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1ovf

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{{STRUCTURE_1ovf| PDB=1ovf | SCENE= }}
{{STRUCTURE_1ovf| PDB=1ovf | SCENE= }}
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'''NMR Structure of ActD/5'-CCGTTTTGTGG-3' Complex'''
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===NMR Structure of ActD/5'-CCGTTTTGTGG-3' Complex===
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==Overview==
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Binding of actinomycin D (ActD) to the seemingly single-stranded DNA (ssDNA) oligomer 5'-CCGTT3 GTGG-3' has been studied in solution using high-resolution nuclear magnetic resonance (NMR) techniques. A strong binding constant (8 x 10(6) M(-1)) and high quality NMR spectra have allowed us to determine the initial DNA structure using distance geometry as well as the final ActD-5'-CCGTT3 GTGG-3' complex structure using constrained molecular dynamics calculations. The DNA oligomer 5'-CCGTT3GTGG-3' in the complex forms a hairpin structure with tandem G.T mismatches at the stem region next to a loop of three stacked thymine bases pointing toward the major groove. Bipartite T2O-GH1 and T2O-G2NH2 hydrogen bonds were detected for the G.T mismatches that further stabilize this unusual DNA hairpin. The phenoxazone chromophore of ActD intercalates nicely between the tandem G.T mismatches in essentially one major orientation. Additional hydrophobic interactions between the ActD quinoid amino acid residues with the loop T5-T6-T7 backbone protons were also observed. The hydrophobic G-phenoxazone-G interaction in the ActD-5'-CCGTT3GTGG-3' complex is more robust than that of the classical ActD- 5'-CCGCT3GCGG-3' complex, consistent with the roughly 2-fold stronger binding of ActD to the 5'-CCGTT3GTGG-3' sequence than to its 5'-CCG CT3GCGG-3' counterpart. Stabilization by ActD of a hairpin containing non-canonical stem base pairs further strengthens the notion that ActD or other related compounds may serve as a sequence- specific ssDNA-binding agent that inhibits human immunodeficiency virus (HIV) and other retroviruses replicating through ssDNA intermediates.
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(as it appears on PubMed at http://www.pubmed.gov), where 12736312 is the PubMed ID number.
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{{ABSTRACT_PUBMED_12736312}}
==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=1OVF OCA].
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Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OVF OCA].
==Reference==
==Reference==
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[[Category: Nmr]]
[[Category: Nmr]]
[[Category: Tandem gt mismatch]]
[[Category: Tandem gt mismatch]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 04:19:25 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 14:18:39 2008''

Revision as of 11:18, 29 July 2008

Image:1ovf.png

Template:STRUCTURE 1ovf

NMR Structure of ActD/5'-CCGTTTTGTGG-3' Complex

Template:ABSTRACT PUBMED 12736312

About this Structure

Full experimental information is available from OCA.

Reference

Solution structure of the ActD-5'-CCGTT3GTGG-3' complex: drug interaction with tandem G.T mismatches and hairpin loop backbone., Chin KH, Chen FM, Chou SH, Nucleic Acids Res. 2003 May 15;31(10):2622-9. PMID:12736312

Page seeded by OCA on Tue Jul 29 14:18:39 2008

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