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Nucleic Acids Research 2006 34(2):755-763; doi:10.1093/nar/gkj480
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Published online 30 January 2006

© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

Sequence effects of aminofluorene-modified DNA duplexes: thermodynamic and circular dichroism properties

Srinivasa Rao Meneni, Rhijuta D'Mello, Gregory Norigian, Gregory Baker, Lan Gao1, M. Paul Chiarelli1 and Bongsup P. Cho*

Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island Kingston, RI 02881, USA 1Department of Chemistry, Loyola University Chicago, IL 60626, USA

*To whom correspondence should be addressed at Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, 41 Lower College Road, Kingston, RI 02881, USA. Tel: +1 401 874 5024; Fax: +1 401 874 5766; Email: bcho{at}uri.edu

Received December 7, 2005. Revised January 14, 2005. Accepted January 14, 2005.

Circular dichroism (CD) and UV-melting experiments were conducted with 16 oligodeoxynucleotides modified by the carcinogen 2-aminofluorene, whose sequence around the lesion was varied systematically [d(CTTCTNG[AF]NCCTC), N = G, A, C, T], to gain insight into the factors that determine the equilibrium between base-displaced stacked (S) and external B-type (B) duplex conformers. Differing stabilities among the duplexes can be attributed to different populations of S and B conformers. The AF modification always resulted in sequence-dependent thermal (Tm) and thermodynamic (–{Delta}G°) destabilization. The population of B-type conformers derived from eight selected duplexes (i.e. -AG*N- and -CG*N-) was inversely proportional to the –{Delta}G° and Tm values, which highlights the importance of carcinogen/base stacking in duplex stabilization even in the face of disrupted Watson–Crick base pairing in S-conformation. CD studies showed that the extent of the adduct-induced negative ellipticities in the 290–350 nm range is correlated linearly with –{Delta}G° and Tm, but inversely with the population of B-type conformations. Taken together, these results revealed a unique interplay between the extent of carcinogenic interaction with neighboring base pairs and the thermodynamic properties of the AF-modified duplexes. The sequence-dependent S/B heterogeneities have important implications in understanding how arylamine–DNA adducts are recognized in nucleotide excision repair.


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