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 A⅐(G⅐G⅐G⅐G) pentad sandwiched between two G⅐G⅐G⅐G 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 G⅐G⅐G⅐G 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 A⅐(G⅐G⅐G⅐G) 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 channel͞canyon formed between subunits of a dimer of dimers of HIV-1 integrase. dimeric quadruplex ͉ DNA aptamer H IV-1 integrase catalyzes the integration of proviral DNA into the host-cell genome, a reaction critical for efficient viral replication. HIV-1 integrase is necessary and sufficient for the first two steps of DNA integration (1): (i) 3Ј-end processing, where two nucleotides are removed from each 3Ј-end of the viral DNA; (ii) strand transfer, where each 3Ј-processed viral DNA end is attached to the host-cell DNA. As a result, HIV-1 integrase constitutes an attractive target for drugs against AIDS (2, 3).Guanine-rich oligonucleotides have been identified as potent inhibitors of HIV-1 integrase (4, 5). In particular, a recent study (6) has identified a 16-nt guanine-rich sequence d(GGGGTGG-GAGGAGGGT), designated 93del, which inhibits both the processing and strand transfer functions of HIV-1 integrase at nanomolar concentrations.Guanine-rich oligonucleotides can form a variety of Gquadruplex architectures involving stacked planar G⅐G⅐G⅐G tetrads. This polymorphism of G-quadruplex topologies reflects the range of alternate strand directionalities, loop connectivities, and syn͞anti distribution of guanine bases around G-tetrads (7-16). Higher order pairing alignments involving G-tetrads have been recently identified, and these include pentads (17), hexads (18), and heptads (19) for sequences containing guanine stretches separated by adenine residues.Here, we present the NMR-based solution structure of 93del. We establish that this 16-nt DNA sequence adopts an unusually stable dimeric quadruplex architecture in K ϩ solution. Each monomer subunit contains two G⅐G⅐G⅐G tetrads and one A⅐(G⅐G⅐G⅐G) pentad, where all of the G-stretches are parallel and linked by three single-nucleotide double-chain-reversal loops. In our attempts to design potent...

G-rich nucleic acids can form non-canonical G-quadruplex structures (G4s) in which four guanines fold in a planar arrangement through Hoogsteen hydrogen bonds. Although many biochemical and structural studies have focused on DNA sequences containing successive, adjacent guanines that spontaneously fold into G4s, evidence for their in vivo relevance has recently begun to accumulate. Complete sequencing of the human genome highlighted the presence of ∼300 000 sequences that can potentially form G4s. Likewise, the presence of putative G4-sequences has been reported in various viruses genomes [e.g., Human immunodeficiency virus (HIV-1), Epstein–Barr virus (EBV), papillomavirus (HPV)]. Many studies have focused on telomeric G4s and how their dynamics are regulated to enable telomere synthesis. Moreover, a role for G4s has been proposed in cellular and viral replication, recombination and gene expression control. In parallel, DNA aptamers that form G4s have been described as inhibitors and diagnostic tools to detect viruses [e.g., hepatitis A virus (HAV), EBV, cauliflower mosaic virus (CaMV), severe acute respiratory syndrome virus (SARS), simian virus 40 (SV40)]. Here, special emphasis will be given to the possible role of these structures in a virus life cycle as well as the use of G4-forming oligonucleotides as potential antiviral agents and innovative tools.

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