1qsx: Difference between revisions

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[[Image:1qsx.gif|left|200px]]
{{Seed}}
[[Image:1qsx.png|left|200px]]


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{{STRUCTURE_1qsx|  PDB=1qsx  |  SCENE=  }}  
{{STRUCTURE_1qsx|  PDB=1qsx  |  SCENE=  }}  


'''SOLUTION NMR STRUCTURE OF THE 2:1 HOECHST 33258-D(CTTTTGCAAAAG)2 COMPLEX'''
===SOLUTION NMR STRUCTURE OF THE 2:1 HOECHST 33258-D(CTTTTGCAAAAG)2 COMPLEX===




==Overview==
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The solution structure of the dodecamer duplex d(CTTTTGCAAAAG)(2)and its 2:1 complex with the bis -benzimidazole Hoechst 33258 has been investigated by NMR and NOE-restrained molecular dynamics (rMD) simulations. Drug molecules are bound in each of the two A-tracts with the bulky N-methylpiperazine ring of each drug located close to the central TG (CA) step, binding essentially to the narrow minor groove of each A-tract. MD simulations over 1 ns, using an explicit solvation model, reveal time-averaged sequence-dependent narrowing of the minor groove from the 3'-end towards the 5'-end of each TTTT sequence. Distinct junctions at the TpG (CpA) steps, characterised by large positive roll, low helical and propeller twists and rapid AT base pair opening rates, add to the widening of the groove at these sites and appear to account for the bound orientation of the two drug molecules with the N-methylpiperazine ring binding in the wider part of the groove close to the junctions. Comparisons between the free DNA structure and the 2:1 complex (heavy atom RMSD 1.55 A) reveal that these sequence-dependent features persist in both structures. NMR studies of the sequence d(GAAAAGCTTTTC)(2), in which the A-tracts have been inverted with the elimination of the TpG junctions, results in loss of orientational specificity of Hoechst 33258 and formation of multiple bound species in solution, consistent with the drug binding in a number of different orientations.
The line below this paragraph, {{ABSTRACT_PUBMED_10637324}}, adds the Publication Abstract to the page
(as it appears on PubMed at http://www.pubmed.gov), where 10637324 is the PubMed ID number.
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{{ABSTRACT_PUBMED_10637324}}


==About this Structure==
==About this Structure==
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QSX OCA].  
Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QSX OCA].  


==Reference==
==Reference==
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[[Category: Minor groove recognition]]
[[Category: Minor groove recognition]]
[[Category: Nmr spectroscopy]]
[[Category: Nmr spectroscopy]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 06:40:17 2008''
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 23:36:32 2008''

Revision as of 20:36, 27 July 2008

File:1qsx.png

Template:STRUCTURE 1qsx

SOLUTION NMR STRUCTURE OF THE 2:1 HOECHST 33258-D(CTTTTGCAAAAG)2 COMPLEX

Template:ABSTRACT PUBMED 10637324

About this Structure

Full experimental information is available from OCA.

Reference

Sequence-dependent variation in DNA minor groove width dictates orientational preference of Hoechst 33258 in A-tract recognition: solution NMR structure of the 2:1 complex with d(CTTTTGCAAAAG)(2)., Gavathiotis E, Sharman GJ, Searle MS, Nucleic Acids Res. 2000 Feb 1;28(3):728-35. PMID:10637324

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