1y8d: Difference between revisions

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[[Image:1y8d.gif|left|200px]]
{{Seed}}
[[Image:1y8d.png|left|200px]]


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{{STRUCTURE_1y8d|  PDB=1y8d  |  SCENE=  }}  
{{STRUCTURE_1y8d|  PDB=1y8d  |  SCENE=  }}  


'''Dimeric parallel-stranded tetraplex with 3+1 5' G-tetrad interface, single-residue chain reversal loops and GAG triad in the context of A(GGGG) pentad'''
===Dimeric parallel-stranded tetraplex with 3+1 5' G-tetrad interface, single-residue chain reversal loops and GAG triad in the context of A(GGGG) pentad===




==Overview==
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We report on the NMR-based solution structure of the 93del d(GGGGTGGGAGGAGGGT) aptamer, a potent nanomolar inhibitor of HIV-1 integrase. This guanine-rich DNA sequence adopts an unusually stable dimeric quadruplex architecture in K+ solution. Within each 16-nt monomer subunit, which contains one A.(G.G.G.G) pentad sandwiched between two G.G.G.G tetrads, all G-stretches are parallel, and all guanines are anti with the exception of G1, which is syn. Dimer formation is achieved through mutual pairing of G1 of one monomer, with G2, G6, and G13 of the other monomer, to complete G.G.G.G tetrad formation. There are three single-nucleotide double-chain-reversal loops within each monomer fold, such that the first (T5) and third (A12) loops bridge three G-tetrad layers, whereas the second (A9) loop bridges two G-tetrad layers and participates in A.(G.G.G.G) pentad formation. Results of NMR and of integrase inhibition assays on loop-modified sequences allowed us to propose a strategy toward the potential design of improved HIV-1 integrase inhibitors. Finally, we propose a model, based on molecular docking approaches, for positioning the 93del dimeric DNA quadruplex within a basic channel/canyon formed between subunits of a dimer of dimers of HIV-1 integrase.
The line below this paragraph, {{ABSTRACT_PUBMED_15637158}}, adds the Publication Abstract to the page
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{{ABSTRACT_PUBMED_15637158}}


==About this Structure==
==About this Structure==
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y8D OCA].  
Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y8D OCA].  


==Reference==
==Reference==
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[[Category: Gag triad]]
[[Category: Gag triad]]
[[Category: Single nucleotide chain reversal loop]]
[[Category: Single nucleotide chain reversal loop]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 16:00:07 2008''
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 13:27:13 2008''

Revision as of 10:27, 28 July 2008

File:1y8d.png

Template:STRUCTURE 1y8d

Dimeric parallel-stranded tetraplex with 3+1 5' G-tetrad interface, single-residue chain reversal loops and GAG triad in the context of A(GGGG) pentad

Template:ABSTRACT PUBMED 15637158

About this Structure

Full experimental information is available from OCA.

Reference

An interlocked dimeric parallel-stranded DNA quadruplex: a potent inhibitor of HIV-1 integrase., Phan AT, Kuryavyi V, Ma JB, Faure A, Andreola ML, Patel DJ, Proc Natl Acad Sci U S A. 2005 Jan 18;102(3):634-9. Epub 2005 Jan 6. PMID:15637158

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