G-Quadruplexes: Prediction, Characterization, and Biological Application

Recent methodological advances allow us to study G-quadruplex structures at higher resolution and throughput. Approaches to use G-quadruplex structures as molecular tools are highlighted. Computational and experimental methods for G-quadruplex studies are reviewed. The works reviewed herein provide unique insights to explore the biological roles and uses of G-quadruplexes in basic and applied research. Guanine (G)-rich sequences in nucleic acids can assemble into G-quadruplex structures that involve G-quartets linked by loop nucleotides. The structural and topological diversity of G-quadruplexes have attracted great attention for decades. Recent methodological advances have advanced the identification and characterization of G-quadruplexes in vivo as well as in vitro, and at a much higher resolution and throughput, which has greatly expanded our current understanding of G-quadruplex structure and function. Accumulating knowledge about the structural properties of G-quadruplexes has helped to design and develop a repertoire of molecular and chemical tools for biological applications. This review highlights how these exciting methods and findings have opened new doors to investigate the potential functions and applications of G-quadruplexes in basic and applied biosciences. Guanine (G)-rich sequences in nucleic acids can assemble into G-quadruplex structures that involve G-quartets linked by loop nucleotides. The structural and topological diversity of G-quadruplexes have attracted great attention for decades. Recent methodological advances have advanced the identification and characterization of G-quadruplexes in vivo as well as in vitro, and at a much higher resolution and throughput, which has greatly expanded our current understanding of G-quadruplex structure and function. Accumulating knowledge about the structural properties of G-quadruplexes has helped to design and develop a repertoire of molecular and chemical tools for biological applications. This review highlights how these exciting methods and findings have opened new doors to investigate the potential functions and applications of G-quadruplexes in basic and applied biosciences. a biological molecule – usually a peptide or oligonucleotide – that binds to a specific target such as a protein or small molecule. Oligonucleotide aptamers (which may form G-quadruplexes) can be generated by combinatorial nucleic acid library screening, SELEX experiment, and other methods. a technique to locate proteins – and also DNA motifs such as G-quadruplexes – in native chromatin. Chromatin is formaldehyde fixed, extracted from cells, fragmented, and treated with an antibody to the entity of interest to isolate associated DNA fragments. These are then identified by sequencing (ChIP-seq) or by hybridization to a microarray (ChIP-on-chip). formed from runs of guanines on more than one DNA strand, or from a hybrid of DNA and RNA strands. See Figure 1B. formed from a single DNA strand, which bears four runs of guanine residues in close proximity. See Figure 1B. undergoes fluorescence quenching upon binding to its target. displays enhanced fluorescence upon binding to its target. modern, high-throughput sequencing techniques, such as Illumina, Ion Torrent, and 454, all of which produce sequence data concurrently on a genomic/transcriptomic scale in the form of millions of short sequence fragments (usually <1 kb). a parallel G-quadruplex has all of the guanine-bearing strands in the same 5′/3′ polarity, necessitating linking by ‘propeller-type’ loops that run top-to-bottom of the folded motif. In an antiparallel quadruplex, the strands do not all have the same polarity, and thus the linking loops can be at the top or bottom of the folded motif. See Figure 1B. ‘systematic evolution of ligands by exponential enrichment’. A technique for generating highly target-selective oligonucleotides with strong binding affinity from a library of random sequences via repeated rounds of binding to the target ligand, washing, elution, reverse transcription (for RNA aptamer), and PCR amplification. ‘selective 2′-hydroxyl acylation analysed by primer extension. SHAPE is used to determine RNA secondary structures by treating RNA with an acylation reagent that selectively acylates the flexible (unpaired) nucleotides of the RNA at the 2′-hydroxyl (2′-OH) group. These modifications can stall reverse transcriptase and thus provide an electrophoresis-based or NGS-based readout of nucleotide reactivity, which can then be used to infer RNA structure.