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DNA polymorphism as an origin of adenine-thymine tract length-dependent threading intercalation rate

DNA polymorphism as an origin of adenine-thymine tract length-dependent threading intercalation rate
DNA polymorphism as an origin of adenine-thymine tract length-dependent threading intercalation rate
Binuclear ruthenium complexes that bind DNA by threading intercalation have recently been found to exhibit an exceptional kinetic selectivity for long polymeric adenine?thymine (AT) DNA. A series of oligonucleotide hairpin duplexes containing a central tract of 6?44 alternating AT base pairs have here been used to investigate the nature of the recognition mechanism.

We find that, above a threshold AT tract length corresponding to one helix turn of B-DNA, a dramatic increase in threading intercalation rate occurs. In contrast, such length dependence is not observed for rates of unthreading. Intercalation by any mechanism that depends on the open end of the hairpin was found not to be important in the series of oligonucleotides used, as verified by including in the study a hairpin duplex cyclized by a copper-catalyzed “click” reaction.

Our observations are interpreted in terms of a conformational pre-equilibrium, determined by the length of the AT tract. We finally find that mismatches or loops in the oligonucleotide facilitate the threading process, of interest for the development of mismatch-recognizing probes.
0002-7863
14651-14658
Nordell, Pär
d45f21fe-1b10-4f75-b95d-681ee9eaba17
Westerlund, Fredrik
08fb049e-9c6c-4f9f-a2a2-23c3743ade9f
Reymer, Anna
42d91b4e-dd25-4add-8eff-81921a02d167
El-Sagheer, Afaf H.
0bf56d90-78ee-4772-add8-453ccacc39be
Brown, Tom
a64aae36-bb30-42df-88a2-11be394e8c89
Nordén, Bengt
64d4009e-7456-4490-ac87-8d587334c7e0
Lincoln, Per
f1edcf40-411d-4f54-bd94-d13394c011d4
Nordell, Pär
d45f21fe-1b10-4f75-b95d-681ee9eaba17
Westerlund, Fredrik
08fb049e-9c6c-4f9f-a2a2-23c3743ade9f
Reymer, Anna
42d91b4e-dd25-4add-8eff-81921a02d167
El-Sagheer, Afaf H.
0bf56d90-78ee-4772-add8-453ccacc39be
Brown, Tom
a64aae36-bb30-42df-88a2-11be394e8c89
Nordén, Bengt
64d4009e-7456-4490-ac87-8d587334c7e0
Lincoln, Per
f1edcf40-411d-4f54-bd94-d13394c011d4

Nordell, Pär, Westerlund, Fredrik, Reymer, Anna, El-Sagheer, Afaf H., Brown, Tom, Nordén, Bengt and Lincoln, Per (2008) DNA polymorphism as an origin of adenine-thymine tract length-dependent threading intercalation rate. Journal of the American Chemical Society, 130 (44), 14651-14658. (doi:10.1021/ja804427q).

Record type: Article

Abstract

Binuclear ruthenium complexes that bind DNA by threading intercalation have recently been found to exhibit an exceptional kinetic selectivity for long polymeric adenine?thymine (AT) DNA. A series of oligonucleotide hairpin duplexes containing a central tract of 6?44 alternating AT base pairs have here been used to investigate the nature of the recognition mechanism.

We find that, above a threshold AT tract length corresponding to one helix turn of B-DNA, a dramatic increase in threading intercalation rate occurs. In contrast, such length dependence is not observed for rates of unthreading. Intercalation by any mechanism that depends on the open end of the hairpin was found not to be important in the series of oligonucleotides used, as verified by including in the study a hairpin duplex cyclized by a copper-catalyzed “click” reaction.

Our observations are interpreted in terms of a conformational pre-equilibrium, determined by the length of the AT tract. We finally find that mismatches or loops in the oligonucleotide facilitate the threading process, of interest for the development of mismatch-recognizing probes.

Full text not available from this repository.

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Published date: 2008

Identifiers

Local EPrints ID: 146703
URI: http://eprints.soton.ac.uk/id/eprint/146703
ISSN: 0002-7863
PURE UUID: 9532a416-3fbe-4895-8eb0-a7f20a36297c

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Date deposited: 22 Apr 2010 09:10
Last modified: 17 Jul 2019 00:04

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