Base Pairing

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  Subject Areas on Research

  • 2'-O-Methylation can increase the abundance and lifetime of alternative RNA conformational states. 
  • A 'Semi-Protected Oligonucleotide Recombination' Assay for DNA Mismatch Repair in vivo Suggests Different Modes of Repair for Lagging Strand Mismatches. 
  • A 32 kb critical region excluding Y402H in CFH mediates risk for age-related macular degeneration. 
  • A complex intronic enhancer regulates expression of the CFTR gene by direct interaction with the promoter. 
  • A historical account of Hoogsteen base-pairs in duplex DNA. 
  • A nested double pseudoknot is required for self-cleavage activity of both the genomic and antigenomic hepatitis delta virus ribozymes. 
  • A potentially abundant junctional RNA motif stabilized by m6A and Mg2. 
  • A quantitative model predicts how m6A reshapes the kinetic landscape of nucleic acid hybridization and conformational transitions. 
  • A single AT-GC exchange can modulate charge transfer-induced p53-DNA dissociation. 
  • A truncated progesterone receptor (PR-M) localizes to the mitochondrion and controls cellular respiration. 
  • Atomic structures of excited state A-T Hoogsteen base pairs in duplex DNA by combining NMR relaxation dispersion, mutagenesis, and chemical shift calculations. 
  • B-DNA to zip-DNA: simulating a DNA transition to a novel structure with enhanced charge-transport characteristics. 
  • Base-pairing potential identified by in vitro selection predicts the kinked RNA backbone observed in the crystal structure of the alfalfa mosaic virus RNA-coat protein complex. 
  • Bayesian analysis of mutational spectra. 
  • Boranophosphates support the RNase H cleavage of polyribonucleotides. 
  • Characterization of long G4-rich enhancer-associated genomic regions engaging in a novel loop:loop 'G4 Kissing' interaction. 
  • Characterizing Watson-Crick versus Hoogsteen Base Pairing in a DNA-Protein Complex Using Nuclear Magnetic Resonance and Site-Specifically 13C- and 15N-Labeled DNA. 
  • Characterizing the protonation state of cytosine in transient G·C Hoogsteen base pairs in duplex DNA. 
  • Charge Transport across DNA-Based Three-Way Junctions. 
  • Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes. 
  • DNA chain length dependence of formation and dynamics of hMutSalpha.hMutLalpha.heteroduplex complexes. 
  • DNA mismatches reveal conformational penalties in protein-DNA recognition. 
  • Direct NMR Evidence that Transient Tautomeric and Anionic States in dG·dT Form Watson-Crick-like Base Pairs. 
  • Direct evidence for (G)O6···H2-N4(C)+ hydrogen bonding in transient G(syn)-C+ and G(syn)-m5C+ Hoogsteen base pairs in duplex DNA from cytosine amino nitrogen off-resonance R1ρ relaxation dispersion measurements. 
  • Direct measurements of base stacking interactions in DNA by single-molecule atomic-force spectroscopy. 
  • Electron transfer characteristics of 2'-deoxy-2'-fluoro-arabinonucleic acid, a nucleic acid with enhanced chemical stability. 
  • Energetic contribution of non-essential 5' sequence to catalysis in a hepatitis delta virus ribozyme. 
  • Environmental Effects on Guanine-Thymine Mispair Tautomerization Explored with Quantum Mechanical/Molecular Mechanical Free Energy Simulations. 
  • Epigenome characterization at single base-pair resolution. 
  • Error-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymerase. 
  • Evidence for a near-resonant charge transfer mechanism for double-stranded peptide nucleic acid. 
  • Expanding the diversity of DNA base modifications with N⁶-methyldeoxyadenosine. 
  • Field- and phage-induced dipolar couplings in a homodimeric DNA quadruplex: relative orientation of G.(C-A) triad and G-tetrad motifs and direct determination of C2 symmetry axis orientation. 
  • Flipping of the ribosomal A-site adenines provides a basis for tRNA selection. 
  • Generation of an anticoagulant aptamer that targets factor V/Va and disrupts the FVa-membrane interaction in normal and COVID-19 patient samples. 
  • Group II introns designed to insert into therapeutically relevant DNA target sites in human cells. 
  • Guanine to inosine substitution leads to large increases in the population of a transient G·C Hoogsteen base pair. 
  • Hierarchy of RNA functional dynamics. 
  • Hoogsteen base pairs increase the susceptibility of double-stranded DNA to cytotoxic damage. 
  • Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure. 
  • Identification of a naturally occurring 21 bp deletion in alpha 2c noradrenergic receptor gene and cognitive correlates to antipsychotic treatment. 
  • Impact of static and dynamic A-form heterogeneity on the determination of RNA global structural dynamics using NMR residual dipolar couplings. 
  • Increasing occurrences and functional roles for high energy purine-pyrimidine base-pairs in nucleic acids. 
  • Infrared Spectroscopic Observation of a G-C+ Hoogsteen Base Pair in the DNA:TATA-Box Binding Protein Complex Under Solution Conditions. 
  • Insights into Watson-Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A. 
  • Integrated CMOS microchip system with capillary array electrophoresis. 
  • Invisible RNA state dynamically couples distant motifs. 
  • Letter by Gurbel et al regarding article, "Cytochrome 2C19*17 allelic variant, platelet aggregation, bleeding events, and stent thrombosis in clopidogrel-treated patients with coronary stent placement". 
  • Mismodeled purines: implicit alternates and hidden Hoogsteens. 
  • Modulation of Hoogsteen dynamics on DNA recognition. 
  • Mutational hot spot potential of a novel base pair mutation of the CSPG2 gene in a family with Wagner syndrome. 
  • NMR studies of nucleic acid dynamics. 
  • New insights into Hoogsteen base pairs in DNA duplexes from a structure-based survey. 
  • New insights into the fundamental role of topological constraints as a determinant of two-way junction conformation. 
  • New tools provide a second look at HDV ribozyme structure, dynamics and cleavage. 
  • Novelty seeking and the dopamine D4 receptor gene (DRD4) revisited in Asians: haplotype characterization and relevance of the 2-repeat allele. 
  • Pervasive tertiary structure in the dengue virus RNA genome. 
  • Probing Watson-Crick and Hoogsteen base pairing in duplex DNA using dynamic nuclear polarization solid-state NMR spectroscopy. 
  • Probing conformational transitions towards mutagenic Watson-Crick-like G·T mismatches using off-resonance sugar carbon R1ρ relaxation dispersion. 
  • Probing the interplay between the two steps of group I intron splicing: competition of exogenous guanosine with omega G. 
  • Protein-DNA binding in the absence of specific base-pair recognition. 
  • Rapid chiral assembly of rigid DNA building blocks for molecular nanofabrication. 
  • Resolving fast and slow motions in the internal loop containing stem-loop 1 of HIV-1 that are modulated by Mg2+ binding: role in the kissing-duplex structural transition. 
  • Resolving the motional modes that code for RNA adaptation. 
  • Revealing A-T and G-C Hoogsteen base pairs in stressed protein-bound duplex DNA. 
  • Revisiting the Hole Size in Double Helical DNA with Localized Orbital Scaling Corrections. 
  • Robust IR-based detection of stable and fractionally populated G-C+ and A-T Hoogsteen base pairs in duplex DNA. 
  • Signatures of protein-DNA recognition in free DNA binding sites. 
  • Structural basis for impaired 5' processing of a mutant tRNA associated with defects in neuronal homeostasis. 
  • The evolution of homing endonuclease genes and group I introns in nuclear rDNA. 
  • The poly(A) site sequence in HDV RNA alters both extent and rate of self-cleavage of the antigenomic ribozyme. 
  • Thermodynamics of RNA melting, one base pair at a time. 
  • Topology links RNA secondary structure with global conformation, dynamics, and adaptation. 
  • Transcriptional Timers Regulating Mitosis in Early Drosophila Embryos. 
  • Transcriptional regulation of Src homology 2 domain-containing leukocyte phosphoprotein of 76 kDa: dissection of key promoter elements. 
  • Transient Hoogsteen base pairs in canonical duplex DNA. 
  • Understanding the characteristics of nonspecific binding of drug-like compounds to canonical stem-loop RNAs and their implications for functional cellular assays. 
  • Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution. 
  • Visualizing transient Watson-Crick-like mispairs in DNA and RNA duplexes. 
  • Visualizing transient low-populated structures of RNA. 
  • Why are Hoogsteen base pairs energetically disfavored in A-RNA compared to B-DNA? 
  • Widespread transient Hoogsteen base pairs in canonical duplex DNA with variable energetics. 
  • m(1)A and m(1)G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs. 
  • m6A minimally impacts the structure, dynamics, and Rev ARM binding properties of HIV-1 RRE stem IIB.