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Intramolecular DNA quadruplexes with different arrangements of short and long loops
We have examined the folding, stability and kinetics of intramolecular quadruplexes formed by DNA sequences containing four G(3) tracts separated by either single T or T(4) loops. All these sequences fold to form intramolecular quadruplexes and 1D-NMR spectra suggest that they each adopt unique stru...
Autores principales: | , , , , |
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Formato: | Texto |
Lenguaje: | English |
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Oxford University Press
2007
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1919480/ https://www.ncbi.nlm.nih.gov/pubmed/17576685 http://dx.doi.org/10.1093/nar/gkm316 |
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author | Rachwal, Phillip A. Findlow, I. Stuart Werner, Joern M. Brown, Tom Fox, Keith R. |
author_facet | Rachwal, Phillip A. Findlow, I. Stuart Werner, Joern M. Brown, Tom Fox, Keith R. |
author_sort | Rachwal, Phillip A. |
collection | PubMed |
description | We have examined the folding, stability and kinetics of intramolecular quadruplexes formed by DNA sequences containing four G(3) tracts separated by either single T or T(4) loops. All these sequences fold to form intramolecular quadruplexes and 1D-NMR spectra suggest that they each adopt unique structures (with the exception of the sequence with all three loops containing T(4), which is polymorphic). The stability increases with the number of single T loops, though the arrangement of different length loops has little effect. In the presence of potassium ions, the oligonucleotides that contain at least one single T loop exhibit similar CD spectra, which are indicative of a parallel topology. In contrast, when all three loops are substituted with T(4) the CD spectrum is typical of an antiparallel arrangement. In the presence of sodium ions, the sequences with two and three single T loops also adopt a parallel folded structure. Kinetic studies on the complexes with one or two T(4) loops in the presence of potassium ions reveal that sequences with longer loops display slower folding rates. |
format | Text |
id | pubmed-1919480 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2007 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-19194802007-07-24 Intramolecular DNA quadruplexes with different arrangements of short and long loops Rachwal, Phillip A. Findlow, I. Stuart Werner, Joern M. Brown, Tom Fox, Keith R. Nucleic Acids Res Structural Biology We have examined the folding, stability and kinetics of intramolecular quadruplexes formed by DNA sequences containing four G(3) tracts separated by either single T or T(4) loops. All these sequences fold to form intramolecular quadruplexes and 1D-NMR spectra suggest that they each adopt unique structures (with the exception of the sequence with all three loops containing T(4), which is polymorphic). The stability increases with the number of single T loops, though the arrangement of different length loops has little effect. In the presence of potassium ions, the oligonucleotides that contain at least one single T loop exhibit similar CD spectra, which are indicative of a parallel topology. In contrast, when all three loops are substituted with T(4) the CD spectrum is typical of an antiparallel arrangement. In the presence of sodium ions, the sequences with two and three single T loops also adopt a parallel folded structure. Kinetic studies on the complexes with one or two T(4) loops in the presence of potassium ions reveal that sequences with longer loops display slower folding rates. Oxford University Press 2007-06 2007-06-18 /pmc/articles/PMC1919480/ /pubmed/17576685 http://dx.doi.org/10.1093/nar/gkm316 Text en © 2007 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Structural Biology Rachwal, Phillip A. Findlow, I. Stuart Werner, Joern M. Brown, Tom Fox, Keith R. Intramolecular DNA quadruplexes with different arrangements of short and long loops |
title | Intramolecular DNA quadruplexes with different arrangements of short and long loops |
title_full | Intramolecular DNA quadruplexes with different arrangements of short and long loops |
title_fullStr | Intramolecular DNA quadruplexes with different arrangements of short and long loops |
title_full_unstemmed | Intramolecular DNA quadruplexes with different arrangements of short and long loops |
title_short | Intramolecular DNA quadruplexes with different arrangements of short and long loops |
title_sort | intramolecular dna quadruplexes with different arrangements of short and long loops |
topic | Structural Biology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1919480/ https://www.ncbi.nlm.nih.gov/pubmed/17576685 http://dx.doi.org/10.1093/nar/gkm316 |
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