2020
Assembly of a DNA Origami Chinese Knot by Only 15% of the Staple Strands
He K, Li Z, Liu L, Zheng M, Mao C. Assembly of a DNA Origami Chinese Knot by Only 15% of the Staple Strands. ChemBioChem 2020, 21: 2132-2136. PMID: 32196869, DOI: 10.1002/cbic.202000106.Peer-Reviewed Original Research
2018
DNA melting initiates the RAG catalytic pathway
Ru H, Mi W, Zhang P, Alt FW, Schatz DG, Liao M, Wu H. DNA melting initiates the RAG catalytic pathway. Nature Structural & Molecular Biology 2018, 25: 732-742. PMID: 30061602, PMCID: PMC6080600, DOI: 10.1038/s41594-018-0098-5.Peer-Reviewed Original ResearchConceptsRecombination signal sequencesDNA meltingCryo-EM structureBase-specific contactsSignal sequenceDNA transpositionSubstrate bindingRetroviral integrationRAG endonucleaseDimer openingTerminal sequenceGTG sequenceDNA cleavageScissile phosphateDNAUniversal mechanismPiston-like movementSequenceActive siteHeptamerRetrotransposonsCatalytic pathwayTransposonComplexesEndonuclease
2012
Formation of triple-helical structures by the 3′-end sequences of MALAT1 and MENβ noncoding RNAs
Brown JA, Valenstein ML, Yario TA, Tycowski KT, Steitz JA. Formation of triple-helical structures by the 3′-end sequences of MALAT1 and MENβ noncoding RNAs. Proceedings Of The National Academy Of Sciences Of The United States Of America 2012, 109: 19202-19207. PMID: 23129630, PMCID: PMC3511071, DOI: 10.1073/pnas.1217338109.Peer-Reviewed Original ResearchConceptsRich internal loopMetastasis-associated lung adenocarcinoma transcript 1Rich tractSarcoma-associated herpesvirusDuplex-triplex junctionsTriple helical structureCellular noncoding RNAsNuclear retention elementBase triplesInternal loopKaposi's sarcoma-associated herpesvirusU base triplesPAN RNATriple helixNoncoding RNAsNuclear RNAThermal denaturation profilesReporter RNALung adenocarcinoma transcript 1C nucleotidesC base pairsMolecular mechanismsUnpaired nucleotidesBase pairsRNA
2010
Pathway of ATP utilization and duplex rRNA unwinding by the DEAD-box helicase, DbpA
Henn A, Cao W, Licciardello N, Heitkamp SE, Hackney DD, De La Cruz EM. Pathway of ATP utilization and duplex rRNA unwinding by the DEAD-box helicase, DbpA. Proceedings Of The National Academy Of Sciences Of The United States Of America 2010, 107: 4046-4050. PMID: 20160110, PMCID: PMC2840157, DOI: 10.1073/pnas.0913081107.Peer-Reviewed Original Research
2005
A Nuclear Magnetic Resonance Investigation of the Energetics of Basepair Opening Pathways in DNA
Coman D, Russu IM. A Nuclear Magnetic Resonance Investigation of the Energetics of Basepair Opening Pathways in DNA. Biophysical Journal 2005, 89: 3285-3292. PMID: 16126830, PMCID: PMC1366824, DOI: 10.1529/biophysj.105.065763.Peer-Reviewed Original ResearchConceptsOpening reactionFree energyNuclear magnetic resonance investigationFree energy relationshipsMagnetic resonance investigationNMR spectroscopySolvent protonsProton exchangeEnergy relationshipsTransition stateExchange catalystResonance investigationOpening pathwaysRate of exchangeEquilibrium constantsEnthalpy changeDNA duplexImino protonsReactionNeighboring basesProtonsDifferent temperaturesEnergeticsOpen stateCatalyst
2004
Estimating the relative risk of developing melanoma in INK4A carriers
Berwick M, Orlow I, Mahabir S, Myskowski P, Coit D, Brady M, Roy P, Song Y, Canchola R, Barz A, Halpern A, Bolognia J, Eng S, Elahi A, Begg C. Estimating the relative risk of developing melanoma in INK4A carriers. European Journal Of Cancer Prevention 2004, 13: 65-70. PMID: 15075790, DOI: 10.1097/00008469-200402000-00010.Peer-Reviewed Original ResearchMeSH KeywordsAdolescentAdultCase-Control StudiesChromatography, LiquidCyclin-Dependent Kinase Inhibitor p16FemaleGerm-Line MutationHumansMaleMelanomaMiddle AgedNeoplasms, Multiple PrimaryNevusNucleic Acid DenaturationOdds RatioPilot ProjectsPolymerase Chain ReactionPrevalenceRisk FactorsSkin NeoplasmsSurveys and QuestionnairesConceptsRisk factorsRelative riskMemorial Sloan-Kettering Cancer CenterStudy designSingle primaryCancer risk factorsMultiple primary melanomasRisk of melanomaNumber of neviPigmented lesion clinicNovel study designRare germline mutationsDermatology clinicCancer CenterNew study designsPrimary melanomaLesion clinicHigh prevalencePrimary casesPatientsMultiple primariesMelanomaGermline mutationsPilot studyFair skin
2003
An Alternative Route for the Folding of Large RNAs: Apparent Two-state Folding by a Group II Intron Ribozyme
Su LJ, Brenowitz M, Pyle AM. An Alternative Route for the Folding of Large RNAs: Apparent Two-state Folding by a Group II Intron Ribozyme. Journal Of Molecular Biology 2003, 334: 639-652. PMID: 14636593, DOI: 10.1016/j.jmb.2003.09.071.Peer-Reviewed Original Research
2001
Improvements in cytogenetic slide preparation: Controlled chromosome spreading, chemical aging and gradual denaturing
Henegariu O, Heerema N, Wright L, Bray‐Ward P, Ward D, Vance G. Improvements in cytogenetic slide preparation: Controlled chromosome spreading, chemical aging and gradual denaturing. Cytometry 2001, 43: 101-109. PMID: 11169574, DOI: 10.1002/1097-0320(20010201)43:2<101::aid-cyto1024>3.0.co;2-8.Peer-Reviewed Original ResearchMeSH KeywordsCell LineCentrifugationChromosome BandingChromosome PaintingDNADNA, NeoplasmHumansIn Situ Hybridization, FluorescenceNucleic Acid DenaturationTumor Cells, CulturedConceptsComparative genomic hybridizationClassical banding techniquesSitu hybridization applicationsChromosomal integrityChromosome spreadsMultiplex FISHMolecular cytogeneticsFISH applicationsChromosome spreadingFISH techniqueGenomic hybridizationEnvironmental conditionsSitu hybridizationBanding techniquesChromosomesHybridizationReproducible protocolFISH resultsCytogenetic slidesCell suspensionsSlide preparationFishMetaphase
1999
Triplex Formation by Oligonucleotides Containing 5-(1-Propynyl)-2‘-deoxyuridine: Decreased Magnesium Dependence and Improved Intracellular Gene Targeting †
Lacroix L, Lacoste J, Reddoch J, Mergny J, Levy D, Seidman M, Matteucci M, Glazer P. Triplex Formation by Oligonucleotides Containing 5-(1-Propynyl)-2‘-deoxyuridine: Decreased Magnesium Dependence and Improved Intracellular Gene Targeting †. Biochemistry 1999, 38: 1893-1901. PMID: 10026270, DOI: 10.1021/bi982290q.Peer-Reviewed Original Research
1998
N2-Methylguanosine is iso-energetic with guanosine in RNA duplexes and GNRA tetraloops
Rife J, Cheng C, Moore P, Strobel S. N2-Methylguanosine is iso-energetic with guanosine in RNA duplexes and GNRA tetraloops. Nucleic Acids Research 1998, 26: 3640-3644. PMID: 9685477, PMCID: PMC147776, DOI: 10.1093/nar/26.16.3640.Peer-Reviewed Original ResearchMeSH KeywordsBase CompositionBase SequenceGuanosineMagnetic Resonance SpectroscopyNucleic Acid ConformationNucleic Acid DenaturationRNAThermodynamicsConceptsM2GGNRA tetraloopRNA duplexesG substitutionSecondary structural stabilityHypermethylated regionsRNA structureNatural RNAPossible functionsRNAWatson-Crick pairsTetraloopNucleotidesN2-methylguanosineRibosomesRRNADuplexMethylationThermodynamic consequencesSubstitutionWide varietyDuplex stabilityPairsFunctionGuanosine
1997
UvrAB activity at a damaged DNA site: is unpaired DNA present?
Gordienko I, Rupp W. UvrAB activity at a damaged DNA site: is unpaired DNA present? The EMBO Journal 1997, 16: 880-888. PMID: 9049316, PMCID: PMC1169688, DOI: 10.1093/emboj/16.4.880.Peer-Reviewed Original ResearchMeSH Keywords2-AcetylaminofluoreneAdenosine TriphosphatasesBacterial ProteinsDNA AdductsDNA DamageDNA HelicasesDNA RepairDNA-Binding ProteinsDNA, Single-StrandedEndodeoxyribonucleasesEscherichia coliEscherichia coli ProteinsModels, GeneticMutationNucleic Acid ConformationNucleic Acid DenaturationOligodeoxyribonucleotides
1995
A DNA enzyme with Mg2+-dependent RNA phosphoesterase activity
Breaker R, Joyce G. A DNA enzyme with Mg2+-dependent RNA phosphoesterase activity. Cell Chemical Biology 1995, 2: 655-660. PMID: 9383471, DOI: 10.1016/1074-5521(95)90028-4.Peer-Reviewed Original Research
1994
Replacement of the conserved G.U with a G-C pair at the cleavage site of the Tetrahymena ribozyme decreases binding, reactivity, and fidelity.
Pyle AM, Moran S, Strobel SA, Chapman T, Turner DH, Cech TR. Replacement of the conserved G.U with a G-C pair at the cleavage site of the Tetrahymena ribozyme decreases binding, reactivity, and fidelity. Biochemistry 1994, 33: 13856-63. PMID: 7947794, DOI: 10.1021/bi00250a040.Peer-Reviewed Original Research
1993
Synthesis and properties of adenosine oligonucleotide analogues containing methylene groups in place of phosphodiester 5'-oxygens.
Breaker R, Gough G, Gilham P. Synthesis and properties of adenosine oligonucleotide analogues containing methylene groups in place of phosphodiester 5'-oxygens. Biochemistry 1993, 32: 9125-8. PMID: 8396423, DOI: 10.1021/bi00086a017.Peer-Reviewed Original ResearchTranslational Repression by the Bacteriophage T4 Gene 32 Protein Involves Specific Recognition of an RNA Pseudoknot Structure
Shamoo Y, Tam A, Konigsberg W, Williams K. Translational Repression by the Bacteriophage T4 Gene 32 Protein Involves Specific Recognition of an RNA Pseudoknot Structure. Journal Of Molecular Biology 1993, 232: 89-104. PMID: 8331672, DOI: 10.1006/jmbi.1993.1372.Peer-Reviewed Original Research
1992
Excision repair at individual bases of the Escherichia coli lacI gene: relation to mutation hot spots and transcription coupling activity.
Kunala S, Brash DE. Excision repair at individual bases of the Escherichia coli lacI gene: relation to mutation hot spots and transcription coupling activity. Proceedings Of The National Academy Of Sciences Of The United States Of America 1992, 89: 11031-11035. PMID: 1438309, PMCID: PMC50477, DOI: 10.1073/pnas.89.22.11031.Peer-Reviewed Original ResearchConceptsTranscribed strandMutation hot spotsChromosomal DNAExcision repairIndividual nucleotidesEscherichia coli chromosomeExcision repair systemColi chromosomeMfd geneDistribution of mutationsGene fragmentsDNA fragmentsEnzymatic incisionCell extractsLacI geneUV-induced mutationsSite of labelingEscherichia coliRepair systemSpecific gene fragmentsUV photoproductsGenesBase variationsMutationsNucleotidesModeling of heteroduplex formation during PCR from mixtures of DNA templates.
Ruano G, Kidd K. Modeling of heteroduplex formation during PCR from mixtures of DNA templates. Genome Research 1992, 2: 112-116. PMID: 1362127, DOI: 10.1101/gr.2.2.112.Peer-Reviewed Original ResearchShuffling of amino acid sequence: an important control in synthetic peptide studies of nucleic acid-binding domains. Binding properties of fragments of a conserved eukaryotic RNA binding motif.
Nadler S, Kapouch J, Elliott J, Williams K. Shuffling of amino acid sequence: an important control in synthetic peptide studies of nucleic acid-binding domains. Binding properties of fragments of a conserved eukaryotic RNA binding motif. Journal Of Biological Chemistry 1992, 267: 3750-3757. PMID: 1740426, DOI: 10.1016/s0021-9258(19)50589-0.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceBinding SitesCarrier ProteinsCircular DichroismFungal ProteinsGenes, FungalHot TemperatureMolecular Sequence DataNucleic Acid DenaturationNucleic AcidsPeptide FragmentsPoly APoly A-UPoly(A)-Binding ProteinsRNA-Binding ProteinsRNA, FungalSaccharomyces cerevisiaeSpectrometry, FluorescenceSubstrate SpecificityConceptsNucleic acidsPeptide studiesResidue peptideSynthetic peptide studiesSynthetic peptidesSynthetic peptide analoguesFree energyProperties of fragmentsPeptide analoguesNucleic acid-binding domainParent proteinLatter peptideNucleic acid bindingAmino acidsStructure/function studiesAmino acid sequenceSignificant affinityAcidEukaryotic RNAPeptidesRNA specificityAmino acid compositionSimilar RNACarboxyl halfMolecular basis
1991
Interactions of the A1 heterogeneous nuclear ribonucleoprotein and its proteolytic derivative, UP1, with RNA and DNA: evidence for multiple RNA binding domains and salt-dependent binding mode transitions.
Nadler S, Merrill B, Roberts W, Keating K, Lisbin M, Barnett S, Wilson S, Williams K. Interactions of the A1 heterogeneous nuclear ribonucleoprotein and its proteolytic derivative, UP1, with RNA and DNA: evidence for multiple RNA binding domains and salt-dependent binding mode transitions. Biochemistry 1991, 30: 2968-76. PMID: 1848781, DOI: 10.1021/bi00225a034.Peer-Reviewed Original ResearchAmino Acid SequenceCircular DichroismDNA HelicasesDNA-Binding ProteinsHeterogeneous Nuclear Ribonucleoprotein A1Heterogeneous-Nuclear Ribonucleoprotein Group A-BHeterogeneous-Nuclear RibonucleoproteinsKineticsMolecular Sequence DataNucleic Acid DenaturationPoly A-UPoly dA-dTPolydeoxyribonucleotidesPolyribonucleotidesRibonucleoproteinsSpectrometry, FluorescenceThermodynamicsThymus Hormones
1989
Site-specific mutagenesis of T4 gene 32: the role of tyrosine residues in protein-nucleic acid interactions.
Shamoo Y, Ghosaini L, Keating K, Williams K, Sturtevant J, Konigsberg W. Site-specific mutagenesis of T4 gene 32: the role of tyrosine residues in protein-nucleic acid interactions. Biochemistry 1989, 28: 7409-17. PMID: 2684276, DOI: 10.1021/bi00444a039.Peer-Reviewed Original ResearchMeSH KeywordsCalorimetry, Differential ScanningCircular DichroismDNA-Binding ProteinsDNA, Single-StrandedDNA, ViralElectrophoresis, Polyacrylamide GelEscherichia coliGene Expression RegulationGenes, ViralMutationNucleic Acid DenaturationPoly dA-dTPoly TProtein DenaturationT-PhagesTemperatureThermodynamicsTrypsinTyrosineViral ProteinsZinc
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