Abstract:
:Abstract 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 A(n)C motif of unbound DNA duplexes might be the initial recognition site for proteins which bind to such junctions; and that in A(n)C 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.
journal_name
J Biomol Struct Dynjournal_title
Journal of biomolecular structure & dynamicsauthors
Kamath S,Sarma MH,Zhurkin VB,Turner CJ,Sarma RHdoi
10.1080/07391102.2000.10506637subject
Has Abstractpub_date
2000-01-01 00:00:00pages
317-25eissn
0739-1102issn
1538-0254journal_volume
17 Suppl 1pub_type
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