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Nucleic Acids Research Advance Access published online on November 19, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp1045
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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

Verification of specific G-quadruplex structure by using a novel cyanine dye supramolecular assembly: II. The binding characterization with specific intramolecular G-quadruplex and the recognizing mechanism

Qianfan Yang1,2, Junfeng Xiang1, Shu Yang1,2, Qian Li1,2, Qiuju Zhou1,2, Aijiao Guan1,2, Xiufeng Zhang1, Hong Zhang1, Yalin Tang1,* and Guangzhi Xu1

1Beijing National Laboratory for Molecular Sciences (BNLMS), Center for Molecular Sciences, State Key Laboratory for Structural Chemistry for Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences (ICCAS), Beijing, 100190, P. R. China and 2Graduate University of Chinese Academy of Sciences, Beijing, 100049, P. R. China

*To whom correspondence should be addressed. Tel: +86 10 82617304; Fax: +86 10 62522090; Email: tangyl{at}iccas.ac.cn

Received May 4, 2009. Revised October 27, 2009. Accepted October 27, 2009.

The supramolecular assembly of a novel cyanine dye, 3,3'-di(3-sulfopropyl)-4,5,4',5'-dibenzo-9-ethyl-thiacarbocyanine triethylammonium salt (ETC) was designed to verify specific intramolecular G-quadruplexes from duplex and single-strand DNAs. Spectral results have shown that ETC presented two major distinct signatures with specific intramolecular G-quadruplexes in vitro: (i) dramatic changes in the absorption spectra (including disappearance of absorption peak around 660 nm and appearance of independent new peak around 584 nm); (ii) ~70 times enhancement of fluorescence signal at 600 nm. Furthermore, based on 1H-nuclear magnetic resonance and circular dichroism results, the preferring binding of ETC to specific intramolecular G-quadruplexes probably result from end-stacking, and the loop structure nearby also plays an important role.


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