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[[Image:179d.jpg|left|200px]]
{{Seed}}
[[Image:179d.png|left|200px]]


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{{STRUCTURE_179d|  PDB=179d  |  SCENE=  }}  
{{STRUCTURE_179d|  PDB=179d  |  SCENE=  }}  


'''SOLUTION STRUCTURE OF THE D(T-C-G-A) DUPLEX AT ACIDIC PH: A PARALLEL-STRANDED HELIX CONTAINING C+.C, G.G AND A.A PAIRS'''
===SOLUTION STRUCTURE OF THE D(T-C-G-A) DUPLEX AT ACIDIC PH: A PARALLEL-STRANDED HELIX CONTAINING C+.C, G.G AND A.A PAIRS===




==Overview==
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The solution structure of the d(T-C-G-A) sequence at acidic pH has been determined by a combination of NMR and molecular dynamics calculations including NOE intensity based refinements. This sequence forms a right-handed parallel-stranded duplex with C+ .C (three hydrogen bonds along Watson-Crick edge), G.G (two symmetry related N2-H.. N3 hydrogen bonds) and A.A (two symmetry related N6-H..N7 hydrogen bonds) homo base-pair formation at acidic pH. The duplex is stabilized by intra-strand base stacking at the C2-G3 step and cross-strand base stacking at the G3-A4 step. The thymine residues on partner strands are directed towards each other and are positioned over the C+ .C base-pair. All four residues adopt anti glycosidic torsion angles and C2'-endo type sugar conformations in the parallel-stranded d(T-C-G-A) duplex which exhibits large changes in twist angles between adjacent steps along the duplex. This study rules out previously proposed models for the structure of the d(T-C-G-A) duplex at acidic pH and supports earlier structural contributions, which established that d(C-G) and d(C-G-A) containing sequences at acidic pH pair through parallel-stranded alignment. We have also monitored hydration patterns in the symmetry related grooves of the parallel-stranded d(T-C-G-A) duplex.
The line below this paragraph, {{ABSTRACT_PUBMED_7932707}}, adds the Publication Abstract to the page
(as it appears on PubMed at http://www.pubmed.gov), where 7932707 is the PubMed ID number.
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{{ABSTRACT_PUBMED_7932707}}


==About this Structure==
==About this Structure==
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=179D OCA].  
Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=179D OCA].  


==Reference==
==Reference==
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[[Category: Wang, Y.]]
[[Category: Wang, Y.]]
[[Category: Dna]]
[[Category: Dna]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 09:33:40 2008''
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 15:36:46 2008''

Revision as of 12:36, 30 June 2008

File:179d.png

Template:STRUCTURE 179d

SOLUTION STRUCTURE OF THE D(T-C-G-A) DUPLEX AT ACIDIC PH: A PARALLEL-STRANDED HELIX CONTAINING C+.C, G.G AND A.A PAIRS

Template:ABSTRACT PUBMED 7932707

About this Structure

Full experimental information is available from OCA.

Reference

Solution structure of the d(T-C-G-A) duplex at acidic pH. A parallel-stranded helix containing C+ .C, G.G and A.A pairs., Wang Y, Patel DJ, J Mol Biol. 1994 Sep 30;242(4):508-26. PMID:7932707

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