1d63

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{{STRUCTURE_1d63| PDB=1d63 | SCENE= }}
{{STRUCTURE_1d63| PDB=1d63 | SCENE= }}
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'''CRYSTAL STRUCTURE OF A BERENIL-D(CGCAAATTTGCG) COMPLEX; AN EXAMPLE OF DRUG-DNA RECOGNITION BASED ON SEQUENCE-DEPENDENT STRUCTURAL FEATURES'''
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===CRYSTAL STRUCTURE OF A BERENIL-D(CGCAAATTTGCG) COMPLEX; AN EXAMPLE OF DRUG-DNA RECOGNITION BASED ON SEQUENCE-DEPENDENT STRUCTURAL FEATURES===
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==Overview==
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The AT-selective drug berenil has been co-crystallized with the dodecanucleotide sequence d(CGCAAATTTGCG)2. The crystal structure has been solved to a resolution of 2.0 A and an R factor of 18.3%, with the location of 65 water molecules. The drug is symmetrically bound in the 5'-AATT region of the minor groove, with its amidinium groups hydrogen-bonding to O-2 atoms of the thymine base at each end of the binding site. This arrangement is distinct from that previously found for berenil with the sequence d(CGCGAATTCGCG)2, which has the drug bound to the sequencing 5'-ATT via hydrogen bonds to adenine N-3 atoms with the involvement of a bridging water molecule at one end of the binding site. The reasons for these differences are discussed in terms of changes in helical parameters; in particular propeller twist and base-pair roll are considered to be important. The conformational and base-pair geometry of the dodecanucleotide in the structure reported here, is closely similar to that for the native structure, suggesting that the 5'-AAATTT sequence does not significantly alter during drug binding, either because of its inflexibility or because its geometry is nearly ideal for berenil binding.
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(as it appears on PubMed at http://www.pubmed.gov), where 1640462 is the PubMed ID number.
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{{ABSTRACT_PUBMED_1640462}}
==About this Structure==
==About this Structure==
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[[Category: Complexed with drug]]
[[Category: Complexed with drug]]
[[Category: Double helix]]
[[Category: Double helix]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 22:31:03 2008''

Revision as of 19:31, 30 June 2008

Image:1d63.png

Template:STRUCTURE 1d63

CRYSTAL STRUCTURE OF A BERENIL-D(CGCAAATTTGCG) COMPLEX; AN EXAMPLE OF DRUG-DNA RECOGNITION BASED ON SEQUENCE-DEPENDENT STRUCTURAL FEATURES

Template:ABSTRACT PUBMED 1640462

About this Structure

Full crystallographic information is available from OCA.

Reference

Crystal structure of a berenil-d(CGCAAATTTGCG) complex. An example of drug-DNA recognition based on sequence-dependent structural features., Brown DG, Sanderson MR, Garman E, Neidle S, J Mol Biol. 1992 Jul 20;226(2):481-90. PMID:1640462

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