Nucleic Acids Research Advance Access originally published online on April 11, 2007
Nucleic Acids Research 2007 35(9):2846-2860; doi:10.1093/nar/gkm155
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Nucleic Acids Research, 2007, Vol. 35, No. 9 2846-2860
© 2007 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.
Chemistry |
Investigation of spectral conversion of d(TTAGGG)4 and d(TTAGGG)13 upon potassium titration by a G-quadruplex recognizer BMVC molecule
1Institute of Atomic and Molecular Sciences, Academia Sinica, PO Box 23-166, Taipei, 106, Taiwan, Republic of China, 2Department of Chemistry, National Chung-Hsin University, Taichung, Taiwan, Republic of China and 3Institute of Biophotonics Engineering, National Yang-Ming University Taipei, 11221, Taiwan, Republic of China
*To whom correspondence should be addressed. Tel: +8862 2366 8231; Fax: +8862 2362 0200; Email: tcchang{at}po.iams.sinica.edu.tw
Received September 5, 2006. Revised November 15, 2006. Accepted February 28, 2007.
We have introduced a G-quadruplex-binding ligand, 3,6-bis(1-methyl-4-vinylpyridinium)carbazole diiodide (BMVC), to verify the major structure of d(T2AG3)4 (H24) in potassium solution and examine the structural conversion of H24 in sodium solution upon potassium titration. The studies of circular dichroism, induced circular dichroism, spectral titration and gel competition have allowed us to determine the binding mode and binding ratio of BMVC to the H24 in solution and eliminate the parallel form as the major G-quadruplex structure. Although the mixed-type form could not be eliminated as a main component, the basket and chair forms are more likely the main components of H24 in potassium solution. In addition, the circular dichroism spectra and the job plots reveal that a longer telomeric sequence d(T2AG3)13 (H78) could form two units of G4 structure both in sodium or potassium solutions. Of particular interest is that no appreciable change on the induced circular dichroism spectra of BMVC is found during the change of the circular dichroism patterns of H24 upon potassium titration. Considering similar spectral conversion detected for H24 and a long sequence H78 together with the G4 structure stabilized by BMVC, it is therefore unlikely that the rapid spectral conversion of H24 and H78 is due to structural change between different types of the G4 structures. With reference to the circular dichroism spectra of d(GAA)7 and d(GAAA)5, we suggest that the spectral conversion of H24 upon potassium titration is attributed to fast ion exchange resulting in different loop base interaction and various hydrogen bonding effects.
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