Nucleic Acids Research Advance Access originally published online on September 12, 2007
Nucleic Acids Research 2007 35(18):6181-6195; doi:10.1093/nar/gkm670
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Nucleic Acids Research, 2007, Vol. 35, No. 18 6181-6195
© 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.
Structural Biology |
A study of 7-deaza-2'-deoxyguanosine–2'-deoxycytidine base pairing in DNA
1Eppley Institute for Research in Cancer, 2Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE-68198-6025, 3Department of Chemistry, Vanderbilt University, Nashville, TN-37235 and 4Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA-15261, USA
*To whom correspondence should be addressed. Tel: +1 412 383 9593; Fax: +1 412 383 7436; Email: goldbi{at}pitt.edu
Received May 22, 2007. Revised July 26, 2007. Accepted August 13, 2007.
The incorporation of 7-deazaguanine modifications into DNA is frequently used to probe protein recognition of H-bonding information in the major groove of DNA. While it is generally assumed that 7-deazaguanine forms a normal Watson–Crick base pair with cytosine, detailed thermodynamic and structural analyses of this modification have not been reported. The replacement of the 7-N atom on guanine with a C–H, alters the electronic properties of the heterocycle and eliminates a major groove cation-binding site that could affect the organization of salts and water in the major groove. We report herein the characterization of synthetic DNA oligomers containing 7-deazaguanine using a variety of complementary approaches: UV thermal melting, differential scanning calorimetry (DSC), circular dichroism (CD), chemical probing and NMR. The results indicate that the incorporation of a 7-deazaguanine modification has a significant effect on the dynamic structure of the DNA at the flanking residue. This appears to be mediated by changes in hydration and cation organization.
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