DNA and Nucleic Acid Chemistry

The paper determines the molecular structures of SYTOX Orange and SYTOX Green, characterizes their effects on DNA mechanics using magnetic tweezers, and reports their photophysical properties.

The paper identifies trinucleotide symmetry in G4 motifs and introduces MSI and nMSI to quantify it, showing higher symmetry in functional G4s compared to mutants and non-G4 sequences.

The paper introduces a framework to analyze DNA sequence space using symmetry filters and identifies G-quadruplex-forming sequences as linked to recombination hotspots.

This study identifies a WRNIP1-ATM-FANCJ pathway that resolves G-quadruplexes by stabilizing FANCJ, preventing genome instability.

The paper investigates how DNA ligases handle non-canonical base pairs in hachimoji DNA, finding that consecutive non-canonical bases at the 3-end reduce ligation efficiency.

This study investigates how molecular crowding affects the activity of the 10-23 DNAzyme using osmolytes, PEG, and dextran, showing concentration-dependent changes in stability and activity.

The paper analyzes G-quadruplexes across the human pangenome, finding that they show distinct selection patterns and influence gene expression.

The paper visualizes RRS function in vitro, showing gap formation during replisome passage and varying gap frequency based on strand positioning.

The paper introduces a topology-aware thermodynamics framework for DNA probe design, showing that mismatch placement and retained paired boxes significantly affect specificity and signal ratios.

The paper identifies G-quadruplex motifs in cancer-related circulating lncRNAs and uses them to discover RNA-binding protein networks through experimental validation and computational analysis.

The paper shows that SYBR Gold fluorescence is strongly influenced by guanosines in single-stranded nucleic acids, impacting its use in nucleic acid quantification.

QuadCleave provides an inexpensive, efficient method to validate G4-forming sequences and assess their repeat counts using two enzymes, with application to C9ORF72 in ALS and FTD.

QuadStack predicts in vivo BG4-binding motifs using deep learning, showing better performance than in vitro-based predictors and revealing discrepancies in G4 sequence grammar.

The paper investigates how Cre recognizes loxP sites through noncontacted DNA positions, showing that these positions influence binding and conformational changes.

This study shows that macromolecular crowding promotes DNA writhe under tension by inducing a contractile force dependent on crowder concentration and molecular weight.

This study shows ZBP1 cannot convert unmodified dsRNA to Z-conformation, unlike ADAR1, revealing a competitive mechanism between these proteins in immune responses.

This study investigates TMPyP4's selective binding to HRAS2 i-Motif DNA using multimodal biophysical and thermodynamic methods, revealing its stabilization and fluorescent response properties.

This study identifies the NS3 protease domain of Yellow Fever Virus as a high-affinity G4 binder, revealing its interaction mechanism and potential as an antiviral target.

The paper analyzes 101 amniote genomes to show that CGGBP1 restricts cytosine methylation, preserving G4-forming potential in mammalian and avian promoters through C-T transition rate differences.

This study shows that G-quadruplexes regulate chromatin accessibility and gene expression in Bloom Syndrome by stabilizing G4s, which enhances chromatin accessibility and promotes gene expression in BLM-deficient cells.

This paper identifies SERBP1 as a G4-binding protein that regulates translation through topology-driven recognition of G-quadruplex structures in RNA, with implications for cancer therapy.

This study investigates RNA i-motif stability at neutral pH, finding that while ensemble experiments show global unfolding, single-molecule experiments reveal a small fraction remains folded.

This study identifies RNA G-quadruplexes in the 5'UTR of KRAS mRNA and demonstrates their interaction with hnRNPA1, revealing a post-transcriptional regulatory mechanism.

This study shows QN-302 damages DNA at G4 sites in cancer cells and its anticancer effect is enhanced by Olaparib, a DNA repair inhibitor.

This study shows that G-quadruplex formation regulates RNA catalytic activity, with linear RNA (linM1) being more prone to it than circular RNA (circM1).

The paper investigates whether the antisense lncRNA THAP9-AS1 can bind to the product of its sense pair, THAP9, by analyzing G-quadruplex forming sequences and validating their structural importance.

This paper introduces a new fluorescent nucleobase, oxo-Ade BZT, with high brightness and universal hybridizing properties for use in nucleic acid-based applications.

The paper characterizes Z-DNA dynamics across different lineages using ZSeeker, finding lineage-specific enrichment and depletion patterns in cellular and viral genomes.

ZSeekerDB catalogs Z-nucleic acid sequences across organismal genomes, enabling cross-species analysis of their distribution and evolutionary significance.