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| | {{STRUCTURE_1juu| PDB=1juu | SCENE= }} | | {{STRUCTURE_1juu| PDB=1juu | SCENE= }} |
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| - | '''NMR Structure of a Parallel Stranded DNA Duplex at Atomic Resolution'''
| + | ===NMR Structure of a Parallel Stranded DNA Duplex at Atomic Resolution=== |
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| - | ==Overview==
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| - | 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.
| + | The line below this paragraph, {{ABSTRACT_PUBMED_11917010}}, adds the Publication Abstract to the page |
| | + | (as it appears on PubMed at http://www.pubmed.gov), where 11917010 is the PubMed ID number. |
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| | + | {{ABSTRACT_PUBMED_11917010}} |
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| | ==About this Structure== | | ==About this Structure== |
| - | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JUU OCA]. | + | Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JUU OCA]. |
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| | ==Reference== | | ==Reference== |
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| | [[Category: Dna duplex]] | | [[Category: Dna duplex]] |
| | [[Category: Parallel stranded]] | | [[Category: Parallel stranded]] |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 21:57:18 2008'' | + | |
| | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 1 20:56:18 2008'' |
Revision as of 17:56, 1 July 2008
Template:STRUCTURE 1juu
NMR Structure of a Parallel Stranded DNA Duplex at Atomic Resolution
Template:ABSTRACT PUBMED 11917010
About this Structure
Full experimental 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
Page seeded by OCA on Tue Jul 1 20:56:18 2008
