Interaction of a Short Peptide with G-Quadruplex-Forming Sequences: An SRCD and CD Study

Locking up G-Quadruplexes with Light-Triggered Staples Leads to Increased Topological, Thermodynamic, and Metabolic Stability

G-quadruplexes (G4 s) are secondary, tetraplexed DNA structures abundant in non-coding regions of the genome, implicated in gene transcription processes and currently firmly recognised as important potential therapeutic targets. Given their affinity for human proteins, G4 structures are investigated as potential decoys and aptamers. However, G4 s tend to adopt different conformations depending on the exact environmental conditions, and often only one displays the specifically desired biological activity. Their less intensively studied counterparts, the elusive tetraplexed intercalated-motifs (IMs) are typically unstable at neutral pH, hampering the investigation of their potential involvement in a biological context. We herein report on a photochemical method for "stapling" such tetraplexed-structures, to increase their stability, lock their topology and enhance their enzymatic resistance, while maintaining biological activity. The chemical structure and topology of the stapled Thrombin Binding Aptamer (TBA) was spectroscopically characterised and rationalised in silico. The method was then extended to other biologically relevant G4- and IM-prone sequences, hinting towards potential application of such stapled structures in a therapeutic context.

Exploring the Interactions Between RHAU Peptide and G-Quadruplex Dimers Based on Chromatographic Retention Behaviors

G-quadruplex (G4), an important secondary structure of nucleic acids, is polymorphic in structure. G4 monomers can associate with each other to form multimers, which show better application performance than monomers in some aspects. G4 dimers, the simplest and most widespread multimeric structures, are often used as a representative for studying multimers. RHAU, a G4 ligand, has been reported to recognize G4 dimers. However, there are few reports focusing on interactions between RHAU and different G4 dimers. In this work, interactions between RHAU peptide and six G4 dimers were investigated by size-exclusion chromatography (SEC). It was revealed that compared to the hybrid G4 monomer, the hybrid tandem unstacked G4 dimer could form special binding sites, leading to a weak interaction with RHAU. It was also found that the steric hindrance at terminal G-tetrads of a special Z-G4 structure greatly weakened their interactions with RHAU. Additionally, RHAU exhibited stronger interactions with intermolecular stacked/interlocked parallel dimers than with intramolecular tandem stacked parallel dimers. This work enriches the understanding of interactions between RHAU and G4 dimers, which is conducive to the elucidation of G4 polymorphism, and provides a strong reference for studying G4 multimer-peptide interactions.

A CD Study of a Structure-Based Selection of N-Heterocyclic Bis-Carbene Gold(I) Complexes as Potential Ligands of the G-Quadruplex-Forming Human Telomeric hTel23 Sequence

Herein, we report the structure-based selection via molecular docking of four N-heterocyclic bis-carbene gold(I) complexes, whose potential as ligands for the hTel23 G-quadruplex structure has been investigated using circular dichroism (CD) spectroscopy, CD melting, and polyacrylamide gel electrophoresis (PAGE). The complex containing a bis(1,2,3,4,6,7,8,9-octahydro-11H-11λ3-pyridazino[1,2-a]indazol-11-yl) scaffold induces a transition from the hybrid (3 + 1) topology to a prevalent parallel G-quadruplex conformation, whereas the complex featuring a bis(2-(2-acetamidoethyl)-3λ3-imidazo[1,5-a]pyridin-3(2H)-yl) moiety disrupted the original G-quadruplex structure. These results deserve particular attention in light of the recent findings on the pathological involvements of G-quadruplexes in neurodegenerative diseases.

Why to target G-quadruplexes using peptides: Next-generation G4-interacting ligands

Guanine-rich oligonucleotides existing in both DNA and RNA are able to fold into four-stranded DNA secondary structures via Hoogsteen type hydrogen-bonding, where four guanines self-assemble into a square planar arrangement, which, when stacked upon each other, results in the formation of higher-order structures called G-quadruplexes. Their distribution is not random; they are more frequently present at telomeres, proto-oncogenic promoters, introns, 5'- and 3'-untranslated regions, stem cell markers, ribosome binding sites and so forth and are associated with various biological functions, all of which play a pivotal role in various incurable diseases like cancer and cellular ageing. Several studies have suggested that G-quadruplexes could not regulate biological processes by themselves; instead, various proteins take part in this regulation and can be important therapeutic targets. There are certain limitations in using whole G4-protein for therapeutics purpose because of its high manufacturing cost, laborious structure prediction, dynamic nature, unavailability for oral administration due to its degradation in the gut and inefficient penetration to reach the target site because of the large size. Hence, biologically active peptides can be the potential candidates for therapeutic intervention instead of the whole G4-protein complex. In this review, we aimed to clarify the biological roles of G4s, how we can identify them throughout the genome via bioinformatics, the proteins interacting with G4s and how G4-interacting peptide molecules may be the potential next-generation ligands for targeting the G4 motifs located in biologically important regions.

Optimization of an aptamer against Prorocentrum minimum - A common harmful algae by truncation and G-quadruplex-forming mutation

Harmful algal blooms (HABs) caused by Prorocentrum minimum have seriously posed economic losses and ecological disasters. To reduce these losses, aptamers are used as a new molecular probe to establish rapid methods. Herein, to improve the affinity and application of aptamers in the detection of harmful algae, the optimization was performed on the previously reported aptamers against P. minimum. First, a total of seven candidate aptamers, including three truncated aptamers (TA1, TA2 and TA3) and four mutant aptamers (MA1, MA2, MA3 and MA4), were obtained by truncation and G-quadruplex (GQ)-forming mutation. Next, the specificity and affinity test by flow cytometry revealed that except for TA1 and TA2, all of the candidate aptamers are specific with the equilibrium dissociation constant of (40.4 ± 5.5) nM for TA3, (63.3 ± 24.0) nM for MA1, (71.7 ± 14.6) nM for MA2, (365.9 ± 74.4) nM for MA3, and (21.1 ± 0.5) nM for MA4, respectively. The circular dichroism analysis of the mutant aptamers demonstrated that the GQ structures formed by MA1/MA2, MA3 and MA4 were antiparallel, mixed parallel and parallel, respectively. The affinity of aptamers with various GQ is in the order of parallel structure > antiparallel structure > mixed parallel structure. In addition, to further improve binding ability, the binding conditions of MA4 were optimized as follows: binding time, 60 min; binding temperature, 37 °C; pH of the binding buffer, 7.5; and Na⁺/Mg²⁺ concentration in the binding buffer, 100 mM/0.5 mM. The binding examination by fluorescence microscopy showed that MA4 had a stronger binding ability to P. minimum than the original aptamer. Taken together, this study not only obtained an aptamer with higher affinity than the original aptamer, which laid a good foundation for subsequent application, but also may provide a feasible reference method for aptamer optimization.

Study on the Interaction of a Peptide Targeting Specific G-Quadruplex Structures Based on Chromatographic Retention Behavior

G-quadruplexes (G4s) are of vital biological significance and G4-specific ligands with conformational selectivity show great application potential in disease treatment and biosensing. RHAU, a RNA helicase associated with AU-rich element, exerts biological functions through the mediation of G4s and has been identified to be a G4 binder. Here, we investigated the interactions between the RHAU peptide and G4s with different secondary structures using size exclusion chromatography (SEC) in association with circular dichroism (CD), ultraviolet-visible (UV-Vis) absorption, and native polyacrylamide gel electrophoresis (Native-PAGE). Spectral results demonstrated that the RHAU peptide did not break the main structure of G4s, making it more reliable for G4 structural analysis. The RHAU peptide was found to display a structural selectivity for a preferential binding to parallel G4s as reflected by the distinct chromatographic retention behaviors. In addition, the RHAU peptide exhibited different interactions with intermolecular parallel G4s and intramolecular parallel G4s, providing a novel recognition approach to G4 structures. The findings of this study enriched the insight into the binding of RHAU to G4s with various conformations. It is noteworthy that SEC technology can be easy and reliable for elucidating G4-peptide interactions, especially for a multiple G4 coexisting system, which supplied an alternative strategy to screen novel specific ligands for G4s.

Targeting the RNA G-Quadruplex and Protein Interactome for Antiviral Therapy

In recent years, G-quadruplexes (G4s), types of noncanonical four-stranded nucleic acid structures, have been identified in many viruses that threaten human health, such as HIV and Epstein-Barr virus. In this context, G4 ligands were designed to target the G4 structures, among which some have shown promising antiviral effects. In this Perspective, we first summarize the diversified roles of RNA G4s in different viruses. Next, we introduce small-molecule ligands developed as G4 modulators and highlight their applications in antiviral studies. In addition to G4s, we comprehensively review the medical intervention of G4-interacting proteins from both the virus (N protein, viral-encoded helicases, severe acute respiratory syndrome-unique domain, and Epstein-Barr nuclear antigen 1) and the host (heterogeneous nuclear ribonucleoproteins, RNA helicases, zinc-finger cellular nucelic acid-binding protein, and nucleolin) by inhibitors as an alternative way to disturb the normal functions of G4s. Finally, we discuss the challenges and opportunities in G4-based antiviral therapy.

Label free detection of auramine O by G-quadruplex-based fluorescent turn-on strategy

Auramine o (AO) is a synthetic dye used in paper and textile industries. Although it has been an unauthorized food additive in many countries due to its toxic and carcinogenic possibility, its illegal uses have been detected in certain food products such as pasta, semolina and spices and also in pharmaceuticals. The presence of AO in food products should be monitored, therefore, to minimize the negative health effects on consumers. In this study, a simple, highly sensitive and selective label free detection method was investigated for AO by G-quadruplex-based fluorescent turn-on strategy. The optimum fluorescent detection assay was achieved with a specific G-quadruplex DNA sequence, c-myc, at 400 nM in Tris-HCl buffer at pH 7.4. The linearity of fluorescence intensity depending on AO concentration ranged from 0 to 0.07 µM and LOD and LOQ were 3 nM and 10 nM, respectively. The G-quadruplex-based detection assay was highly specific for AO as compared to other two synthetic food colorings and successfully applied to determine AO in pasta, bulgur and curry powder with recoveries in the range from 70.33% to 106.49%. This G-quadruplex-based label free detection assay has a significant potential to be used in the detection of AO in food products.