DNA and Nucleic Acid Chemistry

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.

The paper develops a statistical mechanics approach to identify sequence features controlling DNA cyclizability, finding periodic features in highly cyclizable sequences and distinct patterns in low cyclizability.

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 identifies a hidden intermediate in DNA base-pairing using 1H R1{rho} relaxation dispersion NMR, showing it is stabilized by Actinomycin D.

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

The paper mathematically devises 156 unique quadruplex motifs and develops a tool to model their energy-minimized structures, revealing greater structural complexity than previously known.

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

The paper shows that Zβ domains of ADAR1 and ZBP1 bind to G-quadruplex RNA and DNA with low micromolar affinity, providing experimental evidence for their interaction.

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.

The paper presents cryo-EM structures of anti-Z-DNA antibodies bound to Z-DNA, revealing their recognition mechanism and lack of B-to-Z transition induction.

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 uses NMR spectroscopy to show that FUS condensates cause partial unfolding of TERRA RNA G-quadruplexes, suggesting phase-separated environments modulate RNA structure.

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 identifies sequence and ionic requirements for pUG fold RNA quadruplexes, showing flexibility in nucleotide substitutions and specific ion dependence.

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 paper introduces Gs-Staple oligomers to expand RNAh's target range by alleviating sequence constraints, enabling broader mRNA targeting and precise gene suppression in mammalian cells and in vivo.

This study analyzes substitution patterns and selection at G-quadruplexes in great ape genomes, finding stronger purifying selection on stems than loops, especially in regulatory regions.

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.

The paper uses simulations and dimensionality reduction to identify intermediates in G-quadruplex unfolding and their transitions.

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 study identifies and validates G-quadruplex-forming sequences in archaea, demonstrating their presence and function in vivo and identifying potential resolving enzymes.

The paper shows BMI1 represses G-quadruplex DNA formation by heterochromatinization, preventing replication stress and genomic instability in human cells.

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 uses biased MD simulations to study DNA kink formation and identifies two types of kinks with distinct mechanical properties and biological relevance.