Structure and possible function of a G-quadruplex in the long terminal repeat of the proviral HIV-1 genome.

Anh Tuân Phan,Beatrice De Nicola,Brahim Heddi,Christopher J Lech,Ilaria Frasson,Rosalba Perrone,Sagar Regmi,Sara N Richter

doi:10.1093/nar/gkw432

Anh Tuân Phan, Beatrice De Nicola + Show 6 more

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https://doi.org/10.1093/nar/gkw432

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Abstract

The long terminal repeat (LTR) of the proviral human immunodeficiency virus (HIV)-1 genome is integral to virus transcription and host cell infection. The guanine-rich U3 region within the LTR promoter, previously shown to form G-quadruplex structures, represents an attractive target to inhibit HIV transcription and replication. In this work, we report the structure of a biologically relevant G-quadruplex within the LTR promoter region of HIV-1. The guanine-rich sequence designated LTR-IV forms a well-defined structure in physiological cationic solution. The nuclear magnetic resonance (NMR) structure of this sequence reveals a parallel-stranded G-quadruplex containing a single-nucleotide thymine bulge, which participates in a conserved stacking interaction with a neighboring single-nucleotide adenine loop. Transcription analysis in a HIV-1 replication competent cell indicates that the LTR-IV region may act as a modulator of G-quadruplex formation in the LTR promoter. Consequently, the LTR-IV G-quadruplex structure presented within this work could represent a valuable target for the design of HIV therapeutics.

Highlights

G-quadruplexes are nucleic acid secondary structures that may form in G-rich sequences under physiological conditions [1,2,3]
Considering the value of such target elucidation, we report on the nuclear magnetic resonance (NMR) solution structure of a G-quadruplex formed by the 22-nt G-rich long terminal repeat (LTR)-IV sequence (5 -CTG3CG3ACTG4AGTG2T-3 ) from the promoter region of the human immunodeficiency virus (HIV)-1 LTR
Our results suggest that G-quadruplex formation in LTRIII and LTR-IV may act as a regulatory mechanism for transcription activity, with LTR-IV formation acting as a negative regulator of LTR-III

Summary

Introduction

G-quadruplexes are nucleic acid secondary structures that may form in G-rich sequences under physiological conditions [1,2,3]. G-quadruplex-forming motifs have been found in telomeres, G-rich micro- and mini-satellites and near oncogene promoters [8,9,10,11,12,13,14,15,16,17]. Human G-quadruplex DNA motifs have been reported to be associated with recombination prone regions [18] and to show mutational patterns that preserved the potential to form G-quadruplex DNA structures [14]. Expansion of G-quadruplex-forming motifs has been associated with relevant human neurological disorders [19,20,21,22,23,24,25]. The identification of G-quadruplex binding proteins [26,27] and their visualization in cells with antibodybased technology [28,29] have provided convincing evidence of the existence of G-quadruplexes in vivo

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