1juu
From Proteopedia
| Line 1: | Line 1: | ||
| - | [[Image:1juu.gif|left|200px]] | + | [[Image:1juu.gif|left|200px]] |
| - | + | ||
| - | '''NMR Structure of a Parallel Stranded DNA Duplex at Atomic Resolution''' | + | {{Structure |
| + | |PDB= 1juu |SIZE=350|CAPTION= <scene name='initialview01'>1juu</scene> | ||
| + | |SITE= | ||
| + | |LIGAND= | ||
| + | |ACTIVITY= | ||
| + | |GENE= | ||
| + | }} | ||
| + | |||
| + | '''NMR Structure of a Parallel Stranded DNA Duplex at Atomic Resolution''' | ||
| + | |||
==Overview== | ==Overview== | ||
| Line 7: | Line 16: | ||
==About this Structure== | ==About this Structure== | ||
| - | 1JUU is a [ | + | 1JUU is a [[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:// | + | 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://www.ncbi.nlm.nih.gov/pubmed/11917010 11917010] |
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Bhaumik, S R.]] | [[Category: Bhaumik, S R.]] | ||
| Line 22: | Line 31: | ||
[[Category: parallel stranded]] | [[Category: parallel stranded]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:08:47 2008'' |
Revision as of 10:08, 20 March 2008
| |||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
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
Page seeded by OCA on Thu Mar 20 12:08:47 2008
