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Nucleic Acids Research 2005 33(16):e138; doi:10.1093/nar/gni134
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Published online 12 September 2005

© The Author 2005. 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

Methods Online

Thermal difference spectra: a specific signature for nucleic acid structures

Jean-Louis Mergny*, Jing Li1, Laurent Lacroix, Samir Amrane and Jonathan B. Chaires2

Laboratoire de Biophysique, Muséum National d'Histoire Naturelle USM503, INSERM U 565, CNRS UMR 5153 43 rue Cuvier, 75231 Paris cedex 05, France 1Department of Biochemistry, University of Mississippi Medical Center 2500 N. State St., Jackson, MS 39216-4505, USA 2James Graham Brown Cancer Center, Department of Medicine, Health Sciences Center, University of Louisville 529 South Jackson Street, Louisville KY 40202, USA

*To whom correspondence should be addressed. Tel: +33 1 40 79 36 89; Fax: +33 1 40 79 37 05; Email: faucon{at}mnhn.fr

Received July 20, 2005. Revised August 11, 2005. Accepted August 11, 2005.

We show that nucleic acid structures may be conveniently and inexpensively characterized by their UV thermal difference spectra. A thermal difference spectrum (TDS) is obtained for a nucleic acid by simply recording the ultraviolet absorbance spectra of the unfolded and folded states at temperatures above and below its melting temperature (Tm). The difference between these two spectra is the TDS. The TDS has a specific shape that is unique for each type of nucleic acid structure, a conclusion that is based on a comparison of >900 spectra from 200 different sequences. The shape of the TDS reflects the subtleties of base stacking interactions that occur uniquely within each type of nucleic acid structure. TDS provides a simple, inexpensive and rapid method to obtain structural insight into nucleic acid structures, which is applicable to both DNA and RNA from short oligomers to polynucleotides. TDS complements circular dichroism as a tool for the structural characterization of nucleic acids in solution.


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