Strategies for increasing the stability of triple helical DNA
Strategies for increasing the stability of triple helical DNA
By targeting a 17 base oligopurine tract with different 9-mer oligonucleotides and examining the interaction by quantitative DNase I footprinting, I have shown that C+.GC triplets impart a greater triplex stability than T.AT triplets. Experiments using propargylamino-dU, thymine analogue with a charged side group, show that when incorporated in place of thymine in the oligonucleotide 5'-TTTTTCTT, the stability is increased by at least 20,000-fold.
A further means of stabilising DNA triplexes is to use components which bind selectively to triplex and not duplex DNA. I have used DNase I footprinting experiments to explore the structure-activity relationships of a series of disubstituted amidoanthraquinones, examining how the position of the substituents affects their ability to stabilise triplex DNA. The results demonstrate that, with parallel (CT-containing) triplexes, the triplex binding activity of the anthraquinones decreases in the order 2,7 > 1,5 = 1, 8 >>2, 6. UV thermal melting studies with polyd(A).2polyd(T) gave the ranking order 1,8>1,5 = 2,7 >> 2,6.
Coralyne displayed a weaker affinity than the 2,6-disubstituted anthraquinone, while a naphthylquinoline showed similar affinity to the 1,5- and 1,8- anthraquinones. A series of 2,7-disubstituted proflavine derivatives had varying affinities, the best being comparable to the 2,7-disubstituted anthraquinone. BePI bound to triplexes with a similar affinity to the 2,7-anthraquinone.
Triplex stabilisation has also been achieved using an oligonucleotide in which a naphthylquinoline triplex-binding ligand has been covalently tethered to the 5'-end of the oligonucleotide. This derivative shows much greater stabilisation than the untethered compound when used at equivalent concentrations. DNase I footprinting has also been used to examine the interaction of a series of naphthylquinoline dimers with triplex DNA. The best of these ligands generate triplexes which are 40 times more stable than those with the 2,7-disubstituted anthraquinone. The results are consistent with the suggestion that these are the first examples of triplex-specific bis-intercalators.
University of Southampton
1999
Keppler, Melanie Dawn
(1999)
Strategies for increasing the stability of triple helical DNA.
University of Southampton, Doctoral Thesis.
Record type:
Thesis
(Doctoral)
Abstract
By targeting a 17 base oligopurine tract with different 9-mer oligonucleotides and examining the interaction by quantitative DNase I footprinting, I have shown that C+.GC triplets impart a greater triplex stability than T.AT triplets. Experiments using propargylamino-dU, thymine analogue with a charged side group, show that when incorporated in place of thymine in the oligonucleotide 5'-TTTTTCTT, the stability is increased by at least 20,000-fold.
A further means of stabilising DNA triplexes is to use components which bind selectively to triplex and not duplex DNA. I have used DNase I footprinting experiments to explore the structure-activity relationships of a series of disubstituted amidoanthraquinones, examining how the position of the substituents affects their ability to stabilise triplex DNA. The results demonstrate that, with parallel (CT-containing) triplexes, the triplex binding activity of the anthraquinones decreases in the order 2,7 > 1,5 = 1, 8 >>2, 6. UV thermal melting studies with polyd(A).2polyd(T) gave the ranking order 1,8>1,5 = 2,7 >> 2,6.
Coralyne displayed a weaker affinity than the 2,6-disubstituted anthraquinone, while a naphthylquinoline showed similar affinity to the 1,5- and 1,8- anthraquinones. A series of 2,7-disubstituted proflavine derivatives had varying affinities, the best being comparable to the 2,7-disubstituted anthraquinone. BePI bound to triplexes with a similar affinity to the 2,7-anthraquinone.
Triplex stabilisation has also been achieved using an oligonucleotide in which a naphthylquinoline triplex-binding ligand has been covalently tethered to the 5'-end of the oligonucleotide. This derivative shows much greater stabilisation than the untethered compound when used at equivalent concentrations. DNase I footprinting has also been used to examine the interaction of a series of naphthylquinoline dimers with triplex DNA. The best of these ligands generate triplexes which are 40 times more stable than those with the 2,7-disubstituted anthraquinone. The results are consistent with the suggestion that these are the first examples of triplex-specific bis-intercalators.
This record has no associated files available for download.
More information
Published date: 1999
Identifiers
Local EPrints ID: 464010
URI: http://eprints.soton.ac.uk/id/eprint/464010
PURE UUID: 92911120-e06f-49f3-9521-61c28027fb55
Catalogue record
Date deposited: 04 Jul 2022 21:00
Last modified: 04 Jul 2022 21:00
Export record
Contributors
Author:
Melanie Dawn Keppler
Download statistics
Downloads from ePrints over the past year. Other digital versions may also be available to download e.g. from the publisher's website.
View more statistics