Nucleic Acid Aptamers Based on the G-Quadruplex Structure: Therapeutic and Diagnostic Potential

Abstract

Aptamers are short DNA- or RNA-based oligonucleotides selected from large combinatorial pools of sequences for their capacity to efficiently recognize targets ranging from small molecules to proteins or nucleic acid structures. Like antibodies, they exhibit high specificity and affinity for target binding. As a result, they may display effective interference in biological processes, which renders them not only valuable diagnostic tools, but also promising therapeutic agents. In fact, one aptamer that inhibits human VEGF already received approval for the treatment of age-related macular degeneration, while several others are undergoing clinical trials. Aptamers display a large number of structural arrangements, which accounts for their binding efficiency and selectivity for unrelated targets. Among several architectures, the G-quadruplex (G-4) is adopted by several aptamers, the most popular of which shows inhibitory properties against thrombin, a pharmacologically relevant protein. G-4 structures consist of planar arrays of four guanines, each guanine pairing with two neighbours by Hoogsteen bonding. Recent work shows that G-4 arrangement is highly polymorphic and therefore represents a large family of stable structures with a common overall fold, but with well differentiated recognition elements that allow prominent diversity to be explored. Conformational plasticity consents fine tuning of target recognition as obtained by aptamer selection. Here, we will review the present knowledge on aptamers based on the G-4 structures and assess their diagnostic and therapeutic potential as biotech drugs for the detection and treatment of severe pathologies including vascular, cancer and viral diseases.

Specific loop modifications of the thrombin‐binding aptamer trigger the formation of parallel structures

“…TBA and most of the derivatives showed clear antiparallel quadruplex spectra (see CD spectra in KCl/cacodylate buffer in Fig. 1A), with positive bands at approximately 250 nm and 295 nm, and a negative band at approximately 270 nm, whereas TBA derivatives containing two or more guanines at the lateral loops (TBA2G [4,13], TBA2G [3,12], and TBA4G [3,4,12,13]) showed very different CD spectra, which match with those expected for a parallel G-quadruplex (note the positive band at 265 nm and the negative one at 245 nm).…”

Potential uses of G-quadruplex-forming aptamers

“…This is largely due to the fact that the negative charge density of G-quadruplexes is twice as high as that of linear DNA (Gatto et al 2009), although other forces, such as Van der Waals, π-π stacking and hydrophobic interactions are also important. The stability of the G-quadruplex is crucial in providing a high affinity of aptamers to the ligands.…”

Guanine-Centric Self-Assembly of Nucleotides in Water: An Important Consideration in Prebiotic Chemistry

“…First, G-rich genomic sequences that form Gtetrad-based structures are widespread throughout living organisms (Simonsson, 2005), from ''evolutionarily distant genomes of prokaryotes'' (Fry, 2007) to modern mammalian species (Rawal et al, 2006;Todd et al, 2006;Fry, 2007), and these sequences exhibit selective interactions with biomolecules such as proteins (Wang et al, 2009;Xiao et al, 2009;Zhang et al, 2012). They are abundant in telomeres, gene promoter regions, rDNA gene clusters, and recombination ''hotspots'' (Gatto et al, 2009). The prevalence of G-tetrad-forming sequences dating back to primitive terrestrial life suggests a driving force to select G-rich sequences at an early point in biological evolution and, possibly, even earlier in prebiotic selection.…”

“…The prevalence of G-tetrad-forming sequences dating back to primitive terrestrial life suggests a driving force to select G-rich sequences at an early point in biological evolution and, possibly, even earlier in prebiotic selection. Additionally, intramolecular G-quadruplex structures comprising two or more G-tetrads are common structural motifs in RNA and DNA aptamers (Gatto et al, 2009) selected through combinatorial ''molecular evolution'' for highly selective, highaffinity binding to molecular and macromolecular targets. Selective affinity interactions of prebiotic, RNA-like oligomers with amino acids, peptides, primitive cofactors, and inorganic cations would serve to facilitate and regulate catalysis and autocatalysis.…”