DNA and Nucleic Acid Chemistry

This study investigates how DNA damage affects the folding kinetics of G-quadruplex sequences in a DGD motif, showing accelerated folding with specific damage types and locations.

The paper introduces TTSBBC, a platform for analyzing and visualizing TFO target site sequences to aid in designing and validating TTSs.

The paper uses molecular dynamics simulations to study base pair formation at the HIV-1 LTR-III G-quadruplex:duplex junction, revealing electrostatic and geometric factors influencing base pair stability.

This study shows Znf706 promotes protein aggregation but binds G-quadruplexes, which suppresses aggregation and affects mRNA levels.

The paper develops a computational model to study ion-DNA interactions and shows it accurately predicts experimental results without parameter tuning.

The paper introduces a new antibody capture method to accurately capture G4 structures in human cells and shows that G4 formation is constrained by sequence properties and nuclear environment.

The paper uses in-cell NMR to study DNA i-motif formation in human cells, finding that i-motifs are rare and cell cycle-dependent.

The paper investigates the structural polymorphism of RFC1 pentanucleotide repeats associated with CANVAS, showing different G-quadruplex and hairpin structures in DNA and RNA.

The paper develops a method to selectively target and stabilize individual G4 DNA structures using ligand-conjugated oligonucleotides, demonstrating specificity without affecting off-target G4 formations.

The paper shows DNA G-quadruplex regulates gene expression in neurons, affecting memory formation and fear extinction.

This study identifies and evaluates novel chroman derivatives and their borondifluoride complexes as selective G-quadruplex binders through in vitro and cellular assays.

This study shows that pathogenic (A2G3)n repeats in CANVAS stall DNA replication by forming alternative DNA structures like triplexes, while nonpathogenic (A4G)n repeats do not.

This study investigates how TMPyP affects DNA nanomechanics across various conditions and finds it lengthens and softens dsDNA, with NaCl counteracting some effects.

This study examines how mismatches and bulges in DNA/RNA duplexes affect hybridization kinetics and shows that transient low-specificity states can support prebiotic copying reactions.

The paper introduces a machine learning tool, iM-Seeker, to predict DNA i-Motif folding status and strength using CUT&Tag data and biophysical experiments.

The paper identifies and structures the G-quadruplex formed by RFC1 AAGGG repeats, showing its role in replication stalling and transcription inhibition in CANVAS.

This study uses NMR to show that G*T/U mismatches in RNA:DNA hybrids can form Watson-Crick-like conformations, potentially contributing to transcription errors and CRISPR/Cas9 off-target effects.

This paper uses machine learning to classify mutational hotspots by analyzing helical distortion from molecular dynamics simulations of DNA adducts.

This paper introduces a new fluorescent probe, TOR-G4, for visualizing G-quadruplex RNA in cells using fluorescence lifetime imaging microscopy, distinguishing G4s from other structures without relying on intensity changes.

This paper uses molecular dynamics to show that BABAP derivatives induce sequence-selective DNA kinks, mimicking DNA-bound Cre recombinase structures.

This paper introduces a single-molecule fluorescence method to measure DNA breathing dynamics using (iCy3)2 dimer probes, revealing four conformational macrostates in DNA fork constructs.

This study analyzes G4 structures in bacterial pathogenicity islands and finds their non-random distribution and correlation with GC content, suggesting functional roles in DNA integration and pathogenicity.

This paper introduces a framework using hydrogen-deuterium exchange native mass spectrometry to analyze G-quadruplex DNA structures and dynamics, revealing exchange mechanisms and stability relationships.

The paper investigates how G4 prone sequences upstream of a minimal promoter in yeast affect transcriptional activity, finding that they increase basal promoter activity and enhance P53 family protein-dependent expression.

The paper analyzes SNVs in G4-forming regions across databases to identify their impact on G4 structure and disease associations.

The paper examines how the position and sequence environment of an abasic site affect DNA duplex stability and dynamics using spectroscopy and simulations.

The paper uses a DNA microarray to study how proteins and small molecules bind to DNA i-motifs, finding that hnRNP K broadly recognizes iMs while others prefer G-quadruplexes.

The paper introduces pyDNA-EPBD, a software tool for simulating DNA breathing dynamics using the EPBD model, and demonstrates its ability to calculate DNA bubble probabilities and mutation effects.

This study presents a quantitative model showing how DNA topology modulates binding, with experiments using fluorescent intercalators and psoralen to demonstrate topology-dependent effects.

The paper quantifies ion binding effects on G-quadruplex dynamics and free energies, revealing differences between telomeric and TERRA GQs.