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Nucleic Acids Research Advance Access originally published online on June 4, 2008
Nucleic Acids Research 2008 36(12):4079-4087; doi:10.1093/nar/gkn351
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Nucleic Acids Research, 2008, Vol. 36, No. 12 4079-4087
© 2008 The Author(s)
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.

Structural Biology

Structural polymorphism of intramolecular quadruplex of human telomeric DNA: effect of cations, quadruplex-binding drugs and flanking sequences

Timur I. Gaynutdinov, Ronald D. Neumann and Igor G. Panyutin*

Department of Nuclear Medicine, Warren G. Magnuson Clinical Center, National Institutes of Health, Bethesda, MD 20892-1180, USA

*To whom correspondence should be addressed. Tel: +1 301 496 8308; Fax: +1 301 480 9712; Email: igorp{at}helix.nih.gov

Received March 27, 2008. Revised May 12, 2008. Accepted May 15, 2008.

G-quadruplex structures formed in the telomeric DNA are thought to play a role in the telomere function. Drugs that stabilize the G-quadruplexes were shown to have anticancer effects. The structures formed by the basic telomeric quadruplex-forming unit G3(TTAG3)3 were the subject of multiple studies. Here, we employ 125I-radioprobing, a method based on analysis of the distribution of DNA breaks after decay of 125I incorporated into one of the nucleotides, to determine the fold of the telomeric DNA in the presence of TMPyP4 and telomestatin, G-quadruplex-binding ligands and putative anticancer drugs. We show that d[G3(TTAG3)3125I-CT] adopts basket conformation in the presence of NaCl and that addition of either of the drugs does not change this conformation of the quadruplex. In KCl, the d[G3(TTAG3)3125I-CT] is most likely present as a mixture of two or more conformations, but addition of the drugs stabilize the basket conformation. We also show that d[G3(TTAG3)3125I-CT] with a 5'-flanking sequence folds into (3+1) type 2 conformation in KCl, while in NaCl it adopts a novel (3+1) basket conformation with a diagonal central loop. The results demonstrate the structural flexibility of the human telomeric DNA; and show how cations, quadruplex-binding drugs and flanking sequences can affect the conformation of the telomeric quadruplex.


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