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Contributors

Author: Philip A. Rachwal
Author: Tom Brown
Author: Keith R. Fox ORCID iD

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