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Footprinting Studies on Ligands which Stabilize DNA Triplexes: Effects on Stringency within a Parallel Triple Helix

Footprinting Studies on Ligands which Stabilize DNA Triplexes: Effects on Stringency within a Parallel Triple Helix
Footprinting Studies on Ligands which Stabilize DNA Triplexes: Effects on Stringency within a Parallel Triple Helix

We have examined the effect of four triplex-binding ligands on the interaction of the oligodeoxynucleotides T8NT8 (N = A, G, C, T) with DNA fragments containing the sequences A8XA8.T8- YT8 (X = G, C, T; Y = C, G, A) by DNase I footprinting. The ligands form a series of quinoline derivatives with an alkylamine chain in the 4-position and different aryl substituents in the 2-position. By themselves these compounds do not alter DNase I digestion of the DNA duplexes at concentrations up to 100 µM. At a concentration of 10 µM they potentiate triplex formation, lowering the concentration of oligonucleotide required to produce a clear footprint by as much as 100-fold. As well as stabilizing triplexes which consist of well-characterized DNA triplets, they also promote the formation of complexes which contain central triplet mismatches. This reduction in the stringency of triple helix formation may be used to broaden the range of triplex target sequences and enable recognition at sites which contain short regions for which there are no good triplet matches.

0006-2960
7234-7242
Chandler, Simon P.
839d7f59-0eb0-4fc5-accf-6ff2bc08b243
Strekowski, Lucjan
a671c874-b36b-41ca-affe-ce373f032209
Wilson, W. David
a1c5b993-5265-41c4-a6ac-41c3ea279f94
Fox, Keith R.
9da5debc-4e45-473e-ab8c-550d1104659f
Chandler, Simon P.
839d7f59-0eb0-4fc5-accf-6ff2bc08b243
Strekowski, Lucjan
a671c874-b36b-41ca-affe-ce373f032209
Wilson, W. David
a1c5b993-5265-41c4-a6ac-41c3ea279f94
Fox, Keith R.
9da5debc-4e45-473e-ab8c-550d1104659f

Chandler, Simon P., Strekowski, Lucjan, Wilson, W. David and Fox, Keith R. (1995) Footprinting Studies on Ligands which Stabilize DNA Triplexes: Effects on Stringency within a Parallel Triple Helix. Biochemistry, 34 (21), 7234-7242. (doi:10.1021/bi00021a039).

Record type: Article

Abstract

We have examined the effect of four triplex-binding ligands on the interaction of the oligodeoxynucleotides T8NT8 (N = A, G, C, T) with DNA fragments containing the sequences A8XA8.T8- YT8 (X = G, C, T; Y = C, G, A) by DNase I footprinting. The ligands form a series of quinoline derivatives with an alkylamine chain in the 4-position and different aryl substituents in the 2-position. By themselves these compounds do not alter DNase I digestion of the DNA duplexes at concentrations up to 100 µM. At a concentration of 10 µM they potentiate triplex formation, lowering the concentration of oligonucleotide required to produce a clear footprint by as much as 100-fold. As well as stabilizing triplexes which consist of well-characterized DNA triplets, they also promote the formation of complexes which contain central triplet mismatches. This reduction in the stringency of triple helix formation may be used to broaden the range of triplex target sequences and enable recognition at sites which contain short regions for which there are no good triplet matches.

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Published date: May 1995

Identifiers

Local EPrints ID: 475855
URI: http://eprints.soton.ac.uk/id/eprint/475855
ISSN: 0006-2960
PURE UUID: 8b7f421e-2cfb-4662-b799-1561f770b154
ORCID for Keith R. Fox: ORCID iD orcid.org/0000-0002-2925-7315

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Date deposited: 29 Mar 2023 16:46
Last modified: 17 Mar 2024 02:34

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Contributors

Author: Simon P. Chandler
Author: Lucjan Strekowski
Author: W. David Wilson
Author: Keith R. Fox ORCID iD

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