1juu
From Proteopedia
(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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'''NMR Structure of a Parallel Stranded DNA Duplex at Atomic Resolution'''<br /> | '''NMR Structure of a Parallel Stranded DNA Duplex at Atomic Resolution'''<br /> | ||
==Overview== | ==Overview== | ||
| - | DNA dodecamers have been designed with two cytosines on each end and | + | 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== | ==About this Structure== | ||
| - | 1JUU is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http:// | + | 1JUU is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JUU OCA]. |
==Reference== | ==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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11917010 11917010] | 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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11917010 11917010] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Bhaumik, S | + | [[Category: Bhaumik, S R.]] |
| - | [[Category: Chary, K | + | [[Category: Chary, K V.R.]] |
[[Category: Govil, G.]] | [[Category: Govil, G.]] | ||
| - | [[Category: Howard, F | + | [[Category: Howard, F B.]] |
[[Category: Liu, K.]] | [[Category: Liu, K.]] | ||
| - | [[Category: Miles, H | + | [[Category: Miles, H T.]] |
| - | [[Category: Parvathy, V | + | [[Category: Parvathy, V R.]] |
[[Category: dna duplex]] | [[Category: dna duplex]] | ||
[[Category: parallel stranded]] | [[Category: parallel stranded]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:26:58 2008'' |
Revision as of 11:27, 21 February 2008
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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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