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

spinqualitylabelsall models 1y8d, 10 NMR models Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 1y8d is a 2 chain structure. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance. Related: 1eeg, 1jjp Resources: FirstGlance, OCA, RCSB, PDBsum Publication Abstract from PubMed 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. 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 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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