Conversation 11: No. 2
Volume: Conversation 11
Issue Number 2
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.
1Institute of Biomolecular Stereodynamics
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