1cvy

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{{STRUCTURE_1cvy| PDB=1cvy | SCENE= }}
{{STRUCTURE_1cvy| PDB=1cvy | SCENE= }}
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'''CRYSTAL STRUCTURE OF POLYAMIDE DIMER (IMPYPYPYBETADP)2 BOUND TO CCAGATCTGG'''
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===CRYSTAL STRUCTURE OF POLYAMIDE DIMER (IMPYPYPYBETADP)2 BOUND TO CCAGATCTGG===
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==Overview==
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Synthetic polyamides composed of three types of aromatic amino acids, N-methylimidazole (Im), N-methylpyrrole (Py) and N-methyl-3-hydroxypyrrole (Hp) bind specific DNA sequences as antiparallel dimers in the minor groove. The side-by-side pairings of aromatic rings in the dimer afford a general recognition code that allows all four base-pairs to be distinguished. To examine the structural consequences of changing the DNA sequence context on T.A recognition by Hp/Py pairs in the minor groove, crystal structures of polyamide dimers (ImPyHpPy)(2) and the pyrrole counterpart (ImPyPyPy)(2) bound to the six base-pair target site 5'-AGATCT-3' in a ten base-pair oligonucleotide have been determined to a resolution of 2.27 and 2.15 A, respectively. The structures demonstrate that the principles of Hp/Py recognition of T.A are consistent between different sequence contexts. However, a general structural explanation for the non-additive reduction in binding affinity due to introduction of the hydroxyl group is less clear. Comparison with other polyamide-DNA cocrystal structures reveals structural themes and differences that may relate to sequence preference.
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(as it appears on PubMed at http://www.pubmed.gov), where 10623546 is the PubMed ID number.
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{{ABSTRACT_PUBMED_10623546}}
==About this Structure==
==About this Structure==
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[[Category: Imidazole-pyrrole polyamide]]
[[Category: Imidazole-pyrrole polyamide]]
[[Category: Minor groove recognition]]
[[Category: Minor groove recognition]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 13:10:07 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 21:33:22 2008''

Revision as of 18:33, 30 June 2008

Image:1cvy.png

Template:STRUCTURE 1cvy

CRYSTAL STRUCTURE OF POLYAMIDE DIMER (IMPYPYPYBETADP)2 BOUND TO CCAGATCTGG

Template:ABSTRACT PUBMED 10623546

About this Structure

Full crystallographic information is available from OCA.

Reference

Structural effects of DNA sequence on T.A recognition by hydroxypyrrole/pyrrole pairs in the minor groove., Kielkopf CL, Bremer RE, White S, Szewczyk JW, Turner JM, Baird EE, Dervan PB, Rees DC, J Mol Biol. 2000 Jan 21;295(3):557-67. PMID:10623546

Page seeded by OCA on Mon Jun 30 21:33:22 2008

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