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Nucleic Acids Research Advance Access originally published online on July 3, 2008
Nucleic Acids Research 2008 36(13):4433-4442; doi:10.1093/nar/gkn402
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Nucleic Acids Research, 2008, Vol. 36, No. 13 4433-4442
© 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

Effect of loop length variation on quadruplex-Watson Crick duplex competition

Niti Kumar1, Bankanidhi Sahoo2, K. A. S. Varun2, Sudipta Maiti2 and Souvik Maiti1,*

1Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007 and 2Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India

*To whom correspondence should be addressed. Tel: +91 11 2766 6156; Fax: +91 11 2766 7471; Email: souvik{at}igib.res.in

Received February 4, 2008. Revised June 7, 2008. Accepted June 9, 2008.

The effect of loop length on quadruplex stability has been studied when the G-rich strand is present along with its complementary C-rich strand, thereby resulting in competition between quadruplex and duplex structures. Using model sequences with loop lengths varying from T to T5, we carried out extensive FRET to discover the influence of loop length on the quadruplex-Watson Crick duplex competition. The binding data show an increase in the binding affinity of quadruplexes towards their complementary strands upon increasing the loop length. Our kinetic data reveal that unfolding of the quadruplex in presence of a complementary strand involves a contribution from a predominant slow and a small population of fast opening conformer. The contribution from the fast opening conformer increases upon increasing the loop length leading to faster duplex formation. FCS data show an increase in the interconversion between the quadruplex conformers in presence of the complementary strand, which shifts the equilibrium towards the fast opening conformer with an increase in loop length. The relative free-energy difference ({Delta}{Delta}G°) between the duplex and quadruplex indicates that an increase in loop length favors duplex formation and out competes the quadruplex.


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