Nucleic Acid Conformation

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  Subject Areas on Research

  • "Smart" DNA interfaces. 
  • 'Interactive' recognition in EcoRI restriction enzyme-DNA complex. 
  • 1H NMR spectroscopy of DNA. 
  • 2'-O-Methylation can increase the abundance and lifetime of alternative RNA conformational states. 
  • 2'Fluoro Modification Differentially Modulates the Ability of RNAs to Activate Pattern Recognition Receptors. 
  • 3D maps of RNA interhelical junctions. 
  • A 43-nucleotide RNA cis-acting element governs the site-specific formation of the 3' end of a poxvirus late mRNA. 
  • A Novel Genetic Variant in Long Non-coding RNA Gene NEXN-AS1 is Associated with Risk of Lung Cancer. 
  • A cluster of HIV type 1 subtype C sequences from Ethiopia, observed in full genome analysis, is not sustained in subgenomic regions. 
  • A conserved bulged adenosine in a peripheral duplex of the antigenomic HDV self-cleaving RNA reduceskinetic trapping of inactive conformations. 
  • A discrete chromatin loop in the mouse Tcra-Tcrd locus shapes the TCRδ and TCRα repertoires. 
  • A high affinity, antidote-controllable prothrombin and thrombin-binding RNA aptamer inhibits thrombin generation and thrombin activity. 
  • A hybrid DNA aptamer-dendrimer nanomaterial for targeted cell labeling. 
  • A nested double pseudoknot is required for self-cleavage activity of both the genomic and antigenomic hepatitis delta virus ribozymes. 
  • A new assay to quantify in vivo repair of G:T mispairs by base excision repair. 
  • A novel antidote-controlled anticoagulant reduces thrombin generation and inflammation and improves cardiac function in cardiopulmonary bypass surgery. 
  • A pH-sensitive RNA tertiary interaction affects self-cleavage activity of the HDV ribozymes in the absence of added divalent metal ion. 
  • A potentially abundant junctional RNA motif stabilized by m6A and Mg2. 
  • A pseudoknot in the 3' non-core region of the glmS ribozyme enhances self-cleavage activity. 
  • A quantitative model predicts how m6A reshapes the kinetic landscape of nucleic acid hybridization and conformational transitions. 
  • A re-evaluation of 12S ribosomal RNA variability in Drosophila pseudoobscura. 
  • A sequence-specific conformational epitope on U1 RNA is recognized by a unique autoantibody. 
  • A single nucleotide linked to a switch in metal ion reactivity preference in the HDV ribozymes. 
  • A specific 31-nucleotide domain of U1 RNA directly interacts with the 70K small nuclear ribonucleoprotein component. 
  • A structural basis for a phosphoramide mustard-induced DNA interstrand cross-link at 5'-d(GAC). 
  • A structural perspective on the where, how, why, and what of nucleosome positioning. 
  • A toggle duplex in hepatitis delta virus self-cleaving RNA that stabilizes an inactive and a salt-dependent pro-active ribozyme conformation. 
  • A two-state DNA lattice switched by DNA nanoactuator. 
  • A unidirectional DNA walker that moves autonomously along a track. 
  • Activity of a type 1 picornavirus internal ribosomal entry site is determined by sequences within the 3' nontranslated region. 
  • Advances in the determination of nucleic acid conformational ensembles. 
  • An RNA tertiary switch by modifying how helices are tethered. 
  • An antitumor drug-induced topoisomerase cleavage complex blocks a bacteriophage T4 replication fork in vivo. 
  • An autonomously self-assembling dendritic DNA nanostructure for target DNA detection. 
  • Analysis of repetitive sequence elements containing tRNA-like sequences. 
  • Analysis of trans-acting response decoy RNA-mediated inhibition of human immunodeficiency virus type 1 transactivation. 
  • Analytical Debye-Huckel model for electrostatic potentials around dissolved DNA. 
  • Antitermination by bacteriophage lambda Q protein. 
  • Approximate reconstruction of continuous spatially complex domain motions by multialignment NMR residual dipolar couplings. 
  • Argininamide binding arrests global motions in HIV-1 TAR RNA: comparison with Mg2+-induced conformational stabilization. 
  • Assessing potential functionality of catechol-O-methyltransferase (COMT) polymorphisms associated with pain sensitivity and temporomandibular joint disorders. 
  • Assessment of disparate structural features in three models of the hepatitis delta virus ribozyme. 
  • Atomic structures of excited state A-T Hoogsteen base pairs in duplex DNA by combining NMR relaxation dispersion, mutagenesis, and chemical shift calculations. 
  • Autoantibodies specific for U1 RNA and initiator methionine tRNA. 
  • B-DNA to zip-DNA: simulating a DNA transition to a novel structure with enhanced charge-transport characteristics. 
  • Bacteriophage T4 proteins replicate plasmids with a preformed R loop at the T4 ori(uvsY) replication origin in vitro. 
  • Base stacking and molecular polarizability: effect of a methyl group in the 5-position of pyrimidines. 
  • 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. 
  • Beyond static structures of RNA by NMR: folding, refolding, and dynamics at atomic resolution. 
  • Biochemistry. Scaling up DNA computation. 
  • Biophysics of knotting. 
  • Boranophosphate nucleic acids--a versatile DNA backbone. 
  • Boranophosphates as mimics of natural phosphodiesters in DNA. 
  • Boron-containing aptamers to ATP. 
  • Boron-containing oligodeoxyribonucleotide 14mer duplexes: enzymatic synthesis and melting studies. 
  • Breakage of single-stranded DNA by eukaryotic type 1 topoisomerase occurs only at regions with the potential for base-pairing. 
  • Catalytic strategies of the hepatitis delta virus ribozymes. 
  • Cation-Activated Avidity for Rapid Reconfiguration of DNA Nanodevices. 
  • Characterization of long G4-rich enhancer-associated genomic regions engaging in a novel loop:loop 'G4 Kissing' interaction. 
  • Characterization of reaction intermediates of human excision repair nuclease. 
  • Characterizing RNA Excited States Using NMR Relaxation Dispersion. 
  • 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 complex dynamics in the transactivation response element apical loop and motional correlations with the bulge by NMR, molecular dynamics, and mutagenesis. 
  • Characterizing the protonation state of cytosine in transient G·C Hoogsteen base pairs in duplex DNA. 
  • Characterizing the relative orientation and dynamics of RNA A-form helices using NMR residual dipolar couplings. 
  • Chemical rescue, multiple ionizable groups, and general acid-base catalysis in the HDV genomic ribozyme. 
  • Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content. 
  • Chromatin conformation of yeast centromeres 
  • Chromosome aberrations resulting from double-strand DNA breaks at a naturally occurring yeast fragile site composed of inverted ty elements are independent of Mre11p and Sae2p. 
  • Circular ribozymes generated in Escherichia coli using group I self-splicing permuted intron-exon sequences. 
  • Circular transcripts of the testis-determining gene Sry in adult mouse testis. 
  • Cleavage of oligoribonucleotides by a ribozyme derived from the hepatitis delta virus RNA sequence. 
  • Coarse grained models reveal essential contributions of topological constraints to the conformational free energy of RNA bulges. 
  • Cocrystal structure of an editing complex of Klenow fragment with DNA. 
  • Combinatorial and synergistic properties of CaMV 35S enhancer subdomains. 
  • Comparative analysis of LIN28-RNA binding sites identified at single nucleotide resolution. 
  • Comparative studies on the secondary structure of ovalbumin messenger RNA and its complementary DNA transcript. 
  • Comparison of ribosomal DNA ITS regions among geographic isolates of Cenococcum geophilum. 
  • Computational Methods for RNA Structure Validation and Improvement. 
  • Computational approaches for inferring 3D conformations of chromatin from chromosome conformation capture data. 
  • Computational prediction of efficient splice sites for trans-splicing ribozymes. 
  • Concerted motions in HIV-1 TAR RNA may allow access to bound state conformations: RNA dynamics from NMR residual dipolar couplings. 
  • Conformational Dynamics of Mechanically Compliant DNA Nanostructures from Coarse-Grained Molecular Dynamics Simulations. 
  • Conformational studies of dithymidine boranomonophosphate diastereoisomers. 
  • Conformational studies of the nucleic acid binding sites for Xenopus transcription factor IIIA. 
  • Conformational transition of DNA induced by cationic lipid vesicle in acidic solution: spectroscopy investigation. 
  • Constructing RNA dynamical ensembles by combining MD and motionally decoupled NMR RDCs: new insights into RNA dynamics and adaptive ligand recognition. 
  • Constructing atomic-resolution RNA structural ensembles using MD and motionally decoupled NMR RDCs. 
  • Core sequences and a cleavage site wobble pair required for HDV antigenomic ribozyme self-cleavage. 
  • Core-associated non-duplex sequences distinguishing the genomic and antigenomic self-cleaving RNAs of hepatitis delta virus. 
  • Correlation of doxorubicin footprints with deletion endpoints in lacO of E. coli. 
  • Crystal structure and sequence-dependent conformation of the A.G mispaired oligonucleotide d(CGCAAGCTGGCG). 
  • Crystal structure of LacI member, PurR, bound to DNA: minor groove binding by alpha helices. 
  • Crystal structure of an RNA aptamer bound to thrombin. 
  • Crystal structure of the lactose operon repressor and its complexes with DNA and inducer. 
  • Crystal structure of the promutagen O4-methylthymidine: importance of the anti conformation of the O(4) methoxy group and possible mispairing of O4-methylthymidine with guanine. 
  • Crystal structure of the transcription activator BmrR bound to DNA and a drug. 
  • Crystal structures of T. brucei MRP1/MRP2 guide-RNA binding complex reveal RNA matchmaking mechanism. 
  • Cyanobacterial ribosomal RNA genes with multiple, endonuclease-encoding group I introns 
  • DNA base modification: ionized base pairs and mutagenesis. 
  • DNA bending near the replication origin of IncFII plasmid NR1. 
  • DNA mismatch repair: functions and mechanisms. 
  • DNA network structures on various solid substrates investigated by atomic force microscopy. 
  • DNA sequencing: detecting methylation with force. 
  • DNA-Templated Self-Assembly of Protein Arrays and Highly Conductive Nanowires 
  • DNA-XPA interactions: a (31)P NMR and molecular modeling study of dCCAATAACC association with the minimal DNA-binding domain (M98-F219) of the nucleotide excision repair protein XPA. 
  • DNA-templated self-assembly of protein and nanoparticle linear arrays. 
  • DNA: wire or insulator? 
  • DO-RIP-seq to quantify RNA binding sites transcriptome-wide. 
  • Demonstration that Small Molecules can Bind and Stabilize Low-abundance Short-lived RNA Excited Conformational States. 
  • Design and construction of double-decker tile as a route to three-dimensional periodic assembly of DNA. 
  • Detection of DNA looping due to simultaneous interaction of a DNA-binding protein with two spatially separated binding sites on DNA. 
  • Development of universal antidotes to control aptamer activity. 
  • Differentiation and classification of RNA motifs using small molecule-based pattern recognition. 
  • Direct NMR Evidence that Transient Tautomeric and Anionic States in dG·dT Form Watson-Crick-like Base Pairs. 
  • Direct interactions between autoantigen La and human immunodeficiency virus leader RNA. 
  • Directed nucleation assembly of DNA tile complexes for barcode-patterned lattices. 
  • Discovery of Small Molecule Ligands for MALAT1 by Tuning an RNA-Binding Scaffold. 
  • Discrimination of tRNALeu isoacceptors by the insertion mutant of Escherichia coli leucyl-tRNA synthetase. 
  • Disruptive mRNA folding increases translational efficiency of catechol-O-methyltransferase variant. 
  • Dissecting the differences between the alpha and beta anomers of the oxidative DNA lesion FaPydG. 
  • Dissociation of bacteriophage T4 DNA polymerase and its processivity clamp after completion of Okazaki fragment synthesis. 
  • Domain-elongation NMR spectroscopy yields new insights into RNA dynamics and adaptive recognition. 
  • Donor-bridge-acceptor energetics determine the distance dependence of electron tunneling in DNA. 
  • Dramatic mitochondrial gene rearrangements in the hermit crab Pagurus longicarpus (Crustacea, anomura). 
  • Driving factors in amiloride recognition of HIV RNA targets. 
  • Dual stem loops within the poliovirus internal ribosomal entry site control neurovirulence. 
  • Dynamic ensemble of HIV-1 RRE stem IIB reveals non-native conformations that disrupt the Rev-binding site. 
  • Dynamic motions of the HIV-1 frameshift site RNA. 
  • Dynamics of Forced Nucleosome Unraveling and Role of Nonuniform Histone-DNA Interactions 
  • Dynamics of large elongated RNA by NMR carbon relaxation. 
  • Dynamics-based amplification of RNA function and its characterization by using NMR spectroscopy. 
  • EZH2 RIP-seq Identifies Tissue-specific Long Non-coding RNAs. 
  • Effect of DNA conformation on cisplatin adduct formation. 
  • Effects of the Backbone and Chemical Linker on the Molecular Conductance of Nucleic Acid Duplexes. 
  • Efficient and specific repair of sickle beta-globin RNA by trans-splicing ribozymes. 
  • Efficient random subcloning of DNA sheared in a recirculating point-sink flow system. 
  • Electron transfer characteristics of 2'-deoxy-2'-fluoro-arabinonucleic acid, a nucleic acid with enhanced chemical stability. 
  • Electron transfer mechanisms. 
  • Elevated Genome-Wide Instability in Yeast Mutants Lacking RNase H Activity. 
  • Endocarditis in a dog due to infection with a novel Bartonella subspecies. 
  • Energetic contribution of non-essential 5' sequence to catalysis in a hepatitis delta virus ribozyme. 
  • Engineering nanometre-scale coherence in soft matter. 
  • Enzymatic joining of polynucleotides. XI. Reversal of Escherichia coli deoxyribonucleic acid ligase reaction. 
  • Escherichia coli mutS-encoded protein binds to mismatched DNA base pairs. 
  • Escherichia coli phage T4 topoisomerase. 
  • Evaluating group I intron catalytic efficiency in mammalian cells. 
  • Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions. 
  • Evidence that electrostatic interactions dictate the ligand-induced arrest of RNA global flexibility. 
  • Evidence that genomic and antigenomic RNA self-cleaving elements from hepatitis delta virus have similar secondary structures. 
  • Exon circularization in mammalian nuclear extracts. 
  • Expansion of the human mu-opioid receptor gene architecture: novel functional variants. 
  • Experimental evidence for the secondary structure of the hepatitis delta virus ribozyme. 
  • Exposing Hidden High-Affinity RNA Conformational States. 
  • Expression of linear and novel circular forms of an INK4/ARF-associated non-coding RNA correlates with atherosclerosis risk. 
  • Extent of equilibrium perturbation of the DNA helix upon enzymatic methylation of adenine residues. 
  • Fast and compact DNA logic circuits based on single-stranded gates using strand-displacing polymerase. 
  • Flexible histone tails in a new mesoscopic oligonucleosome model. 
  • Flipping of the ribosomal A-site adenines provides a basis for tRNA selection. 
  • Flow linear dichroism and electron microscopic analysis of protein-DNA complexes of a mutant UvrB protein that binds to but cannot kink DNA. 
  • Following an environmental carcinogen N2-dG adduct through replication: elucidating blockage and bypass in a high-fidelity DNA polymerase. 
  • Formation and resolution of DNA catenanes by DNA gyrase. 
  • Formation of supercoiling domains in plasmid pBR322. 
  • Frameworks for targeting RNA with small molecules. 
  • Free energy landscape of salt-actuated reconfigurable DNA nanodevices. 
  • Functional complexity and regulation through RNA dynamics. 
  • G-quadruplex structures trigger RNA phase separation. 
  • Generation of an anticoagulant aptamer that targets factor V/Va and disrupts the FVa-membrane interaction in normal and COVID-19 patient samples. 
  • Generation of nuclease resistant circular RNA decoys for HIV-Tat and HIV-Rev by autocatalytic splicing. 
  • Generation of nuclease resistant circular RNA decoys for HIV-Tat and HIV-Rev by autocatalytic splicing. 
  • Generation of species cross-reactive aptamers using "toggle" SELEX. 
  • Genetic adaptation to untranslated region-mediated enterovirus growth deficits by mutations in the nonstructural proteins 3AB and 3CD. 
  • Genetic control of chromosome length in yeast. 
  • Genetic determinants of cell type-specific poliovirus propagation in HEK 293 cells. 
  • Genetic evidence for preferential strand transfer during meiotic recombination in yeast. 
  • Genetic relationships and evolution of genotypes of yellow fever virus and other members of the yellow fever virus group within the Flavivirus genus based on the 3' noncoding region. 
  • Genetic variation in the 3' non-coding region of dengue viruses. 
  • Genome-wide high-resolution mapping of exosome substrates reveals hidden features in the Arabidopsis transcriptome. 
  • Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape. 
  • Group I permuted intron-exon (PIE) sequences self-splice to produce circular exons. 
  • Guanine to inosine substitution leads to large increases in the population of a transient G·C Hoogsteen base pair. 
  • HDV ribozyme activity in monovalent cations. 
  • HIV-1 leader RNA dimeric interface revealed by NMR. 
  • Hel-N1, an RNA-binding protein, is a ligand for an A + U rich region of the GLUT1 3' UTR. 
  • Hepatitis delta virus ribozymes fold to generate a solvent-inaccessible core with essential nucleotides near the cleavage site phosphate. 
  • Hidden Structural Modules in a Cooperative RNA Folding Transition. 
  • Hierarchy of RNA functional dynamics. 
  • How the EcoRI endonuclease recognizes and cleaves DNA. 
  • Human La antigen is required for the hepatitis C virus internal ribosome entry site-mediated translation. 
  • Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure. 
  • Human nucleotide excision repair protein XPA: NMR spectroscopic studies of an XPA fragment containing the ERCC1-binding region and the minimal DNA-binding domain (M59-F219). 
  • Hybridoma SLE autoantibodies: insights for the pathogenesis of autoimmune disease. 
  • Identification and characterization of an agonistic aptamer against the T cell costimulatory receptor, OX40. 
  • Identification and utilization of arbitrary correlations in models of recombination signal sequences. 
  • Immune activation by bacterial DNA: a new genetic code. 
  • Immunological properties of bacterial DNA. 
  • Impact of static and dynamic A-form heterogeneity on the determination of RNA global structural dynamics using NMR residual dipolar couplings. 
  • In vitro RNA selection identifies RNA ligands that specifically bind to eukaryotic translation initiation factor 4B: the role of the RNA remotif. 
  • In vitro RNA selection of an autoimmune epitope on stem-loop II of U1 RNA. 
  • In vitro selection of an RNA epitope immunologically cross-reactive with a peptide. 
  • In vitro selection of aptamers from RNA libraries. 
  • Incorporation of CC steps into Z-DNA: interplay between B-Z junction and Z-DNA helical formation. 
  • Incorporation of ribonucleoside 5'-(alpha-P-borano)triphosphates into a 20-mer RNA by T7 RNA polymerase. 
  • Increasing occurrences and functional roles for high energy purine-pyrimidine base-pairs in nucleic acids. 
  • Increasing the length of poly-pyrimidine bulges broadens RNA conformational ensembles with minimal impact on stacking energetics. 
  • Increasing the specificity of CRISPR systems with engineered RNA secondary structures. 
  • Infrared Spectroscopic Observation of a G-C+ Hoogsteen Base Pair in the DNA:TATA-Box Binding Protein Complex Under Solution Conditions. 
  • Inhibition of Rev activity and human immunodeficiency virus type 1 replication by antisense oligodeoxynucleotide phosphorothioate analogs directed against the Rev-responsive element. 
  • Inhibition of cell proliferation by an RNA ligand that selectively blocks E2F function. 
  • Initiation of methyl-directed mismatch repair. 
  • Insight into F plasmid DNA segregation revealed by structures of SopB and SopB-DNA complexes. 
  • Insights into Watson-Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A. 
  • Instability of a plasmid-borne inverted repeat in Saccharomyces cerevisiae. 
  • Interactions of TLC1 (which encodes the RNA subunit of telomerase), TEL1, and MEC1 in regulating telomere length in the yeast Saccharomyces cerevisiae. 
  • Internal ribosomal entry site substitution eliminates neurovirulence in intergeneric poliovirus recombinants. 
  • Intrachromosomal gene conversion and the maintenance of sequence homogeneity among repeated genes. 
  • Intronic enhancers coordinate epithelial-specific looping of the active CFTR locus. 
  • Investigation of the influence on conformational transition of DNA induced by cationic lipid vesicles. 
  • Invisible RNA state dynamically couples distant motifs. 
  • Involvement of a cytosine side chain in proton transfer in the rate-determining step of ribozyme self-cleavage. 
  • Iron-dependent regulation of the divalent metal ion transporter. 
  • Is there left-handed DNA at the ends of yeast chromosomes? 
  • Isolation and characterization of the replicon of a Thiobacillus intermedius plasmid. 
  • Isolation of a nuclease-resistant decoy RNA that selectively blocks autoantibody binding to insulin receptors on human lymphocytes. 
  • Knotty Zika Virus Blocks Exonuclease to Produce Subgenomic Flaviviral RNAs. 
  • Left-handed DNA helices, supercoiling, and the B-Z junction. 
  • Liposome-mediated conformation transition of DNA detected by molecular probe: methyl green. 
  • Logical computation using algorithmic self-assembly of DNA triple-crossover molecules. 
  • Low enzymatic activity haplotypes of the human catechol-O-methyltransferase gene: enrichment for marker SNPs. 
  • MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes. 
  • Measurements of a large anisotropy in the swelling of oriented DNA films in aqueous solution. 
  • Measuring similarity between dynamic ensembles of biomolecules. 
  • Measuring thermodynamic preferences to form non-native conformations in nucleic acids using ultraviolet melting. 
  • Mechanism of corepressor-mediated specific DNA binding by the purine repressor. 
  • Meiotic recombination involving heterozygous large insertions in Saccharomyces cerevisiae: formation and repair of large, unpaired DNA loops. 
  • Messenger RNA intron in the nuclear 18s ribosomal RNA gene of deuteromycetes. 
  • Mg2+-induced variations in the conformation and dynamics of HIV-1 TAR RNA probed using NMR residual dipolar couplings. 
  • MicroRNAs both promote and antagonize longevity in C. elegans. 
  • Microwave-field-driven acoustic modes in DNA. 
  • Mismatch-, MutS-, MutL-, and helicase II-dependent unwinding from the single-strand break of an incised heteroduplex. 
  • Mismatch-containing oligonucleotide duplexes bound by the E. coli mutS-encoded protein. 
  • Mismodeled purines: implicit alternates and hidden Hoogsteens. 
  • Mitochondrial DNA structure and expression in specialized subtypes of mammalian striated muscle. 
  • Mitochondrial mutations in adenoid cystic carcinoma of the salivary glands. 
  • Mode of Action of a Designed Antimicrobial Peptide: High Potency against Cryptococcus neoformans. 
  • Modulating RNA Alignment Using Directional Dynamic Kinks: Application in Determining an Atomic-Resolution Ensemble for a Hairpin using NMR Residual Dipolar Couplings. 
  • Modulation of Hoogsteen dynamics on DNA recognition. 
  • MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. 
  • Molecular biology. Versatility of self-cleaving ribozymes. 
  • Molecular interactions and residues involved in force generation in the T4 viral DNA packaging motor. 
  • Molecular mechanisms of HipA-mediated multidrug tolerance and its neutralization by HipB. 
  • Multiassay Profiling of a Focused Small Molecule Library Reveals Predictive Bidirectional Modulation of the lncRNA MALAT1 Triplex Stability In Vitro . 
  • Multifactorial determinants of protein expression in prokaryotic open reading frames. 
  • Multiple forms of rat liver type I topoisomerase. 
  • Multiple hybrid formation in natural populations: concerted evolution of the internal transcribed spacer of nuclear ribosomal DNA (ITS) in North American Arabis divaricarpa (Brassicaceae). 
  • MutS mediates heteroduplex loop formation by a translocation mechanism. 
  • Mutagenic processing of ribonucleotides in DNA by yeast topoisomerase I. 
  • Mutations within the mepA operator affect binding of the MepR regulatory protein and its induction by MepA substrates in Staphylococcus aureus. 
  • N(6)-Methyladenosine Modification in a Long Noncoding RNA Hairpin Predisposes Its Conformation to Protein Binding. 
  • N6-methyladenosine alters RNA structure to regulate binding of a low-complexity protein. 
  • N6-methyladenosine modification of hepatitis B virus RNA differentially regulates the viral life cycle. 
  • NF-κB- and AP-1-mediated DNA looping regulates osteopontin transcription in endotoxin-stimulated murine macrophages. 
  • NMR and XAS reveal an inner-sphere metal binding site in the P4 helix of the metallo-ribozyme ribonuclease P. 
  • NMR studies of RNA dynamics and structural plasticity using NMR residual dipolar couplings. 
  • NMR studies of nucleic acid dynamics. 
  • Nature of the 3'-terminal sequences of the plus and minus strands of the S1 gene of reovirus serotypes 1, 2 and 3. 
  • 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. 
  • Non-coding RNA prediction and verification in Saccharomyces cerevisiae. 
  • Noncanonical secondary structure stabilizes mitochondrial tRNA(Ser(UCN)) by reducing the entropic cost of tertiary folding. 
  • Norfloxacin-induced DNA gyrase cleavage complexes block Escherichia coli replication forks, causing double-stranded breaks in vivo. 
  • Novel circular DNA viruses in stool samples of wild-living chimpanzees. 
  • Nucleosome structure. 
  • Nucleotide sequences of the RNA subunit of RNase P from several mammals. 
  • Numerous group I introns with variable distributions in the ribosomal DNA of a lichen fungus. 
  • One binding site determines sequence specificity of Tetrahymena pre-rRNA self-splicing, trans-splicing, and RNA enzyme activity. 
  • Optimal self-cleavage activity of the hepatitis delta virus RNA is dependent on a homopurine base pair in the ribozyme core. 
  • Optimizing the substrate specificity of a group I intron ribozyme. 
  • Origin of overstretching transitions in single-stranded nucleic acids. 
  • PNA versus DNA: effects of structural fluctuations on electronic structure and hole-transport mechanisms. 
  • Palindromic sequences in heteroduplex DNA inhibit mismatch repair in yeast. 
  • Parallel molecular computations of pairwise exclusive-or (XOR) using DNA "string tile" self-assembly. 
  • Pervasive tertiary structure in the dengue virus RNA genome. 
  • Phospho-MED1-enhanced UBE2C locus looping drives castration-resistant prostate cancer growth. 
  • Physical detection of heteroduplexes during meiotic recombination in the yeast Saccharomyces cerevisiae. 
  • Plasmid DNA network on a mica substrate investigated by atomic force microscopy. 
  • Predicted group II intron lineages E and F comprise catalytically active ribozymes. 
  • Primary sequence of ovomucoid messenger RNA as determined from cloned complementary DNA. 
  • Probing Na(+)-induced changes in the HIV-1 TAR conformational dynamics using NMR residual dipolar couplings: new insights into the role of counterions and electrostatic interactions in adaptive recognition. 
  • Probing RNA Conformational Equilibria within the Functional Cellular Context. 
  • Probing RNA Structure in Liquid-Liquid Phase Separation Using SHAPE-MaP. 
  • Probing conformational transitions towards mutagenic Watson-Crick-like G·T mismatches using off-resonance sugar carbon R1ρ relaxation dispersion. 
  • Probing motions between equivalent RNA domains using magnetic field induced residual dipolar couplings: accounting for correlations between motions and alignment. 
  • Probing sequence-specific DNA flexibility in a-tracts and pyrimidine-purine steps by nuclear magnetic resonance (13)C relaxation and molecular dynamics simulations. 
  • Probing the architecture of the B. subtilis RNase P holoenzyme active site by cross-linking and affinity cleavage. 
  • Probing the interplay between the two steps of group I intron splicing: competition of exogenous guanosine with omega G. 
  • Probing transient Hoogsteen hydrogen bonds in canonical duplex DNA using NMR relaxation dispersion and single-atom substitution. 
  • Programmable Site-Specific Functionalization of DNA Origami with Polynucleotide Brushes. 
  • Programmable Transformations of DNA Origami Made of Small Modular Dynamic Units. 
  • Programming DNA tube circumferences. 
  • Protein-DNA binding in the absence of specific base-pair recognition. 
  • Protein-DNA conformational changes in the crystal structure of a lambda Cro-operator complex. 
  • Proton nuclear magnetic resonance assignments and structural characterization of an intramolecular DNA triplex. 
  • Pulling geometry-induced errors in single molecule force spectroscopy measurements. 
  • Quadruplex DNA formation in a region of the tRNA gene supF associated with hydrogen peroxide mediated mutations. 
  • Quantification of DNA cleavage specificity in Hi-C experiments. 
  • Quantitative determination that one of two potential RNA-binding domains of the A protein component of the U1 small nuclear ribonucleoprotein complex binds with high affinity to stem-loop II of U1 RNA. 
  • Quantitative modeling of transcription factor binding specificities using DNA shape. 
  • Quasielastic light scattering by biopolymers. Conformation of chromatin multimers. 
  • RNA Structural Differentiation: Opportunities with Pattern Recognition. 
  • RNA Structural Modules Control the Rate and Pathway of RNA Folding and Assembly. 
  • RNA aptamer blockade of osteopontin inhibits growth and metastasis of MDA-MB231 breast cancer cells. 
  • RNA aptamer-based functional ligands of the neurotrophin receptor, TrkB. 
  • RNA aptamers as reversible antagonists of coagulation factor IXa. 
  • RNA backbone is rotameric. 
  • RNA backbone rotamers--finding your way in seven dimensions. 
  • RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution). 
  • RNA conformational propensities determine cellular activity. 
  • RNA dynamics by design: biasing ensembles towards the ligand-bound state. 
  • RNA dynamics: it is about time. 
  • RNA surfaces as functional mimetics of proteins. 
  • RNA-DNA hybrid formation at a bacteriophage T4 replication origin. 
  • RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone. 
  • RNase H activation by stereoregular boranophosphate oligonucleotide. 
  • Rapid chiral assembly of rigid DNA building blocks for molecular nanofabrication. 
  • Recognition of U1 and U2 small nuclear RNAs can be altered by a 5-amino-acid segment in the U2 small nuclear ribonucleoprotein particle (snRNP) B" protein and through interactions with U2 snRNP-A' protein. 
  • Recognition of single-stranded DNA by the bacteriophage T4-induced type II topoisomerase. 
  • Referencing strategy for the direct comparison of nuclear magnetic resonance and molecular dynamics motional parameters in RNA. 
  • Regulatable aptamers in medicine: focus on antithrombotic strategies. 
  • Regulation of MALAT1 triple helix stability and in vitro degradation by diphenylfurans. 
  • Regulation of TCRβ allelic exclusion by gene segment proximity and accessibility. 
  • Removal of N-6-methyladenine by the nucleotide excision repair pathway triggers the repair of mismatches in yeast gap-repair intermediates. 
  • Repair of DNA loops involves DNA-mismatch and nucleotide-excision repair proteins. 
  • Replicating circular DNA molecules in yeast. 
  • Requirement of helix P2.2 and nucleotide G1 for positioning the cleavage site and cofactor of the glmS ribozyme. 
  • 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 sugar puckers in RNA excited states exposes slow modes of repuckering dynamics. 
  • Resolving the motional modes that code for RNA adaptation. 
  • Retargeting mobile group II introns to repair mutant genes. 
  • Revealing A-T and G-C Hoogsteen base pairs in stressed protein-bound duplex DNA. 
  • Ribosome exchange revisited: a mechanism for translation-coupled ribosome detachment from the ER membrane. 
  • Ribozyme activity in the genomic and antigenomic RNA strands of hepatitis delta virus. 
  • Robust IR-based detection of stable and fractionally populated G-C+ and A-T Hoogsteen base pairs in duplex DNA. 
  • Role of Conformational Fluctuations of Protein toward Methylation in DNA by Cytosine-5-methyltransferase. 
  • Role of histone tails in chromatin folding revealed by a mesoscopic oligonucleosome model. 
  • Role of nucleobase energetics and nucleobase interactions in single-stranded peptide nucleic acid charge transfer. 
  • SHAPE reveals transcript-wide interactions, complex structural domains, and protein interactions across the Xist lncRNA in living cells. 
  • Schematic drawings of protein structures. 
  • Secondary structure creates mismatched base pairs required for high-affinity binding of cAMP response element-binding protein to the human enkephalin enhancer. 
  • Secondary structure encodes a cooperative tertiary folding funnel in the Azoarcus ribozyme. 
  • Secondary structure of ovalbumin messenger RNA. 
  • Secondary structure of the self-cleaving RNA of hepatitis delta virus: applications to catalytic RNA design. 
  • Selection of an RNA molecule that mimics a major autoantigenic epitope of human insulin receptor. 
  • Selection of circularization sites in a group I IVS RNA requires multiple alignments of an internal template-like sequence. 
  • Selection of heptapeptides that bind helix 69 of bacterial 23S ribosomal RNA. 
  • Selection of peptides that target the aminoacyl-tRNA site of bacterial 16S ribosomal RNA. 
  • Self-cleavage of hepatitis delta virus genomic strand RNA is enhanced under partially denaturing conditions. 
  • Self-cleaving ribozymes of hepatitis delta virus RNA. 
  • Sensing the impact of environment on small molecule differentiation of RNA sequences. 
  • Sensitive and precise quantification of insulin-like mRNA expression in Caenorhabditis elegans. 
  • Seven-base-pair inverted repeats in DNA form stable hairpins in vivo in Saccharomyces cerevisiae. 
  • Shortening the HIV-1 TAR RNA Bulge by a Single Nucleotide Preserves Motional Modes over a Broad Range of Time Scales. 
  • Single transcriptional and translational preQ1 riboswitches adopt similar pre-folded ensembles that follow distinct folding pathways into the same ligand-bound structure. 
  • Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α. 
  • Site on the vesicular stomatitis virus genome specifying polyadenylation and the end of the L gene mRNA. 
  • Sites of circularization of the Tetrahymena rRNA IVS are determined by sequence and influenced by position and secondary structure. 
  • Sites of copy choice replication involved in generation of vesicular stomatitis virus defective-interfering particle RNAs. 
  • Size and structure of yeast chromosomal DNA. 
  • SlmA forms a higher-order structure on DNA that inhibits cytokinetic Z-ring formation over the nucleoid. 
  • Small Molecule-Based Pattern Recognition To Classify RNA Structure. 
  • Small molecule targeting of biologically relevant RNA tertiary and quaternary structures. 
  • Small molecule-RNA targeting: starting with the fundamentals. 
  • Solution structure of a pyrimidine-purine-pyrimidine triplex containing the sequence-specific intercalating non-natural base D3. 
  • Solution structure of the core NFATC1/DNA complex. 
  • Statistical analysis of RNA backbone. 
  • Stepwise self-assembly of DNA tile lattices using dsDNA bridges. 
  • Steric Communication between Dynamic Components on DNA Nanodevices. 
  • Stimulation of thymocyte proliferation by phosphorothioate DNA oligonucleotides. 
  • Structural and Dynamic Basis for Low-Affinity, High-Selectivity Binding of L-Glutamine by the Glutamine Riboswitch. 
  • Structural basis for cooperative DNA binding by two dimers of the multidrug-binding protein QacR. 
  • Structural basis for impaired 5' processing of a mutant tRNA associated with defects in neuronal homeostasis. 
  • Structural basis of DNA-protein recognition. 
  • Structural basis of core promoter recognition in a primitive eukaryote. 
  • Structural biology of plasmid partition: uncovering the molecular mechanisms of DNA segregation. 
  • Structural biology: Aerial view of the HIV genome. 
  • Structural comparison of the free and DNA-bound forms of the purine repressor DNA-binding domain. 
  • Structural dynamics of a single-stranded RNA-helix junction using NMR. 
  • Structural mechanism of transcription regulation of the Staphylococcus aureus multidrug efflux operon mepRA by the MarR family repressor MepR. 
  • Structural plasticity and Mg2+ binding properties of RNase P P4 from combined analysis of NMR residual dipolar couplings and motionally decoupled spin relaxation. 
  • Structure of DNA in DNA replication mutants of yeast. 
  • Structure of a G.T.A triplet in an intramolecular DNA triplex. 
  • Structure of a Z-DNA with two different backbone chain conformations. Stabilization of the decadeoxyoligonucleotide d(CGTACGTACG) by [Co(NH3)6]3+ binding to the guanine. 
  • Structure of a tethered cationic 3-aminopropyl chain incorporated into an oligodeoxynucleotide: evidence for 3'-orientation in the major groove accompanied by DNA bending. 
  • Structure-first identification of RNA elements that regulate dengue virus genome architecture and replication. 
  • Structures involved in Tetrahymena rRNA self-splicing and RNA enzyme activity. 
  • Structures of MERS1, the 5' processing enzyme of mitochondrial mRNAs in Trypanosoma brucei. 
  • Structures of ParB bound to DNA reveal mechanism of partition complex formation. 
  • Structures of archaeal DNA segregation machinery reveal bacterial and eukaryotic linkages. 
  • Structures of the bacterial ribosome in classical and hybrid states of tRNA binding. 
  • Structures of the nucleoid occlusion protein SlmA bound to DNA and the C-terminal domain of the cytoskeletal protein FtsZ. 
  • Structures of the pleiotropic translational regulator Hfq and an Hfq-RNA complex: a bacterial Sm-like protein. 
  • Studies on sequence recognition by type II restriction and modification enzymes. 
  • Surface-enhanced Raman scattering plasmonic enhancement using DNA origami-based complex metallic nanostructures. 
  • Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits. 
  • Synergistic effect of aptamers that inhibit exosites 1 and 2 on thrombin. 
  • Systemic administration of optimized aptamer-siRNA chimeras promotes regression of PSMA-expressing tumors. 
  • TFBSshape: a motif database for DNA shape features of transcription factor binding sites. 
  • Targeting RNA with small molecules: from fundamental principles towards the clinic. 
  • Targeting Two Coagulation Cascade Proteases with a Bivalent Aptamer Yields a Potent and Antidote-Controllable Anticoagulant. 
  • Tethering telomeric double- and single-stranded DNA-binding proteins inhibits telomere elongation. 
  • The 5'-untranslated region of the N-methyl-D-aspartate receptor NR2A subunit controls efficiency of translation. 
  • The Binding of Monoclonal and Polyclonal Anti-Z-DNA Antibodies to DNA of Various Species Origin. 
  • The Control Centers of Biomolecular Phase Separation: How Membrane Surfaces, PTMs, and Active Processes Regulate Condensation. 
  • The DEXH protein product of the DHX36 gene is the major source of tetramolecular quadruplex G4-DNA resolving activity in HeLa cell lysates. 
  • The Elusive 5'-Deoxyadenosyl Radical: Captured and Characterized by Electron Paramagnetic Resonance and Electron Nuclear Double Resonance Spectroscopies. 
  • The LINK-A lncRNA interacts with PtdIns(3,4,5)P3 to hyperactivate AKT and confer resistance to AKT inhibitors. 
  • The MerR-like protein BldC binds DNA direct repeats as cooperative multimers to regulate Streptomyces development. 
  • The Nuclear Pore Complex in Cell Type-Specific Chromatin Structure and Gene Regulation. 
  • The Staphylococcus aureus pSK41 plasmid-encoded ArtA protein is a master regulator of plasmid transmission genes and contains a RHH motif used in alternate DNA-binding modes. 
  • The U1 RNA-binding site of the U1 small nuclear ribonucleoprotein (snRNP)-associated A protein suggests a similarity with U2 snRNPs. 
  • The colorectal microRNAome. 
  • The complete genome sequence, organization and affinities of carrot red leaf virus. 
  • The crystal structure of the TetR family transcriptional repressor SimR bound to DNA and the role of a flexible N-terminal extension in minor groove binding. 
  • The deafness-associated mitochondrial DNA mutation at position 7445, which affects tRNASer(UCN) precursor processing, has long-range effects on NADH dehydrogenase subunit ND6 gene expression. 
  • The effect of a single boranophosphate substitution with defined configuration on the thermal stability and conformation of a DNA duplex. 
  • The helix-turn-helix DNA binding motif. 
  • The hydrogen bonding of cytosine with guanine: calorimetric and 1H-nmr analysis of the molecular interactions of nucleic acid bases. 
  • The large subunit of the mammalian mitochondrial ribosome. Analysis of the complement of ribosomal proteins present. 
  • The mechanism of the translocation step in DNA replication by DNA polymerase I: a computer simulation analysis. 
  • The pattern of gene amplification is determined by the chromosomal location of hairpin-capped breaks. 
  • The plus strand of reovirus gene S2 is identical with its in vitro transcript. 
  • The poly(A) site sequence in HDV RNA alters both extent and rate of self-cleavage of the antigenomic ribozyme. 
  • The role of lysine 55 in determining the specificity of the purine repressor for its operators through minor groove interactions. 
  • The single-molecule conductance and electrochemical electron-transfer rate are related by a power law. 
  • The small subunit of the mammalian mitochondrial ribosome. Identification of the full complement of ribosomal proteins present. 
  • The structural mechanism for transcription activation by MerR family member multidrug transporter activation, N terminus. 
  • The structural organization of the chicken calmodulin gene. 
  • The structure of PurR mutant L54M shows an alternative route to DNA kinking. 
  • The winged-helix DNA-binding motif: another helix-turn-helix takeoff. 
  • Therapeutic aptamers and antidotes: a novel approach to safer drug design. 
  • Three-Helix Bundle DNA Tiles Self-Assemble into 2D Lattice or 1D Templates for Silver Nanowires. 
  • Tissue-specific expression from CaMV 35S enhancer subdomains in early stages of plant development. 
  • Topological constraints are major determinants of tRNA tertiary structure and dynamics and provide basis for tertiary folding cooperativity. 
  • Topological constraints: using RNA secondary structure to model 3D conformation, folding pathways, and dynamic adaptation. 
  • Topology links RNA secondary structure with global conformation, dynamics, and adaptation. 
  • Towards structural genomics of RNA: rapid NMR resonance assignment and simultaneous RNA tertiary structure determination using residual dipolar couplings. 
  • Trans-activating rev protein of the human immunodeficiency virus 1 interacts directly and specifically with its target RNA. 
  • Trans-splicing reactions by ribozymes. 
  • Transcription Factor-Directed Re-wiring of Chromatin Architecture for Somatic Cell Nuclear Reprogramming toward trans-Differentiation. 
  • Transcription of orthopoxvirus telomeres at late times during infection. 
  • Transcription of the terminal loop region of vaccinia virus DNA is initiated from the telomere sequences directing DNA resolution. 
  • Translation by the adenovirus tripartite leader: elements which determine independence from cap-binding protein complex. 
  • Triplet repeats form secondary structures that escape DNA repair in yeast. 
  • Twist propagation in dinucleosome arrays. 
  • Understanding the Contributions of Conformational Changes, Thermodynamics, and Kinetics of RNA-Small Molecule Interactions. 
  • Understanding the characteristics of nonspecific binding of drug-like compounds to canonical stem-loop RNAs and their implications for functional cellular assays. 
  • Unraveling the structural complexity in a single-stranded RNA tail: implications for efficient ligand binding in the prequeuosine riboswitch. 
  • Unveiling Inherent Degeneracies in Determining Population-Weighted Ensembles of Interdomain Orientational Distributions Using NMR Residual Dipolar Couplings: Application to RNA Helix Junction Helix Motifs. 
  • Using DNA duplex stability information for transcription factor binding site discovery. 
  • Using secondary structure to identify ribosomal numts: cautionary examples from the human genome. 
  • Utility of 1H NMR chemical shifts in determining RNA structure and dynamics. 
  • UvsW protein regulates bacteriophage T4 origin-dependent replication by unwinding R-loops. 
  • Variable helix elongation as a tool to modulate RNA alignment and motional couplings. 
  • Visualizing RNA Conformational Changes via Pattern Recognition of RNA by Small Molecules. 
  • Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms. 
  • Visualizing spatially correlated dynamics that directs RNA conformational transitions. 
  • Visualizing the formation of an RNA folding intermediate through a fast highly modular secondary structure switch. 
  • Visualizing transient low-populated structures of RNA. 
  • Why are Hoogsteen base pairs energetically disfavored in A-RNA compared to B-DNA? 
  • Widespread occurrence of spliceosomal introns in the rDNA genes of ascomycetes. 
  • Widespread transient Hoogsteen base pairs in canonical duplex DNA with variable energetics. 
  • Wrestling with Chromosomes: The Roles of SUMO During Meiosis. 
  • X-ray structure of cytidine-5'-O-dimethylphosphate. Novel stacking between the ribosyl O(2') hydroxyl oxygen atom and the base. 
  • iRED analysis of TAR RNA reveals motional coupling, long-range correlations, and a dynamical hinge. 
  • m6A minimally impacts the structure, dynamics, and Rev ARM binding properties of HIV-1 RRE stem IIB. 
  • mRNA structure determines specificity of a polyQ-driven phase separation. 
• 

  Keywords of People

  • Erickson, Harold Paul, James B. Duke Distinguished Professor Emeritus, Cell Biology
  • Gordan, Raluca Mihaela, Associate Professor in Biostatistics & Bioinformatics, Computer Science
  • Hartemink, Alexander J., Professor in the Department of Computer Science, Biology
  • Krangel, Michael S., George Barth Geller Distinguished Professor of Immunology, Integrative Immunobiology
  • Richardson, David C., Professor Emeritus of Biochemistry, Biochemistry
  • Shinohara, Mari L., Professor of Integrative Immunobiology, Cell Biology