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Nucleic Acids Research Advance Access published online on October 25, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp898
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© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Structural Biology

Molecular crowding creates an essential environment for the formation of stable G-quadruplexes in long double-stranded DNA

Ke-wei Zheng1, Zhao Chen1, Yu-hua Hao2 and Zheng Tan1,2,*

1Laboratory of Biochemistry and Biophysics, College of Life Sciences, Wuhan University, Wuhan 430072 and 2State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P. R. China

*To whom correspondence should be addressed. Tel: +86 (10) 6480 7259; Fax: +86 (10) 6480 7099; Email: z.tan{at}ioz.ac.cn, tanclswu{at}public.wh.hb.cn

Received August 1, 2009. Revised October 6, 2009. Accepted October 6, 2009.

Large numbers of guanine-rich sequences with potential to form G-quadruplexes have been identified in genomes of various organisms. Such sequences are constrained at both ends by long DNA duplex with a complementary strand in close proximity to compete for duplex formation. G-quadruplex/duplex competition in long double-stranded DNA has rarely been studied. In this work, we used DMS footprinting and gel electrophoresis to study G-quadruplex formation in long double-stranded DNA derived from human genome under both dilute and molecular crowding condition created by PEG. G-quadruplex formation was observed in the process of RNA transcription and after heat denaturation/renaturation under molecular crowding condition. Our results showed that the heat denaturation/renaturation treatment followed by gel electrophoresis could provide a simple method to quantitatively access the ability of G-quadruplex formation in long double-stranded DNA. The effect of K+ and PEG concentration was investigated and we found that stable G-quadruplexes could only form under the crowding condition with PEG at concentrations near the physiological concentration of biomass in living cells. This observation reveals a physical basis for the formation of stable G-quadruplexes in genome and supports its presence under the in vivo molecular crowding condition.


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