DNA and Nucleic Acid Chemistry

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

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

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.

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 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.

This study identifies BAZ2 chromatin remodelers as suppressors of G4 DNA structures and shows that their depletion increases G4 formation and genomic instability.

The paper introduces JAX-EPBD, a high-throughput framework for simulating DNA breathing dynamics, showing 30x speedup and improved predictions of transcription factor binding using SELEX datasets.

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.

This study uses DFT to calculate binding energies of base pairs, showing transition mutations are more stable than transversion mutations, supporting their higher frequency in genomes.

This study uses circular dichroism to analyze how environmental factors and DNA sequences affect G-quadruplex and i-motif formation in vitro.

The paper identifies repetitive DNA motifs as overrepresented in mechanical extrema and hypothesizes their abundance is due to unique mechanical properties.

AGAPE predicts G-quadruplex binding affinity using ML, achieving 91% accuracy with molecular descriptors and quantum chemistry data.

The paper investigates pH-dependent i-motif folding in a duplex context and shows stabilization near the i-motif-duplex junction.

This study investigates how an amyloidogenic peptide binds to DNA, showing its structural interactions and effects on DNA function.

G4-Attention is a deep learning model that improves G4 quadruplex prediction accuracy using CNN, Bi-LSTM, and attention layers, outperforming existing methods.

This study uses molecular dynamics to compare Cu2+ and Mg2+ binding to Dickerson DNA, revealing similar binding preferences but distinct binding mechanisms for Cu2+.

This study investigates how protamine compacts DNA through multiple modes, forming bends, loops, and coils that contribute to transcription silencing in sperm cells.

This study identifies phytocompounds that stabilize G4 structures in the hTERT promoter using in silico screening and molecular dynamics simulations.

This study identifies intercalation as the dominant binding mode of palmatine to DNA through long-range molecular dynamics simulations and enhanced sampling.

The paper develops methods to map native co-localized G4s and R-loops in living cells and shows their role in transcriptional regulation.

This study investigates the torsional mechanics of circular DNA, showing that underwound DNA has a torque near the melting threshold and equal force/torque distribution, with implications for DNA-protein interactions.

The paper predicts the atomic structure of a guanine quadruplex in TMPRSS2 mRNA using circular dichroism and molecular modeling.

This study uses molecular dynamics simulations to show that ASO-mRNA complex stability depends on ASO length, triple base pairs, and hairpin loop accessibility, offering insights for ASO design.

This study investigates how RNA modifications affect G-quadruplex structure using molecular dynamics simulations, revealing dynamic and energetic changes in inter-quadruplex interactions.

The paper investigates the B-to-C DNA transition in aqueous LiCl solutions and finds increased helical twist across all tested concentrations, suggesting C-DNA stability above 8 M LiCl.

The paper analyzes 392 experimentally determined DNA quadruplex structures to identify 48 unique motifs, which can be classified into continuous and discontinuous types, aiding in quadruplex engineering and drug design.