This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
1juu
From Proteopedia
| Line 1: | Line 1: | ||
[[Image:1juu.gif|left|200px]] | [[Image:1juu.gif|left|200px]] | ||
| - | + | <!-- | |
| - | + | The line below this paragraph, containing "STRUCTURE_1juu", creates the "Structure Box" on the page. | |
| - | + | You may change the PDB parameter (which sets the PDB file loaded into the applet) | |
| - | + | or the SCENE parameter (which sets the initial scene displayed when the page is loaded), | |
| - | | | + | or leave the SCENE parameter empty for the default display. |
| - | | | + | --> |
| - | + | {{STRUCTURE_1juu| PDB=1juu | SCENE= }} | |
| - | + | ||
| - | + | ||
| - | }} | + | |
'''NMR Structure of a Parallel Stranded DNA Duplex at Atomic Resolution''' | '''NMR Structure of a Parallel Stranded DNA Duplex at Atomic Resolution''' | ||
| Line 19: | Line 16: | ||
==About this Structure== | ==About this Structure== | ||
| - | + | 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://www.ncbi.nlm.nih.gov/pubmed/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://www.ncbi.nlm.nih.gov/pubmed/11917010 11917010] | ||
| - | [[Category: Protein complex]] | ||
[[Category: Bhaumik, S R.]] | [[Category: Bhaumik, S R.]] | ||
[[Category: Chary, K V.R.]] | [[Category: Chary, K V.R.]] | ||
| Line 31: | Line 27: | ||
[[Category: Miles, H T.]] | [[Category: Miles, H T.]] | ||
[[Category: Parvathy, V R.]] | [[Category: Parvathy, V R.]] | ||
| - | [[Category: | + | [[Category: Dna duplex]] |
| - | [[Category: | + | [[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 | + | |
Revision as of 18:57, 2 May 2008
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
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 Fri May 2 21:57:18 2008
