DNA and Nucleic Acid Chemistry

This paper reports the crystal structures of an antibody used in CoolMPS sequencing, revealing the structural basis for its high specificity in recognizing modified nucleotides.

This study investigates APE1's role in repairing damaged telomeric i-motif structures and its interaction with PCBP1 in maintaining telomere integrity.

This study shows pyridostatin stabilizes telomeric G-quadruplexes, inhibiting lagging strand replication, which is overcome by FEN1/DNA2 cleavage and MMEJ repair, suggesting potential for anti-cancer therapies.

The paper identifies G-quadruplex and i-motif structures in SHMT1 5UTR that regulate gene expression, suggesting potential therapeutic targets for multiple sclerosis.

The paper investigates how urea affects the formation of DNA duplexes with mismatched nucleotides, showing that urea stabilizes these structures through energy level shifts.

This paper introduces a method to produce 15N-labeled ssDNA for NMR studies of G-quadruplexes in cell lysates, revealing distinct ligand-binding behaviors in different environments.

The paper analyzes single-stranded DNA (ssDNA) formation in human and non-human ape telomere-to-telomere genomes to identify non-B DNA structures and their functional roles.

This paper investigates triplex stability by showing that dangling ends from both the third strand and duplex enhance stability through bimodal association kinetics.

The paper shows that changes in intracellular Na+/K+ ratio affect gene expression by altering G-quadruplex dynamics in HeLa cells.

The paper shows that DNA sequence-encoded mechanical properties influence DNA gyrase binding by modulating DNA wrapping around its CTDs, revealing asymmetric interactions and GC-rich motifs that enhance binding.

The paper shows how intrinsically disordered protein sequences selectively stabilize specific RNA G-quadruplex structures through weak interactions, without relying on high-affinity binding or cations.

The paper identifies G-quadruplex structures in HTLV-1 3'-LTR and shows they enhance antisense transcription via SP1 binding.

The paper develops a single-step synthesis method for acp3U and cmnm5U phosphoramidites, enabling the creation of oligonucleotides with hypermodified nucleobases.

This study measures DNA twist at high salt concentrations using magnetic tweezers and simulations, showing ion-specific changes but no evidence for a C-form transition.

This study determines the structure and dynamics of 8oxoG:C and 8oxoG:A base pairs in the nucleosome and characterizes MUTYH activity, revealing that 8oxoG:A is less processable by MUTYH.

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

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

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

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.

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.

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.

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

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

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.

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

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

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.

This study shows that both G-quadruplexes and i-motifs are required for glucose-induced transcriptional activation of the insulin gene, with i-motif stability positively correlating with promoter activity.

This study shows that DNA-binding proteins and nicks increase R-loop formation in vitro, revealing their roles in R-loop dynamics and initiation.