title: Novel bimodular DNA aptamers with guanosine quadruplexes inhibit phylogenetically diverse HIV-1 reverse transcriptases.
abstract: DNA aptamers RT5, RT6 and RT47 form a group of related sequences that inhibit HIV-1 reverse transcriptase (RT). The essential inhibitory structure is identified here as bimodular, with a 5' stem-loop module physically connected to a 3'-guanosine quadruplex module. The stem-loop tolerates considerable sequence plasticity. Connections between the guanosine triplets in the quadruplex could be simplified to a single nucleotide or a nonnucleic acid linker, such as hexaethylene glycol. All 12 quadruplex guanosines are required in an aptamer retaining most of the original loop sequence from RT6; only 11 are required for aptamer R1T (single T residue in intra-quadruplex loops). Circular dichroism (CD) spectroscopy gave ellipticity minima and maxima at 240 nm and 264 nm, indicating a parallel arrangement of the quadruplex strands. The simplified aptamers displayed increased overall stability. An aptamer carrying the original intra-quadruplex loops from RT6 inhibited RT in K(+) buffers but not in Na(+) buffers and displayed significant CD spectral broadening in Na(+) buffers, while R1T inhibited RT in both buffers and displayed less broadening in Na(+) buffers. The bimodular ssDNA aptamers inhibited RT from diverse primate lentiviruses with low nM IC(50) values. These data provide insight into the requirements for broad-spectrum RT inhibition by nucleic acid aptamers.
authors.affiliation: Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, Columbia, MO 65211, USA.
authors.forename: Daniel
authors.initials: D
authors.lastname: Michalowski
authors.forename: Rebecca
authors.initials: R
authors.lastname: Chitima-Matsiga
authors.forename: Daniel M
authors.initials: DM
authors.lastname: Held
authors.forename: Donald H
authors.initials: DH
authors.lastname: Burke
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry*; D002412:Cations / Q000737:chemistry; D004277:DNA, Single-Stranded / Q000737:chemistry; D054856:G-Quadruplexes; D006151:Guanosine / Q000737:chemistry*; D054303:HIV Reverse Transcriptase / Q000037:antagonists & inhibitors* / Q000145:classification; D009154:Mutation; D010802:Phylogeny; D018894:Reverse Transcriptase Inhibitors / Q000737:chemistry*
chemical_list: D052157:Aptamers, Nucleotide; D002412:Cations; D004277:DNA, Single-Stranded; D018894:Reverse Transcriptase Inhibitors; D006151:Guanosine; C514824:reverse transcriptase, Human immunodeficiency virus 1; D054303:HIV Reverse Transcriptase