DNA and Nucleic Acid Chemistry

QuadCleave: Enzymatic cleavage and analysis of DNA G-quadruplexes.

QuadCleave provides an inexpensive, efficient method to validate G4-forming sequences and assess their repeat counts using two enzymes, with application to C9ORF72 in ALS and FTD.

Searching for Sequence Features that Control DNA Cyclizability

The paper develops a statistical mechanics approach to identify sequence features controlling DNA cyclizability, finding periodic features in highly cyclizable sequences and distinct patterns in low cyclizability.

QuadStack: Specialized convolutional blocks enable in vivo BG4-binding motif prediction and highlight discrepancies with in vitro G-quadruplexes.

QuadStack predicts in vivo BG4-binding motifs using deep learning, showing better performance than in vitro-based predictors and revealing discrepancies in G4 sequence grammar.

Thermodynamics of Indirect Readout in Cre-loxP Recognition

The paper investigates how Cre recognizes loxP sites through noncontacted DNA positions, showing that these positions influence binding and conformational changes.

1H R1{rho} Relaxation Identifies a Hidden Intermediate in DNA Base-Pairing

This study identifies a hidden intermediate in DNA base-pairing using 1H R1{rho} relaxation dispersion NMR, showing it is stabilized by Actinomycin D.

MACRO-MOLECULAR CROWDING FAVORS WRITHE IN UNWOUND DNA

This study shows that macromolecular crowding promotes DNA writhe under tension by inducing a contractile force dependent on crowder concentration and molecular weight.

Untangling or further entangling? Revelation of the complicated world of nucleic acid quadruplex folds

The paper mathematically devises 156 unique quadruplex motifs and develops a tool to model their energy-minimized structures, revealing greater structural complexity than previously known.

ZBP1's Inability to Convert Unmodified RNAs to the Z-form Underlies a Balanced Mechanism of RNA Recognition with ADAR1

This study shows ZBP1 cannot convert unmodified dsRNA to Z-conformation, unlike ADAR1, revealing a competitive mechanism between these proteins in immune responses.

Zα and Zβ domains of ADAR1 and ZBP1 bind to G-quadruplexes with low micromolar affinity

The paper shows that Zβ domains of ADAR1 and ZBP1 bind to G-quadruplex RNA and DNA with low micromolar affinity, providing experimental evidence for their interaction.

Selective Stabilization of HRAS2 i-Motif DNA by TMPyP4: A Multimodal Biophysical and Thermodynamic Investigation

This study investigates TMPyP4's selective binding to HRAS2 i-Motif DNA using multimodal biophysical and thermodynamic methods, revealing its stabilization and fluorescent response properties.

Cryo-EM structures of anti Z-DNA antibodies in complex with antigen reveal distinct recognition modes of a left-handed geometry

The paper presents cryo-EM structures of anti-Z-DNA antibodies bound to Z-DNA, revealing their recognition mechanism and lack of B-to-Z transition induction.

Unraveling Viral peptide-G4 Interactions: the NS3 Protease Domain of Yellow Fever Virus Binds G-Quadruplexes with High Specificity and Affinity

This study identifies the NS3 protease domain of Yellow Fever Virus as a high-affinity G4 binder, revealing its interaction mechanism and potential as an antiviral target.

CGGBP1-regulated heterogeneous C-T transition rates relate with G-quadruplex potential of terrestrial vertebrate genomes

The paper analyzes 101 amniote genomes to show that CGGBP1 restricts cytosine methylation, preserving G4-forming potential in mammalian and avian promoters through C-T transition rate differences.

Visualizing TERRA RNA G-quadruplex unfolding in FUS biomolecular condensates

This study uses NMR spectroscopy to show that FUS condensates cause partial unfolding of TERRA RNA G-quadruplexes, suggesting phase-separated environments modulate RNA structure.

G-quadruplexes regulate chromatin accessibility and gene expression in Bloom Syndrome

This study shows that G-quadruplexes regulate chromatin accessibility and gene expression in Bloom Syndrome by stabilizing G4s, which enhances chromatin accessibility and promotes gene expression in BLM-deficient cells.

Intrinsically disordered SERBP1 regulates translation through topology-driven G-quadruplex recognition.

This paper identifies SERBP1 as a G4-binding protein that regulates translation through topology-driven recognition of G-quadruplex structures in RNA, with implications for cancer therapy.

Sequence and ionic requirements of pUG fold quadruplexes

This study identifies sequence and ionic requirements for pUG fold RNA quadruplexes, showing flexibility in nucleotide substitutions and specific ion dependence.

RNA i-Motif Formation at Neutral pH

This study investigates RNA i-motif stability at neutral pH, finding that while ensemble experiments show global unfolding, single-molecule experiments reveal a small fraction remains folded.

Expanded gene targeting in RNA hacking with G-tract-supply Staple oligomer

This paper introduces Gs-Staple oligomers to expand RNAh's target range by alleviating sequence constraints, enabling broader mRNA targeting and precise gene suppression in mammalian cells and in vivo.

Substitution spectrum and selection at G-quadruplexes in great ape telomere-to-telomere genomes

This study analyzes substitution patterns and selection at G-quadruplexes in great ape genomes, finding stronger purifying selection on stems than loops, especially in regulatory regions.

Recognition and Resolution of KRAS 5'UTR RNA G-Quadruplexes by hnRNPA1

This study identifies RNA G-quadruplexes in the 5'UTR of KRAS mRNA and demonstrates their interaction with hnRNPA1, revealing a post-transcriptional regulatory mechanism.

Telomeric G-quadruplex Intermediates unveiled by Complex Markov Network Analysis.

The paper uses simulations and dimensionality reduction to identify intermediates in G-quadruplex unfolding and their transitions.

The DNA damaging properties of the experimental G-quadruplex (G4) drug QN-302 are potentiated by the DNA repair inhibitor Olaparib and mitigated by the molecular helicase PhpC

This study shows QN-302 damages DNA at G4 sites in cancer cells and its anticancer effect is enhanced by Olaparib, a DNA repair inhibitor.

The Shape of Control: How Going in Circles Keeps RNA Catalytically Switched On

This study shows that G-quadruplex formation regulates RNA catalytic activity, with linear RNA (linM1) being more prone to it than circular RNA (circM1).

Can Antisense lncRNA bind to the product of its sense pair?

The paper investigates whether the antisense lncRNA THAP9-AS1 can bind to the product of its sense pair, THAP9, by analyzing G-quadruplex forming sequences and validating their structural importance.

Archaeal G-Quadruplexes: A Novel Model for Understanding Unusual DNA/RNA Structures Across the Tree of Life

This study identifies and validates G-quadruplex-forming sequences in archaea, demonstrating their presence and function in vivo and identifying potential resolving enzymes.

BMI1-mediated heterochromatinization represses G-quadruplex DNA formation to maintain genomic stability during replication

The paper shows BMI1 represses G-quadruplex DNA formation by heterochromatinization, preventing replication stress and genomic instability in human cells.

An Adenine-Based Molecular Rotor as a Universal Fluorescent Nucleobase with High Brightness

This paper introduces a new fluorescent nucleobase, oxo-Ade BZT, with high brightness and universal hybridizing properties for use in nucleic acid-based applications.

Inferring DNA kinkability from biased MD simulations

The paper uses biased MD simulations to study DNA kink formation and identifies two types of kinks with distinct mechanical properties and biological relevance.

Chemically Synthesized Ultra-long DNA as Building Blocks to Accelerate Complex Gene Construction in Synthetic Biology

This paper introduces a novel DNA synthesis platform, UCOS, capable of efficiently synthesizing long, complex, and repetitive DNA sequences up to 600nt in length.