Comparison of antiparallel a-at and t-at triplets within an alternate strand DNA triple helix
Comparison of antiparallel a-at and t-at triplets within an alternate strand DNA triple helix
We have examined the formation of alternate strand triple-helices at the target sequence A11(TC)6-(GA)6T11 using the oligonucleotides T11(AG)6 and T11(TG)6, by DNase I footprinting. These third strands were designed so as to form parallel T-AT triplets together with antiparallel G-GC and A-AT or T-AT triplets. We find that, although both oligonucleotides yield clear footprints at similar concentrations (0.3 μM) in the presence of manganese, only T11(TG)6 forms a stable complex in magnesium-containing buffers, albeit at a higher concentration (10-30 μM). Examination of the interaction of (AG)6 and (TG)6 with half the target site confirmed that the complex containing A-AT triplets was only stable in the presence of manganese. In contrast no binding of (TG)6 was detected in the presence of either metal ion, suggesting that the reverse-Hoogsteen T-AT triplet is less stable that GGC. We suggest that, within the context of GGC triplets, the rank order of antiparallel triplet stability is A·AT(Mn2+) > T.AT(Mn2+) > T.AT (Mg2+) > A.AT (Mg2+). Third strands containing a single base substitution in the centre of either the parallel or antiparallel portion showed a (10-fold) weaker interaction in manganese-containing buffers, and no interaction in the presence of magnesium.
3977-3982
Washbrook, Elinor
7f340876-4fd6-4518-858c-e12928fe8180
Fox, Keith R.
9da5debc-4e45-473e-ab8c-550d1104659f
25 September 1994
Washbrook, Elinor
7f340876-4fd6-4518-858c-e12928fe8180
Fox, Keith R.
9da5debc-4e45-473e-ab8c-550d1104659f
Washbrook, Elinor and Fox, Keith R.
(1994)
Comparison of antiparallel a-at and t-at triplets within an alternate strand DNA triple helix.
Nucleic Acids Research, 22 (19), .
(doi:10.1093/nar/22.19.3977).
Abstract
We have examined the formation of alternate strand triple-helices at the target sequence A11(TC)6-(GA)6T11 using the oligonucleotides T11(AG)6 and T11(TG)6, by DNase I footprinting. These third strands were designed so as to form parallel T-AT triplets together with antiparallel G-GC and A-AT or T-AT triplets. We find that, although both oligonucleotides yield clear footprints at similar concentrations (0.3 μM) in the presence of manganese, only T11(TG)6 forms a stable complex in magnesium-containing buffers, albeit at a higher concentration (10-30 μM). Examination of the interaction of (AG)6 and (TG)6 with half the target site confirmed that the complex containing A-AT triplets was only stable in the presence of manganese. In contrast no binding of (TG)6 was detected in the presence of either metal ion, suggesting that the reverse-Hoogsteen T-AT triplet is less stable that GGC. We suggest that, within the context of GGC triplets, the rank order of antiparallel triplet stability is A·AT(Mn2+) > T.AT(Mn2+) > T.AT (Mg2+) > A.AT (Mg2+). Third strands containing a single base substitution in the centre of either the parallel or antiparallel portion showed a (10-fold) weaker interaction in manganese-containing buffers, and no interaction in the presence of magnesium.
This record has no associated files available for download.
More information
Published date: 25 September 1994
Additional Information:
Funding Information:
We thank Dr Terry Jenkins and Mr Tony Reszka (ICR, Sutton) for assistance with the DNA melting curves. This work was supported by grants from the Cancer Research Campaign and the Science and Engineering Research Council. KRF is a Lister Institute Research Fellow.
Identifiers
Local EPrints ID: 475663
URI: http://eprints.soton.ac.uk/id/eprint/475663
ISSN: 0305-1048
PURE UUID: 2c1672eb-471a-458e-8ae5-296de4dee141
Catalogue record
Date deposited: 23 Mar 2023 17:48
Last modified: 18 Mar 2024 02:32
Export record
Altmetrics
Contributors
Author:
Elinor Washbrook
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
