DNA and Nucleic Acid Chemistry

The paper analyzes G-quadruplexes in T2T genomes of great apes, finding shared and species-specific G4s, their methylation patterns, and their potential role in gene regulation and adaptation.

This study identifies G-quadruplex structures in dysregulated lncRNAs of ovarian cancer and their interactions with human serum albumin, suggesting potential diagnostic value.

The paper determines crystal structures of the RhoBAST RNA aptamer complexed with fluorophores to elucidate the mechanism of ring-opening fluorescence.

The paper identifies guanine quadruplexes as mediators of mitochondrial RNA polymerase pausing and shows their impact on mitochondrial transcription and function.

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

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.

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.

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.

The paper shows RNA G-quadruplexes regulate mitochondrial function by modulating cytoplasmic mRNA translation of nuclear-encoded mitochondrial proteins, impacting energy metabolism and cancer cell proliferation.

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.

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

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

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

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

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

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

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

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

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.

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

This paper demonstrates a cost-effective method to monitor G-quadruplex folding transitions using single-dye labeled DNA sequences without quenchers, enabling faster and cheaper synthetic biology applications.

The paper investigates how transcription factors recognize DNA dinucleotides through structural analysis, revealing water-mediated mechanisms that enhance specificity beyond mononucleotide recognition.

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

The paper introduces NBBC, a web-based tool for quantifying non-B DNA motifs in cancer, and provides a detailed protocol for its use in analyzing genomic stability and mutation signatures.

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.

This study introduces a DNA-encoded library screening method called DEL Zipper to improve RNA-targeted small molecule screening by reducing DNA-RNA interaction signals.

The paper investigates DNA dynamics and deformability in Rad4/XPC damage sensing using T-jump and FRET techniques, showing rapid fluctuations and unwound/bent conformations at lesion sites.

This paper introduces PNA-based linkers to enhance RNA imaging probes by improving binding affinity and specificity, demonstrating significant improvements in RNA visualization in live cells.

The paper designs in silico peptides that stabilize VEGF-A G-quadruplexes, reducing gene expression and inhibiting angiogenesis in cancer cells.

This study compares the effects of G-quadruplex stabilization and destabilization on gene expression in human astrocytes using PDS and PhpC, revealing distinct transcriptomic and proteomic responses.