NMR structure of a parallel-stranded DNA duplex at atomic resolution

Rani Parvathy, V. ; Bhaumik, Sukesh R. ; Chary, Kandala V. R. ; Govil, Girjesh ; Liu, Keliang ; Howard, Frank B. ; Todd Miles, H. (2002) NMR structure of a parallel-stranded DNA duplex at atomic resolution Nucleic Acids Research, 30 (7). pp. 1500-1511. ISSN 0305-1048

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Official URL: http://nar.oxfordjournals.org/content/30/7/1500.ab...

Related URL: http://dx.doi.org/10.1093/nar/30.7.1500


DNA dodecamers have been designed with two cytosines on each end and intervening A and T stretches, such that the oligomers have fully complementary A:T base pairs when aligned in the parallel orientation. Spectroscopic (UV, CD and IR), NMR and molecular dynamics studies have shown that oligomers having the sequences d(CCATAATTTACC) and d(CCTATTAAATCC) form a parallel-stranded duplex when dissolved at 1:1 stoichiometry in aqueous solution. This is due to the C:C+ clamps on either end and extensive mismatches in the antiparallel orientation. The structure is stable at neutral and acidic pH. At higher temperatures, the duplex melts into single strands in a highly cooperative fashion. All adenine, cytosine and thymine nucleotides adopt the anti conformation with respect to the glycosidic bond. The A:T base pairs form reverse Watson-Crick base pairs. The duplex shows base stacking and NOEs between the base protons T(H6)/A(H8) and the sugar protons (H1″/H2″/H2″) of the preceding nucleotide, as has been observed in antiparallel duplexes. However, no NOEs are observed between base protons H2/H6/H8 of sequential nucleotides, though such NOEs are observed between T(CH3) and A(H8). A three-dimensional structure of the parallel-stranded duplex at atomic resolution has been obtained using molecular dynamics simulations under NMR constraints. The simulated structures have torsional angles very similar to those found in B-DNA duplexes, but the base stacking and helicoid parameters are significantly different.

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Deposited On:13 Nov 2010 09:27
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