DNA and Nucleic Acid Chemistry

G-quadruplex stabilization induces DNA breaks in pericentromericrepetitive DNA sequences in B lymphocytes

This study shows that G4-stabilizing drugs like pyridostatin cause DNA breaks and chromosomal rearrangements in B cells, with differential effects between primary and malignant cells.

8-Oxoguanine Disrupts G-Quadruplex DNA Stability and Modulates FANCJ AKKQ Binding

This paper investigates how 8-oxoguanine modifications affect G-quadruplex DNA stability and FANCJ AKKQ binding through experimental assays.

G-quadruplex formation in long non-coding RNAs dysregulated in colorectal cancer

This study investigates G-quadruplex (G4) formation in three lncRNAs dysregulated in colorectal cancer and shows their stable G4 structures using in silico and in vitro methods.

DDX41 dissolves G-quadruplexes to maintain erythroid genome integrity and prevent cGAS-mediated cell death

Study on the interaction of Yohimbine with duplex oligonucleotide using spectroscopic and computational tools

This study investigates Yohimbine's interaction with hairpin-duplex oligonucleotides using spectroscopic and computational methods, revealing groove-binding and thermodynamic properties.

Genome-wide mapping of DNA G-quadruplexes in Trypanosoma brucei chromatin reveals enrichment in coding regions

This study maps DNA G-quadruplexes in Trypanosoma brucei, showing enrichment in coding regions and functional impact of G4-stabilizing ligands on gene expression.

Untargeted CUT&Tag and BG4 CUT&Tag are both enriched at G-quadruplexes and accessible chromatin

The paper shows BG4 CUT&Tag and untargeted CUT&Tag signals are both enriched at G-quadruplexes and accessible chromatin, suggesting BG4 CUT&Tag may not reliably distinguish G4s from other accessible regions.

The structure, folding kinetics and dynamics of long poly(UG) RNA

This study investigates the structure, folding kinetics, and dynamics of long poly(UG) RNAs, revealing a dynamic model for segmental register exchange and double pUG fold formation.

Synthetic G-quadruplex components for predictable, precise two-level control of mammalian recombinant protein expression

This paper develops synthetic G-quadruplex elements to precisely control mammalian recombinant protein expression across different hosts and molecular formats.

G-quadruplex structures regulate long-range transcriptional reprogramming to promote drug resistance in ovarian cancer

This study identifies G-quadruplex structures as regulators of long-range transcriptional reprogramming in drug-resistant ovarian cancer, showing their role in promoting resistance and potential as therapeutic targets.

AT vs. GC binding of protamine-template: A microscopic understanding through molecular dynamics and binding free energies

This study uses molecular dynamics simulations to show that a protamine-mimicking peptide binds preferentially to GC-rich sequences in the major groove and AT-rich sequences in the minor groove of DNA.

The Effects of DMSO on DNA Conformations and Mechanics

This paper investigates how DMSO affects DNA structure and mechanics using single-molecule techniques and simulations, finding that DMSO increases DNA flexibility and compaction up to 50% concentration.

Phase Separation Tunes the Stability and Dynamics of G-quadruplex and i-Motif DNA in the Nuclei of Living Cells

This study investigates how phase separation affects the stability and dynamics of G-quadruplex and i-motif DNA structures in living cells.

Systematic DNA nicking reveals the structural logic of protein recognition

This study introduces PIC-NIC, a method to systematically perturb DNA binding sites without altering base sequences, revealing how DNA backbone structure influences transcription factor binding.

Towards the Development of Isoenergetic Peptide Nucleic Acid Based Probes Targeting Double-Stranded RNAs Through Enhancing Sequence-Specific Stacking Interactions

This paper investigates how modifying PNA with s2U adjacent to Q residues enhances binding affinity and functional activity toward dsRNAs, demonstrating broader applicability in targeting structured RNA structures.

Resveratrol targets G-quadruplexes to exert its pharmacological effects

This study identifies G-quadruplex stabilization as the mechanism by which resveratrol exerts its multi-target pharmacological effects.

Landscape and mutational dynamics of G-quadruplexes in the complete human genome and in haplotypes of diverse ancestry

The paper maps G-quadruplexes across the human genome and haplotypes, showing their enrichment in repetitive regions and association with genomic instability and PRDM9 binding.

Loss of DHX36/G4R1, a G4 resolvase, drives genome instability and regulates innate immune gene expression in cancer cells

This study shows that loss of DHX36/G4R1 increases genome instability and innate immune gene expression in cancer cells, correlating with improved survival in B-cell acute lymphoblastic leukemia.

Impact of Molecular Crowding on Accessibility of Telomeric Overhangs Forming Multiple G-quadruplexes

This study investigates how molecular crowding affects the accessibility and structure of telomeric overhangs with multiple G-quadruplexes using smFRET and FRET-PAINT.

G-quadruplex topologies determine the functional outcome of guanine-rich bioactive oligonucleotides

This study shows that G-quadruplex topology determines the functional outcome of G-rich oligonucleotides, with parallel topologies inhibiting translation while antiparallel ones do not.

Evolutionary Dynamics of G-Quadruplexes in Human and Other Great Ape Telomere-to-Telomere Genomes

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.

G-quadruplex Structures in Dysregulated Long Non-Coding RNA of Ovarian Cancer and their Binding Interactions with Human Serum Albumin

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

Structural basis for ring-opening fluorescence by the RhoBAST RNA aptamer.

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

Thermally activated irreversible homogenization of G-quadruplexes in an ALS/FTD-associated nucleotide expansion

This paper investigates thermally activated irreversible homogenization of G-quadruplexes in C9ORF72 hexanucleotide repeats, linking conformational changes to disease mechanisms.

In vivo guanine quadruplex structure dynamics and role in genome maintenance in Deinococcus radiodurans

This study investigates G4 structure dynamics and their role in genome maintenance in Deinococcus radiodurans under stress.

A Guanine-quadruplex located on the negative strand of the hepatitis C virus facilitates efficient genomic RNA synthesis

This paper identifies a conserved G4 structure in the HCV negative strand 3 UTR that is essential for efficient RNA synthesis by facilitating NS3 helicase recruitment and NS5B polymerase access.

Guanine quadruplexes mediate mitochondrial RNA polymerase pausing

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

Antibody targeting the anti-parallel topology of human telomeric G-quadruplex DNA

This study develops an antibody that selectively recognizes the antiparallel topology of human telomeric G-quadruplex DNA, distinguishing it from parallel conformations.

Specificity and mechanism of the double-stranded RNA-specific J2 monoclonal antibody

This study defines the epitope, specificity, and mechanism of the J2 monoclonal antibody, revealing its unique recognition of dsRNA and implications for RNA research.

Chemical Environment of the Confinement Governs Thermal Stability of the Folded Telomere G-Quadruplex

This study investigates how the chemical nature of confinement affects the folding and thermal stability of telomere G-quadruplexes, finding that cationic water pools reduce thermal stability compared to anionic ones.