Kinetic and Thermodynamic Control of G-Quadruplex Polymorphism by Na+ and K+ Cations

DNA conductance modulation via aptamer binding

The electronic properties of DNA make it an attractive candidate for applications in biosensing and molecular electronics. One approach to utilizing DNA in these fields involves binding molecules, such as aptamers, to control DNA's electrical conductance. By combining molecular dynamics simulations and density functional theory with Green's function-based charge transport calculations, we gain insights into aptamer induced structural realignment of DNA base pairs near the binding site. We find that this structural realignment enhances the electronic coupling, creating a conductive path near the highest occupied molecular orbital. This interaction results in a significant modulation of conductance by at least an order of magnitude compared to the dsDNA without the aptamer. We anticipate that our findings will promote the development of DNA-aptamer complexes for use in molecular electronics and biosensing applications.

A facile optical sensing strategy for glyphosate detection based on structure-switching signaling aptamers

A facile and highly specific optical sensing strategy is established for glyphosate (GLYP) detection using structure-switching signaling aptamers (F-SSSAs) with fluorescence signal reporting functionality. The strategy involves two domains: the FITC-labeled signal transduction domain for fluorescence signal reporting, while the functional domain (specific structure-switching aptamers) controls the target recognition. Graphene oxide (GO) works as a robust F-SSSAs quencher in the absence of GLYP. However, the F-SSSAs structure is switched in the presence of GLYP, prominently affecting the interaction with GO. The fluorescence of the structure-switching signaling aptamer-based sensing system is subsequently restored. The present strategy exhibits two dynamic linear relationships for GLYP detection in the ranges 0.2 to 80 ng·mL-1 and 100 to 800 ng·mL-1, with a low detection limit (LOD) of 0.07 ng·mL-1. Significantly, the proposed sensing system has been successfully utilized to detect GLYP in water, soil, and rice, demonstrating its potential applications in GLYP monitoring.

RHPS4 Targeted the G-Quadruplex of the 1a Gene of Cucumber Mosaic Virus to Inhibit Viral Proliferation

Small molecules targeting G-quadruplexes (G4s) in viruses could inhibit viral proliferation. The 1a protein of cucumber mosaic virus (CMV) act as RNA-dependent RNA polymerase (RdRp) that plays a crucial role in regulating the replication of CMV. In this study, four putative G4 sequences (CMV PQS1-PQS4) in the genetic coding region of CMV 1a were identified, and three of them (PQS2, PQS3, and PQS4) were confirmed to fold into G4 structures. The G4-ligand, RHPS4, could bind to CMV PQS2 and PQS4 with a strong binding affinity and preferred to interact with the 3' terminal G-quartet surfaces of CMV PQS2, and 5' terminal of CMV PQS4. RHPS4 was also found to stabilize the CMV PQS2 and PQS4 G4s. Further studies revealed that RHPS4 exhibited an excellent anti-CMV activity. This study suggested that CMV PQS2 and PQS4 could be considered potential targets for screening viral inhibitors.

Insights into the Molecular Structure, Stability, and Biological Significance of Non-Canonical DNA Forms, with a Focus on G-Quadruplexes and i-Motifs

This article provides a comprehensive examination of non-canonical DNA structures, particularly focusing on G-quadruplexes (G4s) and i-motifs. G-quadruplexes, four-stranded structures formed by guanine-rich sequences, are stabilized by Hoogsteen hydrogen bonds and monovalent cations like potassium. These structures exhibit diverse topologies and are implicated in critical genomic regions such as telomeres and promoter regions of oncogenes, playing significant roles in gene expression regulation, genome stability, and cellular aging. I-motifs, formed by cytosine-rich sequences under acidic conditions and stabilized by hemiprotonated cytosine-cytosine (C:C+) base pairs, also contribute to gene regulation despite being less prevalent than G4s. This review highlights the factors influencing the stability and dynamics of these structures, including sequence composition, ionic conditions, and environmental pH. Molecular dynamics simulations and high-resolution structural techniques have been pivotal in advancing our understanding of their folding and unfolding mechanisms. Additionally, the article discusses the therapeutic potential of small molecules designed to selectively bind and stabilize G4s and i-motifs, with promising implications for cancer treatment. Furthermore, the structural properties of these DNA forms are explored for applications in nanotechnology and molecular devices. Despite significant progress, challenges remain in observing these structures in vivo and fully elucidating their biological functions. The review underscores the importance of continued research to uncover new insights into the genomic roles of G4s and i-motifs and their potential applications in medicine and technology. This ongoing research promises exciting developments in both basic science and applied fields, emphasizing the relevance and future prospects of these intriguing DNA structures.

Role of Alkali Cations in DNA-Thioflavin T Interaction

This study investigates the role of alkali cations in modulating the interaction between deoxyribonucleic acid (DNA) and Thioflavin T (ThT) in dilute and condensed phases. The emission characteristics of ThT were analyzed in the presence of double-stranded DNA and G-quadruplex structures with a focus on the effects of four cations: sodium, potassium, calcium, and magnesium. The ThT emission in double-stranded DNA was influenced by direct DNA binding and steric hindrance within the hydration shell of DNA, which was modulated by the presence of alkali cations. Lasing spectroscopy experiments further highlighted ThT sensitivity to the spatial arrangement of water molecules in the DNA hydration shell. Lasing was exclusively observed in the presence of Mg2+ in the G-quadruplex structure, suggesting that the parallel propeller configuration of G4 provides an optimal environment for ThT light amplification. This study highlights the critical role of cations in DNA-dye interactions and reaffirms the significance of ThT in biophysical studies.

Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations

Guanine quadruplex (GQ) is a noncanonical nucleic acid structure formed by guanine-rich DNA and RNA sequences. Folding of GQs is a complex process, where several aspects remain elusive, despite being important for understanding structure formation and biological functions of GQs. Pulling experiments are a common tool for acquiring insights into the folding landscape of GQs. Herein, we applied a computational pulling strategy─steered molecular dynamics (SMD) simulations─in combination with standard molecular dynamics (MD) simulations to explore the unfolding landscapes of tetrameric parallel GQs. We identified anisotropic properties of elastic conformational changes, unfolding transitions, and GQ mechanical stabilities. Using a special set of structural parameters, we found that the vertical component of pulling force (perpendicular to the average G-quartet plane) plays a significant role in disrupting GQ structures and weakening their mechanical stabilities. We demonstrated that the magnitude of the vertical force component depends on the pulling anchor positions and the number of G-quartets. Typical unfolding transitions for tetrameric parallel GQs involve base unzipping, opening of the G-stem, strand slippage, and rotation to cross-like structures. The unzipping was detected as the first and dominant unfolding event, and it usually started at the 3'-end. Furthermore, results from both SMD and standard MD simulations indicate that partial spiral conformations serve as a transient ensemble during the (un)folding of GQs.

G-quadruplex DNA-based colorimetric biosensor for the ultrasensitive visual detection of strontium ions using MnO2 nanorods as oxidase mimetics

Strontium-90 (90Sr) is a major radioactive component that has attracted great attention, but its detection remains challenging since there are no specific energy rays indicative of its presence. Herein, a biosensor that is capable of rapidly detecting Sr2+ ions is demonstrated. Simple colorimetric method for sensitive detection of Sr2+ with the help of single-stranded DNA was developed by preparing MnO2 nanorods as oxidase mimic catalysis 3,3',5,5'-tetramethylbenzidine (TMB). Under weakly acidic conditions, MnO2 exhibited a strong oxidase-mimicking activity to oxidize colorless TMB into blue oxidation products (oxTMB) with discernible absorbance signals. Nevertheless, the introduction of a guanine-rich DNA aptamer inhibited MnO2-mediated TMB oxidation and reduced oxTMB formation, resulting in blue fading and diminished absorbance. Upon the addition of strontium ions to the system, the aptamers formed a stable G-quadruplex structure with strontium ions, thereby restoring the oxidase-mimicking activity of MnO2. Under the best experimental conditions, the absorbance exhibits a linear relationship with the Sr2+ concentration within the range 0.01-200 μM, with a limit of detection of 0.0028 µM. When the concentration of Sr2+ from 10-8 to 10-6 mol L-1, a distinct color change gradient could be observed in paper-based sensor. We successfully applied this approach to determine Sr2+ in natural water samples, obtaining recoveries ranging from 97.6 to 103% with a relative standard deviation of less than 5%. By providing technical solutions for detection, our work contributed to the effective monitoring of transportation of radioactive Sr in the environment.