DNA and Nucleic Acid Chemistry

Massively parallel characterization of RNA G-quadruplex stability and molecular recognition

The paper characterizes RNA G-quadruplex stability and recognition by ligands and proteins using a synthetic library and reverse-transcriptase stop sequencing.

G4All: a database of experimentally confirmed G-quadruplex-forming sequences

G4All is a curated database of experimentally validated G-quadruplex-forming DNA and RNA sequences with controls, enabling comparative analysis and predictive model development.

G-quadruplex structures act as a novel recognition motif for the meiosis-specific histone methyltransferase PRDM9

This study shows PRDM9 binds G-quadruplex structures, enhancing meiotic recombination by creating chromatin accessibility.

Compartment-dependent selection regimes maintain the G-quadruplex paradox across the eukaryotic kingdoms

The paper investigates the G4 paradox across eukaryotic genomes, finding compartment-dependent selection regimes that maintain G4 structures in regulatory regions and suppress them in coding sequences.

The effect of DNA methylation on DNA structure and DNA-small molecule interactions

This study investigates how DNA methylation affects DNA structure and small molecule interactions, showing increased stability in fully methylated DNA and specific hydrophobic interactions with drugs like Dox.

Anti-Z-NA antibodies can distinguish accessible Z-form states across DNA, RNA, and DNA-RNA substrates

This study compares Z22 and Z-D11 antibodies' binding to Z-NA substrates, finding they have distinct specificities and functional capabilities.

G-quadruplex folding uncouples cis-activation from collateral trans-cleavage by Cas12a

This study shows that G-quadruplex structures can separate Cas12a cis-activation from trans-cleavage, enabling controlled diagnostic signals.

Direct detection of alternative DNA conformations with long-read sequencing and machine learning approaches

This study uses long-read sequencing and machine learning to detect alternative DNA conformations, achieving ~90% accuracy in distinguishing G4 from B-form DNA.

Telomeric G-Quadruplexes Formed by Six G-overhang Permutation Repeats

The paper investigates G-quadruplex formation from six G-overhang permutations in telomeres, revealing differences in stability and folding that affect DNA polymerase activity.

Visualising diverse extracellular nucleic acids in biofilms with DNA-binding dyes

This paper evaluates DNA-binding dyes for visualizing non-canonical extracellular nucleic acids in biofilms and identifies dyes with specific binding preferences.

Parallel DNA Holliday Junctions: Myth or Reality? An Atomistic Molecular Dynamics Study

This study uses molecular dynamics simulations to investigate whether parallel Holliday junctions exist in solution, finding they are thermodynamically metastable but rarely observed.

HSeeker: an algorithm for systematic H-DNA sequence identification

HSeeker identifies and scores H-DNA-forming sequences using a three-part algorithm, providing genomic coordinates and stability scores for further analysis.

G4 DNA structures induced by UV radiation: a multi-omic approach

This study identifies UV radiation-induced G4 DNA structures in human cells using multi-omic analyses and reveals their role in genotoxic stress responses.

A genetically buffered helicase network promotes tolerance of G-quadruplex stabilization in Saccharomyces cerevisiae

This paper investigates G-quadruplex tolerance in yeast by testing helicase mutants, finding that redundancy across multiple helicases, not single families, is required for G4 resolution.

Molecular Structure, DNA Binding, and Photophysical Properties of SYTOX Orange and SYTOX Green

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.

Trinucleotide Distribution, Symmetry Elements and Formulation of Mirror Symmetry Index for G4 Motifs

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.

Recombinogenic G-quadruplexes in the Newtonian DNA Sequence Space

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

WRNIP1-ATM signaling promotes G-quadruplex resolution by preserving FANCJ stability

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

DNA Ligases Discriminate Between Natural and Non-Natural Base Pairs

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.

Molecular crowding: impacts on the activity of the 10-23 DNAzyme

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.

Variation and selection at predicted G-quadruplexes across the human pangenome

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

Accessibility of Telomeric Overhangs to Stabilizing Small-Molecule Ligands

This study investigates how telomeric overhang architecture affects small-molecule ligand accessibility by analyzing binding stoichiometry and cooperativity in G-quadruplex structures.

Direct visualisation of post-replication gap formation at the bacterial RRS

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

Topology-aware thermodynamics for DNA probe design under fixed stringency: Retained paired boxes link mismatch placement, nearest-neighbor stability and room-temperature diagnostic specificity

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.

Putative G-Quadruplex Structures in Cancer-Dysregulated Circulating lncRNAs and their G4-mediated Identification of Protein Interacting Partners

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.

CTCF directly binds G-quadruplex structures to regulate genome topology and gene expression

This study identifies CTCF as a strong G4 DNA binder and shows its role in genome topology and gene expression through chromatin looping and CTCF occupancy.

SYBR Gold staining of single stranded nucleic acids is strongly influenced by the presence of guanosines

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

Visualizing Poloidal Orientation in DNA Minicircles

This study experimentally confirms sequence-dependent poloidal orientations in DNA minicircles using atomic force microscopy.

MDNA: a software module for DNA structure generation and analysis

MDNA is a software module that generates and analyzes complex DNA structures, supporting modifications and providing geometric analysis tools for detailed DNA modeling.

Mechanistic Insights into TMPyP4 Recognition of the HIV-1 LTR-III G-Quadruplex in Dilute and Protein Condensate Environments Reveal Hidden Dual Binding Modes