Conversation 11: No. 2

category image Volume: Conversation 11
Issue Number 2
May 2000
ISBN 0-940030-81-0

DNA Bending and Sugar Switching

Using high frequency antiphase NMR spectroscopy and computer simulations of the antiphase spectra, we studied the equlibria in the sugar conformations in the DNA duplex 11-mer containing the AAA tract surrounded by cytosines. We demonstrate that at the 3'-end of the A-tract, the sugar switches from the common S-conformer (B-like form) to the N-conformer (A-like form) with the probability of 50-60%, thus creating a purine-pyrimidine step with heteronomous characteristics. The presence of this local B-A junction in one strand leads to compression of the interphosphate distance in this strand. We calculate the effect of this sugar switch on the helical parameters that are related to DNA bending. Finally, we suggest that the heteronomous deformation present in the AnC motif of unbound DNA duplexes might be the initial recognition site for proteins which bind to such junctions; and that in AnC stretches, DNA bending is a complicated dynamic process, i.e., locally noncanonical N conformers of the sugar phosphate backbone mix in with the B-like S conformers leading to bending.

Shantaram Kamath1
Mukti H. Sarma1
Victor B. Zhurkin2
Christopher J. Turner3
and Ramaswamy H. Sarma1

1Institute of Biomolecular Stereodynamics
Department of Chemistry
University at Albany, SUNY
1400 Washington Avenue
Albany, NY 12222
2Molecular Structure Section
Laboratory of Computational and Experimental Biology
National Cancer Institute
National Institutes of Health
Bethesda, MD 20892-5677
3Francis Bitter Magnet Laboratory
Massachusetts Institute of Technology
170 Albany Street
Cambridge, MA 02139


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