HIV-1 integrase inhibitor T30177 forms a stacked dimeric G-quadruplex structure containing bulges

Abstract

T30177 is a G-rich oligonucleotide with the sequence (GTGGTGGGTGGGTGGGT) which inhibits the HIV-1 integrase activity at nanomolar concentrations. Here we show that this DNA sequence forms in K+ solution a dimeric G-quadruplex structure comprising a total of six G-tetrad layers through the stacking of two propeller-type parallel-stranded G-quadruplex subunits at their 5′-end. All twelve guanines in the sequence participate in the G-tetrad formation, despite the interruption in the first G-tract by a thymine, which forms a bulge between two adjacent G-tetrads. In this work, we also propose a simple analytical approach to stoichiometry determination using concentration-dependent melting curves.

NMR spectroscopy of G-quadruplexes

“…Complete description of the structure and dynamics of G-quadruplexes would provide fundamental insights towards understanding their existence and function in nature. On the other hand, some artificial G-rich oligomer sequences, capable of forming G-quadruplexes, possess interesting biological activities, such as anticoagulant, anticancer and anti-HIV activities [17][18][19][20][21][22]. G-quadruplexes also have potential applications in various fields such as chemistry and nanotechnology [1,23,24].…”

“…1). UV/CD melting, gel electrophoresis, size exclusion chromatography or mass spectrometry can complement NMR to provide information on the stoichiometry at various concentrations [21,22,39]. In some cases, it is possible to use NMR data, such as NOE restraints and spectral line-width, to indirectly deduce information on the stoichiometry of the structure [22,26].…”

DNA Duplexes with Hydrophobic Modifications Inhibit Fusion between HIV-1 and Cell Membranes

“…Interestingly, some sequences do not act through base pairing but as aptamers. These aptamers fold into defined three-dimensional (3D) structures and interact with HIV-1-associated proteins, such as HIV-1 reverse transcriptases (6,7), RNase H (8), Tat proteins (9), integrase (10)(11)(12)(13), and surface glycoproteins (14,15). A subcategory of aptamers possess an additional intermolecular assembly feature such as the quadruplex d(TGGGAG) 4 described by Hotoda et al, which was assembled by four 6-mer G-rich sequences in parallel with the 5=-end attaching to aromatic substituents of adequate size, such as tert-butyldiphenylsilyl (TBDPS) and 4=4-dimethoxytriphenyl (DMT) (16)(17)(18)(19)(20)(21)(22)(23)(24).…”

Potential uses of G-quadruplex-forming aptamers

“…For example, the overall G-quadruplex is composed of three stacked G-tetrads, and all tetrad guanines adopt anti conformation in parallel-stranded folding topology for many G-rich sequence repeats in K + e.g. promoter sequences c-Myc, HIV aptamers, the four-repeat human telomeric d[AGGG(TTAGGG) 3 ] sequence, the two-repeat human telomeric d[TAGGGTTAGGGT] sequence (Mukundan et al 2011;Tong et al 2011;Trajkovski et al 2012). But once again, it is not a general rule that parallel G-quadruplexes are composed only of anti guanines; for example a RET promoter sequence forms a parallel structure in which one G-tetrad consists of four syn guanines (Tong et al 2011).…”