170d: Difference between revisions

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[[Image:170d.gif|left|200px]]
{{Seed}}
[[Image:170d.png|left|200px]]


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{{STRUCTURE_170d|  PDB=170d  |  SCENE=  }}  
{{STRUCTURE_170d|  PDB=170d  |  SCENE=  }}  


'''SOLUTION STRUCTURE OF A DNA DODECAMER CONTAINING THE ANTI-NEOPLASTIC AGENT ARABINOSYLCYTOSINE: COMBINED USE OF NMR, RESTRAINED MOLECULAR DYNAMICS AND FULL RELAXATION MATRIX REFINEMENT'''
===SOLUTION STRUCTURE OF A DNA DODECAMER CONTAINING THE ANTI-NEOPLASTIC AGENT ARABINOSYLCYTOSINE: COMBINED USE OF NMR, RESTRAINED MOLECULAR DYNAMICS AND FULL RELAXATION MATRIX REFINEMENT===




==Overview==
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The effect of araC incorporation into the dodecamer duplex [d(CGCGAATT) (araC)d(GCG)]2 was examined by comparing its nuclear magnetic resonance (NMR)-determined solution structure with that of the control duplex d[(CGCGAATTCGCG)]2. 1H and 31P resonances in both duplexes were assigned using a combination of 2-D 1H NMR and a 3-D 31P-1H heteroTOCSY-NOESY experiment. Proton-proton distances (determined from NOESY data) and sugar dihedral angles (from NOESY and COSY data) were used in restrained molecular dynamics simulations starting from canonical A- or B-form DNA models. Both the control and araC sets of simulations converged to B-type structures. These structures were subjected to full relaxation matrix refinement to produce final structures which were in excellent agreement (R1/6 &lt; 0.05) with the observed NOE intensities. A detailed comparison of the final control and araC structures revealed a global similarity (overall RMSD approximately 1.3 A), with significant differences localized at the araC site and neighboring bases. These included changes in sugar pucker, backbone torsion angles, base stacking, and other helical parameters. These findings are in general agreement with the previously published X-ray structure of a decamer duplex containing araC. One intriguing feature of the NMR solution structure not found in the crystal structure is the presence of an intramolecular hydrogen bond between the 2' hydroxyl on the araC sugar and the 3' phosphate group.
The line below this paragraph, {{ABSTRACT_PUBMED_7918360}}, adds the Publication Abstract to the page
(as it appears on PubMed at http://www.pubmed.gov), where 7918360 is the PubMed ID number.
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{{ABSTRACT_PUBMED_7918360}}


==About this Structure==
==About this Structure==
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=170D OCA].  
Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=170D OCA].  


==Reference==
==Reference==
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[[Category: Schweitzer, B I.]]
[[Category: Schweitzer, B I.]]
[[Category: Dna]]
[[Category: Dna]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 09:32:38 2008''
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 15:35:00 2008''

Revision as of 12:35, 30 June 2008

File:170d.png

Template:STRUCTURE 170d

SOLUTION STRUCTURE OF A DNA DODECAMER CONTAINING THE ANTI-NEOPLASTIC AGENT ARABINOSYLCYTOSINE: COMBINED USE OF NMR, RESTRAINED MOLECULAR DYNAMICS AND FULL RELAXATION MATRIX REFINEMENT

Template:ABSTRACT PUBMED 7918360

About this Structure

Full experimental information is available from OCA.

Reference

Solution structure of a DNA dodecamer containing the anti-neoplastic agent arabinosylcytosine: combined use of NMR, restrained molecular dynamics, and full relaxation matrix refinement., Schweitzer BI, Mikita T, Kellogg GW, Gardner KH, Beardsley GP, Biochemistry. 1994 Sep 27;33(38):11460-75. PMID:7918360

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