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 hete ronomous characteristics. The presence of this local B-Ajunction in one str and leads to compression of the interphosphate distance in this strand. We calculate the effect of this sugar switch on the helical parameters that ar e related to DNA bending. Finally, we suggest that the heteronomous deforma tion present in the A(n)C motif of unbound DNA duplexes might be the initia l recognition site for proteins which bind to such junctions; and that in A (n)C stretches, DNA bending is a complicated dynamic process, ie., locally noncanonical N conformers of the sugar phosphate backbone mix in with the B -like S conformers leading to bending.