DNA and Nucleic Acid Chemistry

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

The paper characterizes Z-DNA dynamics across different lineages using ZSeeker, finding lineage-specific enrichment and depletion patterns in cellular and viral genomes.

This paper introduces an AI-based method using normalizing flows to accurately model DNA sequence-dependent structure and deformability, capturing complex correlations between internal coordinates.

ZSeekerDB catalogs Z-nucleic acid sequences across organismal genomes, enabling cross-species analysis of their distribution and evolutionary significance.

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 paper introduces ATENA, a method using chemically modified CRISPR-Cas9 to target specific G-quadruplexes and i-motifs, showing ligand-dependent transcriptional changes in c-MYC.

This study investigates how DNA strand polarity affects base-stacking energetics using single-molecule and computational methods, finding polarity-dependent stability differences in purine-purine and purine-pyrimidine interactions.

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.

G4mer identifies G-quadruplexes and disease variants from population-scale genetic data, improving accuracy and highlighting sequence features affecting rG4 formation.

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 uses molecular dynamics simulations to study how DNA sequence and superhelical density affect structural dynamics in minicircles, finding that undercoiling leads to stable denaturation bubbles.

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

The paper identifies peptide ligands that bind i-motif DNA structures and modulate c-Myc gene expression in HEK293 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 shows that HCQ and CQ downregulate c-myc oncogene transcription via G4 stabilization, reducing tumor growth and enhancing chemotherapy in breast cancer models.

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.

The paper analyzes G-quadruplex conformational landscapes by evaluating 20,000 unique structures from 128 DNA sequences, revealing that long-distance propeller loops restrict folding and are influenced by G4 helicity.

The paper uses CRISPR-Cas9 to mutate a G4-forming motif in the adh1+ promoter of yeast, showing its role in regulating transcriptome and metabolome.

This study maps G-quadruplexes in skeletal muscle stem cells and shows their role in promoting activation and regeneration through chromatin looping and transcription factor binding.

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 identifies G-quadruplexes as a source of genome instability in BRCA2-deficient granule cell progenitors and medulloblastoma, suggesting PIF1 helicase as a therapeutic target.