DNA and Nucleic Acid Chemistry

Characterization of Z-DNA dynamics across the tree of life

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

Deciphering DNA's sequence-dependent structure and deformability with normalizing flows

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: A database of Z-nucleic acid sequences across organismal genomes

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

Structural Mechanism of Specific Nucleobase Recognition by a Monoclonal Antibody in CoolMPSTM Sequencing

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.

Apurinic/apyrimidinic endodeoxyribonuclease 1 contributes to the repair of damaged intercalated-motif of telomeric sequences

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

Chemically modified CRISPR-Cas9 enables targeting of individual G-quadruplex and i-motif structures, revealing ligand-dependent transcriptional perturbation.

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.

Design and synthesis of mirror image fluorescent nucleotide reversible terminator, (L)-3'-O-azidomethyl-dGTP-N3-fluorophore, and (D)-9°N mutant DNA polymerase for mirror image (L)-DNA sequencing by synthesis

Investigating polarity effects in DNA base stacking

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.

Rescue from pyridostatin-stabilized telomeric G-quadruplexes by DNA cleavage and microhomology-mediated end joining

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.

G-Quadruplex and i-Motif Structures in the SHMT1 5UTR Modulate Gene Expression

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

G4mer: An RNA language model for transcriptome-wide identification of G-quadruplexes and disease variants from population-scale genetic data

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

Formation of DNA duplexes in the presence of urea as a chaotropic agent.

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

Bio-synthesis of 15N-Labeled G-Quadruplexes to Investigate the Structure and Interactions in the Cell Lysate using Nuclear Magnetic Resonance

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.

Comparative analysis of single-stranded and non-canonical DNA formation in human and other ape cells with telomere-to-telomere genomes

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.

Dangling Ends of Third Strand and Duplex Drive Nucleic Acid Triplex Stabilization through Bimodal Association

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

Sequence and supercoiling-dependent effects on the structural dynamics of DNA minicircles

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.

Alteration in the intracellular Na+/K+ ratio regulates gene expression through the shift of G-quadruplex dynamics in living cells

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

Affinity-selected peptide ligands specifically bind i-motif DNA and modulate c-Myc gene expression

The paper identifies peptide ligands that bind i-motif DNA structures and modulate c-Myc gene expression in HEK293 cells.

The mechanical code of DNA impacts its interaction with DNA gyrase

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.

Specificity of the stabilising interaction between intrinsically disordered protein sequences and G-quadruplexes in RNA

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.

HTLV-1 antisense transcription is promoted by increased SP1 binding at 3'-LTR G-Quadruplexes

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

Towards One-Step and Universal Synthesis of Hypermodified Uracil Nucleosides: acp3U and cmnm5U

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

G-Quadruplex Mediated c-myc Specific Downregulation: A Unique Pathway of the Anticancer Action of Immunomodulator Drugs

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.

DNA Twist at High Alkaline Ion Concentrations: Evidence against C-Form DNA in Solution

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.

Large-scale conformational analysis explains G-quadruplex topological landscape

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.

CRISPR-Cas9 Targeting of G-Quadruplex DNA in ADH1 promoter Highlights its role in Transcriptome and Metabolome Regulation

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.

DNA G-quadruplex Profiling Reveals Functional and Mechanistic Role of G-quadruplexes in Skeletal Muscle Stem Cells

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.

Structure, dynamics, and processing of 8oxoG:A in the nucleosome

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.

G-quadruplexes are a source of vulnerability in BRCA2 deficient granule cell progenitors and medulloblastoma

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.

Sequence-dependent shape and stiffness of DNA and RNA double helices: hexanucleotide scale and beyond

This study presents mechanical properties of DNA and RNA duplexes based on molecular dynamics simulations and proposes a model to predict sequence-dependent shape and stiffness.