DNA and Nucleic Acid Chemistry

Epigenetic CpG Duplex Marks Probed by an Evolved DNA Reader via a Well-Tempered Conformational Plasticity

The paper investigates how a designer DNA reader selectively recognizes oxidized CpG duplex marks through conformational plasticity, revealing insights into DNA-protein interactions.

Stress promotes RNA G-quadruplex folding in human cells

The paper identifies stress-induced RNA G-quadruplexes in human cells and shows they regulate mRNA stability and stress response.

Sequence-independent, site-specific incorporation of chemical modifications to generate light-activated plasmids

This paper introduces a method to create light-activated plasmids by site-specifically incorporating photocages, enabling controlled gene expression in both cell-free and mammalian systems.

The multivalent G-quadruplex (G4)-ligands MultiTASQs allow for versatile click chemistry-based investigations

The paper introduces two clickable G4 ligands for visualizing and identifying G4s in human cells using click chemistry protocols.

Thermodynamic Parameters Contributions of Single Internal Mismatches In RNA/DNA Hybrid Duplexes

The paper measures thermodynamic parameters of RNA/DNA hybrid duplexes and develops a nearest-neighbor parameter set with high accuracy for predicting their properties.

An Atypical RNA Quadruplex Marks RNAs as Vectors for Gene Silencing

The paper identifies a novel RNA quadruplex structure, the pUG fold, that drives gene silencing in C. elegans and is present in human non-coding RNAs.

Spontaneous DNA synapsis by forming noncanonical intermolecular structures

The paper reports the spontaneous formation of DNA-DNA junctions in solution, visualized by atomic force microscopy, and suggests a new role for noncanonical structures in chromatin architecture.

Triple-helix potential of the mouse genome

This study uses S1-seq to evaluate H-DNA triplex-forming potential in the mouse genome, identifying motifs and structural features associated with DNA secondary structure.

rG4-seq 2.0: enhanced transcriptome-wide RNA G-quadruplex structure sequencing for low RNA input samples

This study introduces rG4-seq 2.0, an improved method for detecting RNA G-quadruplexes with lower RNA input requirements and better library quality.

Mutagenesis at non-B DNA motifs in the human genome: a course correction

The paper analyzes mutagenesis at non-B DNA motifs in the human genome, revealing biological mechanisms and correcting previous findings by accounting for confounding factors.

Genomic landscape, polymorphism and possible LINE-associated delivery of G-Quadruplex motifs in the bovine genes.

The paper characterizes G-Quadruplex motifs in bovine genes, showing their distribution, stability, and association with LINE repeats, suggesting a delivery mechanism and potential for agricultural trait studies.

Linking Dynamic DNA Secondary Structures to Genome Instability

The paper identifies dynamic DNA secondary structures in vivo that contribute to genome instability by analyzing ssDNA converted to DSBs using S1-END-seq.

Structure-driven effects on genomic DNA damage propensity at G-quadruplex sites

The paper investigates how G-quadruplex structures influence DNA damage propensity at different sites and shows that damage patterns vary depending on G4 strength and strand localization.

Genome-wide mapping of G-quadruplex structures with CUT&Tag

This study uses CUT&Tag to map G-quadruplex structures in mammalian cells, revealing their genomic distribution and relationship with transcription and R loops.

Regulation of DIM-2-dependent repeat-induced point mutation (RIP) by the recombination-independent homologous DNA pairing in Neurospora crassa

The paper investigates DIM-2-dependent RIP in Neurospora crassa, showing GC-rich repeats and direct repeats enhance RIP efficiency through homologous DNA pairing and quadruplex formation.

Structure-based design of antisense oligonucleotides that inhibit SARS-CoV-2 replication

This paper designs structure-based antisense oligonucleotides (ASOs) that inhibit SARS-CoV-2 replication by targeting RNA structures rather than just sequences.

Identification and Targeting Putative G-Quadruplex Sequences in Candida glabrata: A Route to Virulence and Pathogenesis Control?

The paper identifies putative G-quadruplex sequences in Candida glabrata and evaluates compound A as a potential antifungal agent targeting these sequences.

Characterization of a triad of genes in cyanophage S-2L sufficient to replace adenine by 2-aminoadenine in bacterial DNA

This paper identifies three genes in cyanophage S-2L that enable the synthesis of 2-aminoadenine in bacterial DNA, demonstrating their function in a synthetic system.

Promoter G-quadruplexes and transcription factors cooperate to shape the cell type-specific transcriptome

The paper shows that promoter G-quadruplexes and transcription factors like AP-1 and SP1 work together to regulate cell-specific gene expression in liposarcoma and keratinocytes.

ATRX promotes heterochromatin formation to protect cells from G-quadruplex DNA-mediated stress

This study shows ATRX prevents G-quadruplex DNA stress by interacting with the MCM complex and promoting heterochromatin formation via ESET.

Exploring G and C-quadruplex structures as potential targets against the severe acute respiratory syndrome coronavirus 2

The paper analyzes the 2019-nCoV genome and related viruses to identify potential G and C-quadruplex structures as theranostic targets using an upgraded algorithm and experimental validation.

High-Throughput Measurement of Metastable DNA Secondary Structures Using Multiplexed Low-Yield Bisulfite Sequencing (MLB-seq)

This paper introduces MLB-seq, a method to profile DNA secondary structures using bisulfite sequencing, and finds that 84% of studied human genome subsequences adopt multiple structures.

Whole genome identification of potential G-quadruplexes and analysis of the G-quadruplex binding domain for SARS-CoV-2

The paper identifies potential G-quadruplexes in SARS-CoV-2 and analyzes their binding domain, finding conservation and structural similarities to human transcriptome G-quadruplexes.

PENGUINN: Precise Exploration of Nuclear G-quadruplexes Using Interpretable Neural Networks

PENGUINN uses Convolutional Neural Networks to predict G-quadruplex forming sequences, outperforming existing methods.

G-quadruplex stabilization in the ions and maltose transporters inhibit Salmonella enterica growth and virulence.

The paper identifies conserved G-quadruplex motifs in Salmonella enterica genes and shows that stabilizing these structures inhibits bacterial growth and virulence.

DeepG4 : A deep learning approach to predict active G-quadruplexes from DNA

DeepG4 accurately predicts active G-quadruplexes in DNA using a convolutional neural network, identifying key motifs and showing their impact on transcription and chromatin.

rG4-seeker enables high-confidence identification of novel and non-canonical rG4 motifs from rG4-seq experiments

rG4-seeker improves rG4-seq analysis by reducing false positives and enhancing detection of non-canonical rG4 motifs in human RNA.

High Affinity binding of Yeast Nucleolin Nsr1 to Co-transcriptionally Formed G4 DNA Obstructs Replication and Elevates Genome Instability

This study shows that yeast Nsr1 binds G4 DNA with high affinity, obstructs replication, and increases genome instability, with the RGG domain being essential for this effect.

Transcription-associated topoisomerase activities control DNA-breaks production by G-quadruplex ligands

The paper identifies TOP2A as a key effector of cytotoxicity from G4 ligands and shows its role in DNA break production during transcription.

Integrative analysis reveals RNA G-Quadruplexes in UTRs are selectively constrained and enriched for functional associations

The paper identifies G-quadruplex sequences in UTRs as functionally constrained and enriched for cis-eQTLs and RNA-binding protein interactions, linking them to disease associations.