DNA and Nucleic Acid Chemistry

G-Quadruplexes Act as an On/Off Switch While i-Motifs Regulate Insulin Expression in Reporter Gene Assays

This study shows that both G-quadruplexes and i-motifs are required for glucose-induced transcriptional activation of the insulin gene, with i-motif stability positively correlating with promoter activity.

ZSeeker: An optimized algorithm for Z-DNA detection in genomic sequences

ZSeeker detects potential Z-DNA-forming sequences in genomes with improved accuracy and accessibility through a Python package and web interface.

AMOEBA Polarizable Molecular Dynamics Simulations of Guanine Quadruplexes: from the c-Kit Proto-oncogene to HIV-1

The paper uses AMOEBA polarizable MD simulations to study guanine quadruplexes in c-kit1 and HIV-1 LTR-III, identifying structural motifs and druggable pockets.

Protein-mediated stabilization and nicking of the non-template DNA strand dramatically affect R-loop formation in vitro

This study shows that DNA-binding proteins and nicks increase R-loop formation in vitro, revealing their roles in R-loop dynamics and initiation.

An A-T Hoogsteen base pair in a naked DNA hairpin motif: A Protein-Recognized Conformation

The paper shows that an A-T Hoogsteen base pair forms in naked DNA hairpins without protein binding, and identifies a DNA-specific motif stabilized by this pairing.

Breaking barriers: A new phytomedicine based treatment approach for targeted unrevealed non-canonical DNA structures in tuberculosis bacteria.

This study investigates how flavonoids interact with non-canonical DNA structures in Mtb, showing they stabilize GQ and iM sequences, potentially enhancing TB drug efficacy.

Non-canonical DNA in human and other ape telomere-to-telomere genomes

The paper characterizes non-B DNA motifs in T2T genomes of apes, showing their enrichment in specific genomic regions and potential roles in genome function.

DNA2 and MSH2 activity collectively mediate chemically stabilized G4 for efficient telomere replication

The paper shows DNA2 and MSH2 work together to remove G4 structures at telomeres, preventing replication issues and telomere instability.

G-quadruplex profiling in complex tissues using single-cell CUT&Tag

This study uses G4 scCUT&Tag to profile G-quadruplexes in mouse brain cells, showing lineage-specific G4s and enabling integrative analysis with scRNA-Seq data.

Impacts of sequence and structure on pyrrolocytosine fluorescence in RNA

This paper investigates how sequence and structure affect the fluorescence of pyrrolocytosine (pC) in RNA, showing that pC is brightest in base-stacked, unpaired conformations.

Next generation APOBEC3 inhibitors: Optimally designed for potency and nuclease stability

This study designs and tests optimized oligonucleotide inhibitors for APOBEC3 enzymes, showing improved potency and nuclease stability compared to previous inhibitors.

The "very moment" when UDG recognizes aflipped-out uracil base in dsDNA

This study uses molecular dynamics simulations to show that DNA mechanics can induce base-flipping, facilitating UDG recognition of uracil bases in chromatin.

Thermodynamic Parameter Estimation for Modified Oligonucleotides Using Molecular Dynamics Simulations

This study estimates thermodynamic parameters for RNA/DNA hybrid duplexes using MD simulations, finding MMGBSA provides more accurate predictions than MMPBSA for modified oligonucleotides.

Cryo-EM structures of G4-stalled CMG reveal inchworm mechanism of DNA translocation

The paper uses cryo-EM to study how G4 DNA structures stall replisomes and reveals an inchworm mechanism for DNA translocation.

G-quadruplexes represent promising new targets to overcome multidrug-resistant fungal infections

This study demonstrates that G-quadruplexes are a promising antifungal target, as ligands like PhenDC3 inhibit fungal pathogens and show synergistic effects with existing antifungals.

Systematic study of hybrid triplex topology and stability suggests a general triplex-mediated regulatory mechanism

The paper systematically studies hybrid triplex topology and stability, revealing a regulatory mechanism in the human genome and transcriptome through triplex formation.

Helical foldamers as selective G-quadruplex ligands

This study identifies helical foldamers with quinoline and pyridine units as selective G-quadruplex ligands, showing preference for parallel structures and sequence variants.

Quantitative and systematic NMR measurements of sequence-dependent A-T Hoogsteen dynamics uncovers unique conformational specificity in the DNA double helix

This study measures sequence-dependent A-T Hoogsteen dynamics in DNA using NMR, revealing distinct conformational specificity and sequence dependence.

Small molecules reveal differential shifts in stability and protein binding for G-quadruplex RNA

This paper investigates how small molecules affect RNA G-quadruplex stability and protein binding, revealing bidirectional impacts and specific protein interactions.

The modification of DNA with indole-linked nucleotides alters its sensitivity to enzymatic cleavage

This paper modifies DNA with indole-linked nucleotides, altering its conformation and sensitivity to enzymatic cleavage, with implications for antisense therapeutics and small molecule screening.

G-Quadruplex Structures in 16S rRNA Regions Correlate with Thermal Adaptation in Prokaryotes

This study finds that G-quadruplex structures in 16S rRNA regions correlate with thermal adaptation in prokaryotes, showing higher stability in thermophilic species.

Site-specific free energy surface parameters from single-molecule fluorescence measurements of exciton-coupled (iCy3)2 dimer probes positioned at DNA replication fork junctions

The paper analyzes single-molecule fluorescence data to quantify free energy surfaces of DNA breathing at replication fork junctions.

G-quadruplexes in the RSV genome: potential anti-viral targets.

This study identifies G-quadruplex (G4) structures in the RSV genome and shows they are recognized by ligands and nucleolin, suggesting potential as anti-viral targets.

Early Events in G-quadruplex Folding Captured by Time-Resolved Small-Angle X-Ray Scattering

The paper uses TR-SAXS to study early G-quadruplex folding, revealing a rapid collapse followed by slower conformational changes.

RNA G-Quadruplex Emerges from a Coil-Like Ensemble via Multiple Pathways

This study uses molecular dynamics simulations to explore the folding pathways of an RNA G-quadruplex, revealing multi-pathway mechanisms and highlighting challenges in simulating non-canonical RNA structures.

Single-molecule analysis of PARP1-G-quadruplex interaction

This study investigates PARP1's interaction with G-quadruplexes using single-molecule techniques, revealing dynamic 1:1 binding and PARylation activation.

Refinement of the Sugar Puckering Torsion Potential in the AMBER DNA Force Field

This study refines the AMBER DNA force field parameters to better model A-DNA stability and improve protein-DNA complex modeling.

G-Quadruplex-Protein Interactome at Human Gene Promoters

The paper maps G4-protein interactions at human gene promoters using ENCODE data, revealing three distinct binding sites and dynamic regulation by histone modifications.

Dominant Formation of DNA:RNA Hybrid G-Quadruplexes in the Genomes of Living Human and Mouse Cells

This paper identifies DNA:RNA hybrid G-quadruplexes (hG4s) as the most abundant G4 structures in human and mouse genomes, surpassing intramolecular DNA G4s in abundance and independence of G-tract formation.

The iMab antibody selectively binds to intramolecular and intermolecular i-motif structures

The paper investigates the selectivity of the iMab antibody for i-motif structures, showing it binds both intramolecular and intermolecular iMs, and highlights the impact of experimental conditions on binding.