DNA and Nucleic Acid Chemistry

This paper demonstrates that Z-modified TFOs can repress endogenous gene expression by forming stable triplexes at GC-rich regulatory elements.

The paper discovers a 3'-terminal phosphorothioated mismatch bypass activity by DNA polymerases and demonstrates its use in creating a binary molecular switch.

This paper introduces NLG4, self-assembled nucleolipid G-quadruplexes that inhibit pancreatic cancer by targeting multiple oncogenes and pathways.

This study determines the high-resolution NMR structures of Apt38, a truncated variant of the serotonin-binding aptamer, revealing its G-quadruplex-duplex hybrid structure and serotonin binding mechanism.

The paper determines the molecular structures of RiboGreen, OliGreen, and PicoGreen using NMR and mass spectrometry, revealing their cyanine structure and binding mechanisms to nucleic acids.

This study uses MD simulations to analyze how DNA intercalators affect DNA conformation, revealing distinct intercalation patterns and their impact on mechanical properties.

This study shows DNA damage alters duplex structure and dynamics, potentially signaling repair protein recruitment through changes in DNA flexibility.

The paper investigates how DNA braiding geometry affects supercoiling partitioning during replication, showing that substrate geometry influences torsional resistance and fork rotation.

SOLiD-MaP maps small molecule binding sites on RNA using photoproximity labeling, demonstrating target-selective labeling and mutational profiling to identify binding regions.

The paper reports a cryo-EM structure of a 95-basepair DNA minicircle at 5.3 Å resolution, revealing its B-DNA configuration and structural features.

This study visualizes DNA-DNA pairing using AFM and MD simulations, showing ion-mediated groove alignment as a mechanism for homologous recognition.

This study explores how oligonucleotide design affects G4 ligand-conjugated oligonucleotide binding and stabilization of G-quadruplex structures.

This study identifies G-quadruplex regions in Arabidopsis and shows AtPLH1 regulates gene expression related to stress response and transcription.

The paper identifies conserved long G4-rich (LG4) enhancer regions across 16 species and finds a highly conserved LG4 enhancer regulating over 40 genes in human and mouse.

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

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

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.

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

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

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.

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

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.

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.

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.

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.

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

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.

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.

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

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