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The stability of triplex DNA is affected by the stability of the underlying duplex

The stability of triplex DNA is affected by the stability of the underlying duplex
The stability of triplex DNA is affected by the stability of the underlying duplex
We have studied the formation of DNA triple helices in different sequence contexts and show that, for the most stable triplexes, their apparent stability is affected by the stability of the underlying duplex. For a 14-mer parallel triplex-forming oligonucleotide (generating C+.GC and T.AT triplets) at pH 5.0 the Tm is more than 10 °C lower with an intermolecular 14-mer duplex target, than it is with an intramolecular duplex, or one which is flanked by 6 GC base pairs at either end. A similar effect is seen with triplex-forming oligonucleotides that contain stabilising analogues, for which the Tm is higher for an intramolecular than an intermolecular duplex target. These results suggest that the use of simple intermolecular duplex targets may underestimate the triplex stabilisation that is produced by some nucleotide analogues.

triplex, nucleotide analogue, thermal melting
0301-4622
105-110
Rusling, David A.
d08f1f97-f8a9-4980-a025-ae41c23a938f
Rachwal, Philip A.
97ca8752-9be6-42ec-9dc5-570f7413be51
Brown, Tom
a64aae36-bb30-42df-88a2-11be394e8c89
Fox, Keith R.
9da5debc-4e45-473e-ab8c-550d1104659f
Rusling, David A.
d08f1f97-f8a9-4980-a025-ae41c23a938f
Rachwal, Philip A.
97ca8752-9be6-42ec-9dc5-570f7413be51
Brown, Tom
a64aae36-bb30-42df-88a2-11be394e8c89
Fox, Keith R.
9da5debc-4e45-473e-ab8c-550d1104659f

Rusling, David A., Rachwal, Philip A., Brown, Tom and Fox, Keith R. (2009) The stability of triplex DNA is affected by the stability of the underlying duplex. Biophysical Chemistry, 145 (2-3), 105-110. (doi:10.1016/j.bpc.2009.09.007).

Record type: Article

Abstract

We have studied the formation of DNA triple helices in different sequence contexts and show that, for the most stable triplexes, their apparent stability is affected by the stability of the underlying duplex. For a 14-mer parallel triplex-forming oligonucleotide (generating C+.GC and T.AT triplets) at pH 5.0 the Tm is more than 10 °C lower with an intermolecular 14-mer duplex target, than it is with an intramolecular duplex, or one which is flanked by 6 GC base pairs at either end. A similar effect is seen with triplex-forming oligonucleotides that contain stabilising analogues, for which the Tm is higher for an intramolecular than an intermolecular duplex target. These results suggest that the use of simple intermolecular duplex targets may underestimate the triplex stabilisation that is produced by some nucleotide analogues.

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More information

Published date: December 2009
Keywords: triplex, nucleotide analogue, thermal melting

Identifiers

Local EPrints ID: 146667
URI: http://eprints.soton.ac.uk/id/eprint/146667
ISSN: 0301-4622
PURE UUID: 501d0111-99e3-4563-966a-6bb2a4d68598
ORCID for David A. Rusling: ORCID iD orcid.org/0000-0002-7442-686X
ORCID for Keith R. Fox: ORCID iD orcid.org/0000-0002-2925-7315

Catalogue record

Date deposited: 22 Apr 2010 08:37
Last modified: 20 Jul 2019 01:27

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