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193d

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{{STRUCTURE_193d| PDB=193d | SCENE= }}
{{STRUCTURE_193d| PDB=193d | SCENE= }}
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'''SOLUTION STRUCTURE OF A QUINOMYCIN BISINTERCALATOR-DNA COMPLEX'''
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===SOLUTION STRUCTURE OF A QUINOMYCIN BISINTERCALATOR-DNA COMPLEX===
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==Overview==
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The quinomycin antibiotic UK-63052 (designated QN) exhibits a chemical structure related to the antibiotic echinomycin which is known to bisintercalate into DNA. Common features among these antibiotics include two heterocyclic aromatic ring systems propagating from a cross-bridged cyclic octadepsipeptide scaffold. We report on the solution structure of the QN-d(A1-C2-A3-C4-G5-T6-G7-T8) complex (one QN molecule per duplex) based on a combined NMR-molecular dynamics study including intensity-based refinement. The 3-hydroxy quinaldic acid rings bisintercalate into the duplex at (A3-C4).(G5-T6) steps and stack with flanking Watson-Crick A3.T6 and C4.G5 base-pairs. The intercalation sites at (A3-C4).(G5-T6) steps are wedge-shaped and unwound, with significant unwinding also observed at the (C4-C5).(C4-G5) step bracketed between the intercalation sites. The cross-bridged cyclic octadepsipeptide is positioned in the minor groove with the methyl groups on its Ala and NMe-MCp residues directed towards and making van der Waals contacts with the minor groove edge of the duplex. A pair of adjacent intermolecular hydrogen bonds between the Ala backbone atoms and the G5 minor groove edge (Ala-NH to G5-N(3) and G5-NH2e to Ala-CO) account for the sequence specificity associated with complex formation. The solution structure of the QN-DNA oligomer complex, which contains only Watson-Crick base-pairs flanking the bisintercalation site, is compared with the crystal structure of the related echinomycin-DNA oligomer complex, which contains Hoogsteen base-pairs on either side of the bisintercalation site.
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(as it appears on PubMed at http://www.pubmed.gov), where 7853395 is the PubMed ID number.
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{{ABSTRACT_PUBMED_7853395}}
==About this Structure==
==About this Structure==
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=193D OCA].
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Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=193D OCA].
==Reference==
==Reference==
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[[Category: Nmr]]
[[Category: Nmr]]
[[Category: Quinomycin]]
[[Category: Quinomycin]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 09:35:16 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 15:39:58 2008''

Revision as of 12:40, 30 June 2008

Image:193d.png

Template:STRUCTURE 193d

SOLUTION STRUCTURE OF A QUINOMYCIN BISINTERCALATOR-DNA COMPLEX

Template:ABSTRACT PUBMED 7853395

About this Structure

Full experimental information is available from OCA.

Reference

Solution structure of a quinomycin bisintercalator-DNA complex., Chen H, Patel DJ, J Mol Biol. 1995 Feb 10;246(1):164-79. PMID:7853395

Page seeded by OCA on Mon Jun 30 15:39:58 2008

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