1juu
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(New page: 200px<br /><applet load="1juu" size="450" color="white" frame="true" align="right" spinBox="true" caption="1juu" /> '''NMR Structure of a Parallel Stranded DNA Dup...)
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Revision as of 22:09, 24 November 2007
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NMR Structure of a Parallel Stranded DNA Duplex at Atomic Resolution
Overview
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.
About this Structure
1JUU is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
NMR structure of a parallel-stranded DNA duplex at atomic resolution., Parvathy VR, Bhaumik SR, Chary KV, Govil G, Liu K, Howard FB, Miles HT, Nucleic Acids Res. 2002 Apr 1;30(7):1500-11. PMID:11917010
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