DNA and Nucleic Acid Chemistry

Analysis of live cell data with G-DNABERT supports a role for G-quadruplexes in chromatin looping

The paper uses G4-DNABERT to map G-quadruplexes to enhancer and promoter regions, supporting their role in chromatin looping and gene regulation.

TTSBBC: Triplex Target Site Biomarkers and Barcodes in Cancer

The paper introduces TTSBBC, a platform for analyzing and visualizing TFO target site sequences to aid in designing and validating TTSs.

Stalling of Transcription by Putative G-quadruplex Sequences and CRISPR-dCas9

The paper investigates how CRISPR-dCas9 and G-quadruplex sequences affect transcription by studying their impact on RNA polymerase elongation in specific promoter regions.

G-quadruplex landscape and its regulation revealed by a new antibody capture method

The paper introduces a new antibody capture method to accurately capture G4 structures in human cells and shows that G4 formation is constrained by sequence properties and nuclear environment.

Nucleolar accumulation of APE1 through condensates is mediated by rRNA forming G-quadruplex structures

This study creates an endogenous fluorescent APE1 cell line to show that APE1 accumulates in nucleoli via RNA G-quadruplex structures and lysine residues, linking phase separation to its functional switch between rRNA processing and DNA repair.

DNA G-quadruplex is a transcriptional control device that regulates memory

The paper shows DNA G-quadruplex regulates gene expression in neurons, affecting memory formation and fear extinction.

The Apurinic/Apyrimidinic Endodeoxyribonuclease 1 is an RNA G-quadruplex binding protein and regulates miR-92b expression in cancer cells

This study identifies APE1 as an RNA G-quadruplex binding protein that regulates miR-92b expression by modulating rG4 structure folding and miRNA maturation in cancer cells.

Pathogenic CANVAS (AAGGG)n repeats stall DNA replication due to the formation of alternative DNA structures

This study shows that pathogenic (A2G3)n repeats in CANVAS stall DNA replication by forming alternative DNA structures like triplexes, while nonpathogenic (A4G)n repeats do not.

Long G4-rich enhancer physically interacts with EXOC3 promoter via a G4:G4 DNA-based mechanism

The paper identifies LG4 enhancers that physically interact with gene promoters via G4:G4 DNA structures and links SNPs in these enhancers to CF lung disease severity.

Prediction of DNA i-Motifs Via Machine Learning

The paper introduces a machine learning tool, iM-Seeker, to predict DNA i-Motif folding status and strength using CUT&Tag data and biophysical experiments.

In vivo detection of DNA secondary structures using Permanganate/S1 Footprinting with Direct Adapter Ligation and Sequencing (PDAL-Seq)

The paper introduces PDAL-Seq, a method to detect DNA secondary structures in vivo, and provides a standardized analysis pipeline.

Analysis of nucleotide variations in human g-quadruplex forming regions associated with disease states

The paper analyzes SNVs in G4-forming regions across databases to identify their impact on G4 structure and disease associations.

Examining DNA Breathing with pyDNA-EPBD

The paper introduces pyDNA-EPBD, a software tool for simulating DNA breathing dynamics using the EPBD model, and demonstrates its ability to calculate DNA bubble probabilities and mutation effects.

Genetic variations in G-Quadruplex forming sequences affect the transcription of human disease-related genes

The paper identifies genetic variations in G-quadruplex forming sequences that affect transcription of disease-related genes and may contribute to disease susceptibility.

Replication-induced DNA secondary structures drive fork uncoupling and breakage

This study shows that DNA secondary structures like G4s and iMs cause replication fork arrest and breakage, and that Pif1 helicase is required to resolve stalled forks.

ExoChew: An exonuclease technique to generate single-stranded DNA libraries

ExoChew generates single-stranded DNA libraries by enzymatically converting double-stranded DNA fragments, enabling genome-wide studies of protein-DNA interactions and DNA structures.

Parallel G-quadruplex folds via multiple paths involving G-tract stacking and structuring from coil ensemble

This study uses molecular dynamics simulations to explore the folding pathways of a parallel G-quadruplex DNA structure, revealing multiple folding paths and limitations of current force fields.

A dynamic bias in chromatin protein deposition at G-quadruplex sites

The paper investigates chromatin protein deposition bias at G-quadruplex sites, finding a reciprocal association of parental and new proteins with G4 and C4 DNA strands, respectively.

Ancestral genomes and population sequencing data reveal strand- and context-specificity of polymorphic G4 sites

The paper analyzes polymorphic G4 sites using ancestral genomes and population data to show strand- and context-specific mutation patterns in DNA quadruplexes.

Local G-quadruplexes are not a major determinant of altered gene expression in BLM-deficientcells

This study investigates the role of G-quadruplexes in gene expression changes in BLM-deficient cells and finds they are not a major determinant.

Exploring G-quadruplex structure in PRCC-TFE3 fusion Oncogene: Plausible use as anti cancer therapy for translocation Renal cell carcinoma (tRCC)

The paper identifies G-quadruplex forming sequences in the PRCC-TFE3 fusion gene and demonstrates their stabilization by pyridostatin, suggesting potential as a therapeutic target for tRCC.

Prediction of G4 formation in live cells with epigenetic data: a deep learning approach

The paper develops a deep learning model, epiG4NN, to predict G4 formation in live cells using epigenetic data, showing its effectiveness across different cell lines.

Z-Flipon Variants reveal the many roles of Z-DNA and Z-RNA in health and disease

The paper identifies Z-flipon variants' roles in health and disease by analyzing Z-DNA and Z-RNA effects across multiple genomic features and disease associations.

In Vivo mRNA Hacking with Staple Oligomers Prevents Myocardial Hypertrophy

This paper introduces a method to suppress target protein translation by inducing RNA G-quadruplex structures using Staple oligomers, demonstrating efficacy in preventing cardiac hypertrophy in mice.

Identification and prediction of G-quadruplex RNA-binding proteins with roles in transcription and phase separation

The paper identifies and predicts RNA G-quadruplex-binding proteins, showing their roles in transcription and phase separation, and provides a web tool for prediction.

High throughput screening of a new fluorescent G-quadruplex ligand having telomerase inhibitory activity in human A549 cells

The paper screens a set of compounds from the ZINC database to identify a G-quadruplex ligand with telomerase inhibitory activity in human A549 cells, finding one compound with significant anti-telomerase effects and cytotoxicity.

Estimating the vertical ionization potential of single-stranded DNA molecules

The paper estimates the vertical ionization potential (vIP) of single-stranded DNA sequences using quantum chemistry calculations and validates the results with experimental data.

Structural and functional classification of G-quadruplex families within the human genome

The paper classifies G-quadruplex sequences into families using computational methods and annotates them based on sequence, structure, and functional properties.

G-quadruplexes regulate miRNA biogenesis in live zebrafish embryos

The paper shows that G-quadruplexes in pre-miR-150 regulate miRNA biogenesis in zebrafish embryos by competing with the stem-loop structure.

DNA 5-methylcytosine regulates genome-wide formation of G-quadruplex structures

This study shows that DNA 5-methylcytosine methylation reduces G-quadruplex formation, affecting gene transcription and linking epigenetic regulation to genome structure.