2023
Mapping the in vivo fitness landscape of a tethered ribosome
Radford F, Rinehart J, Isaacs F. Mapping the in vivo fitness landscape of a tethered ribosome. Science Advances 2023, 9: eade8934. PMID: 37115918, PMCID: PMC10146877, DOI: 10.1126/sciadv.ade8934.Peer-Reviewed Original ResearchConceptsPeptidyl transfer centerEpistatic interactionsFitness landscapeMacromolecular machinesLaboratory evolutionRibosome functionDeleterious mutationsVivo fitness landscapeComplete mutagenesisLethal mutationsGenetic elementsRibosomesProtein synthesisDominant lethal mutationsMost nucleotidesMutationsSequence spaceNucleotidesNext-generation biomaterialsLandscapeMutagenesisOrganismsSequenceInteractionDeeper understanding
2021
Metaviromic identification of discriminative genomic features in SARS-CoV-2 using machine learning
Park JJ, Chen S. Metaviromic identification of discriminative genomic features in SARS-CoV-2 using machine learning. Patterns 2021, 3: 100407. PMID: 34812427, PMCID: PMC8598947, DOI: 10.1016/j.patter.2021.100407.Peer-Reviewed Original ResearchAmino acid resolutionSARS-CoV-2 genomeGenomic featuresGenetic elementsCoronavirus genomeGenomeFunctional studiesSequence targetsGenomic profilesUnbiased collectionMajor threatPathogenic virusesUnappreciated featureAnimal originInterpretable signaturesRapid characterizationPathogenic regionsSARS-CoVB cellsSystematic mapRdRpNucleotidesEpitope predictionProteinPathogenicityNoncoding RNAs: biology and applications—a Keystone Symposia report
Cable J, Heard E, Hirose T, Prasanth KV, Chen L, Henninger JE, Quinodoz SA, Spector DL, Diermeier SD, Porman AM, Kumar D, Feinberg MW, Shen X, Unfried JP, Johnson R, Chen C, Wilusz JE, Lempradl A, McGeary SE, Wahba L, Pyle AM, Hargrove AE, Simon MD, Marcia M, Przanowska RK, Chang HY, Jaffrey SR, Contreras LM, Chen Q, Shi J, Mendell JT, He L, Song E, Rinn JL, Lalwani MK, Kalem MC, Chuong EB, Maquat LE, Liu X. Noncoding RNAs: biology and applications—a Keystone Symposia report. Annals Of The New York Academy Of Sciences 2021, 1506: 118-141. PMID: 34791665, PMCID: PMC9808899, DOI: 10.1111/nyas.14713.Peer-Reviewed Original ResearchConceptsPIWI-interacting RNAsKeystone Symposia reportPotential drug targetsRNA biologyHuman transcriptomeEpigenetic modificationsKeystone eSymposiumNoncoding RNAsCell signalingBasic biologyDrug targetsRNABiologyDisease mechanismsNucleotidesSpeciesTranscriptomeImportant roleRNAsTranscriptionSymposium reportSignalingTranslationRoleTargetIdentification of Mg2+ ions next to nucleotides in cryo-EM maps using electrostatic potential maps
Wang J, Natchiar SK, Moore PB, Klaholz BP. Identification of Mg2+ ions next to nucleotides in cryo-EM maps using electrostatic potential maps. Acta Crystallographica Section D, Structural Biology 2021, 77: 534-539. PMID: 33825713, PMCID: PMC8025889, DOI: 10.1107/s2059798321001893.Peer-Reviewed Original Research
2018
Carbodiimide reagents for the chemical probing of RNA structure in cells
Wang PY, Sexton AN, Culligan WJ, Simon MD. Carbodiimide reagents for the chemical probing of RNA structure in cells. RNA 2018, 25: 135-146. PMID: 30389828, PMCID: PMC6298570, DOI: 10.1261/rna.067561.118.Peer-Reviewed Original ResearchConceptsConformation of RNAU nucleotidesIntact cellsChemical probesDimethyl sulfateNucleotides of RNASingle-stranded nucleotidesXist lncRNACellular contextNoncoding RNAsRNA elementsSHAPE reagentsAccessible nucleotidesRNA conformationRNA structureBiological contextChemical probingWatson-Crick faceCellular environmentFunctional roleCarbodiimide reagentRNA nucleotidesRNANucleotidesStructured regionsCharacterization of Natural Colibactin–Nucleobase Adducts by Tandem Mass Spectrometry and Isotopic Labeling. Support for DNA Alkylation by Cyclopropane Ring Opening
Xue M, Shine E, Wang W, Crawford JM, Herzon SB. Characterization of Natural Colibactin–Nucleobase Adducts by Tandem Mass Spectrometry and Isotopic Labeling. Support for DNA Alkylation by Cyclopropane Ring Opening. Biochemistry 2018, 57: 6391-6394. PMID: 30365310, PMCID: PMC6997931, DOI: 10.1021/acs.biochem.8b01023.Peer-Reviewed Original ResearchConceptsGenotoxic secondary metabolitesMethionine auxotrophic strainsE. coliGut commensal Escherichia coliClb gene clusterColibactin biosynthesisElectrophilic CyclopropanesGene clusterDNA alkylationPrevious biosynthetic studiesSecondary metabolitesAuxotrophic strainsEscherichia coliCommensal Escherichia coliBiosynthetic studiesFirst identificationBiosynthesisColiColibactinPUC19 DNAIsotopic labelingNucleotidesDNATandem mass spectrometryCertain strainsMicrohaplotypes in forensic genetics
Oldoni F, Kidd KK, Podini D. Microhaplotypes in forensic genetics. Forensic Science International Genetics 2018, 38: 54-69. PMID: 30347322, DOI: 10.1016/j.fsigen.2018.09.009.Peer-Reviewed Original ResearchBacterial Y RNAs: Gates, Tethers, and tRNA Mimics
Sim S, Wolin S. Bacterial Y RNAs: Gates, Tethers, and tRNA Mimics. 2018, 369-381. DOI: 10.1128/9781683670247.ch21.Peer-Reviewed Original ResearchY RNAsBacterial Y RNAsRing-shaped proteinSubset of bacteriaCharacterized organismsProtein partnersNoncoding RNAsTRNA mimicAnimal cellsHomology searchHuman RNAHuman cellsRNANucleotidesImportant targetBacteriaSystemic autoimmune rheumatic diseasesAutoimmune rheumatic diseasesSystemic lupus erythematosusCellsRNAsOrganismsSpeciesProteinLupus erythematosus
2016
RESA identifies mRNA-regulatory sequences at high resolution
Yartseva V, Takacs CM, Vejnar CE, Lee MT, Giraldez AJ. RESA identifies mRNA-regulatory sequences at high resolution. Nature Methods 2016, 14: 201-207. PMID: 28024160, PMCID: PMC5423094, DOI: 10.1038/nmeth.4121.Peer-Reviewed Original ResearchpiRNAs and Their Functions in the Brain
Zuo L, Wang Z, Tan Y, Chen X, Luo X. piRNAs and Their Functions in the Brain. International Journal Of Human Genetics 2016, 16: 53-60. PMID: 27512315, PMCID: PMC4976825, DOI: 10.1080/09723757.2016.11886278.Peer-Reviewed Original Research
2015
Accelerating SNARE‐Mediated Membrane Fusion by DNA–Lipid Tethers
Xu W, Wang J, Rothman J, Pincet F. Accelerating SNARE‐Mediated Membrane Fusion by DNA–Lipid Tethers. Angewandte Chemie 2015, 127: 14596-14600. DOI: 10.1002/ange.201506844.Peer-Reviewed Original ResearchDNA-lipidMembrane-distal endMembrane-proximal endArtificial tetherSNARE functionCore machinerySNARE proteinsProtein functionTarget membraneMembrane fusionBiological processesNative proteinBase pairsLipid mixingMaximum fusion rateProgrammable toolsBase-pair hybridizationProteinSnareMembraneFusionMachineryTetherNucleotidesVesiclesSensory Receptors
Levitan I, Kaczmarek L. Sensory Receptors. 2015, 295-326. DOI: 10.1093/med/9780199773893.003.0013.Chapters
2014
SNPlice: variants that modulate Intron retention from RNA-sequencing data
Mudvari P, Movassagh M, Kowsari K, Seyfi A, Kokkinaki M, Edwards N, Golestaneh N, Horvath A. SNPlice: variants that modulate Intron retention from RNA-sequencing data. Bioinformatics 2014, 31: 1191-1198. PMID: 25481010, PMCID: PMC4393518, DOI: 10.1093/bioinformatics/btu804.Peer-Reviewed Original ResearchConceptsRNA-seq datasetsExon-intron boundariesImportance of splicingRNA-sequencing dataHigh-throughput approachIntron retentionSplicing eventsAltered splicingSplice junctionsVariant lociVariant nucleotidesAllele-specific sequencingSplicingSupplementary dataLinux computerBinary packagesComputational approachEdUVariantsLociRNANucleotidesBioinformaticsSequencingThe mechanism of Torsin ATPase activation
Brown RS, Zhao C, Chase AR, Wang J, Schlieker C. The mechanism of Torsin ATPase activation. Proceedings Of The National Academy Of Sciences Of The United States Of America 2014, 111: e4822-e4831. PMID: 25352667, PMCID: PMC4234599, DOI: 10.1073/pnas.1415271111.Peer-Reviewed Original Research
2013
Prechemistry Nucleotide Selection Checkpoints in the Reaction Pathway of DNA Polymerase I and Roles of Glu710 and Tyr766
Bermek O, Grindley N, Joyce C. Prechemistry Nucleotide Selection Checkpoints in the Reaction Pathway of DNA Polymerase I and Roles of Glu710 and Tyr766. Biochemistry 2013, 52: 6258-6274. PMID: 23937394, PMCID: PMC3770053, DOI: 10.1021/bi400837k.Peer-Reviewed Original ResearchConceptsFidelity checkpointDNA polymerase IPolymerase IHigh-fidelity DNA polymeraseMutator allelesCheckpoint functionMutator polymeraseIncorrect base pairsSelection checkpointDNA templateConformational changesSubstrate poolBase pairsDNA polymeraseComplementary nucleotidesCheckpointNoncomplementary nucleotidesTemplating baseFinger closingPolymeraseDNTPsNucleotidesCorrect incomingPathwayWeak bindingConformational landscapes of DNA polymerase I and mutator derivatives establish fidelity checkpoints for nucleotide insertion
Hohlbein J, Aigrain L, Craggs T, Bermek O, Potapova O, Shoolizadeh P, Grindley N, Joyce C, Kapanidis A. Conformational landscapes of DNA polymerase I and mutator derivatives establish fidelity checkpoints for nucleotide insertion. Nature Communications 2013, 4: 2131. PMID: 23831915, PMCID: PMC3715850, DOI: 10.1038/ncomms3131.Peer-Reviewed Original ResearchConceptsClosed conformationDNA polymerase IIncorrect nucleotidesPolymerase ITernary complexSingle-molecule FRETActive site side chainsNucleotide selectionMutator phenotypeFidelity checkpointPrimary checkpointPhosphoryl transferFidelity mutantsConformational changesConformational landscapeDNA polymeraseNucleotide insertionConformational transitionDNA synthesisFRET valuesNucleotidesFree energy landscapeReduced affinityCheckpointConformationDevelopment of modified siRNA molecules incorporating 5-fluoro-2′-deoxyuridine residues to enhance cytotoxicity
Wu SY, Chen TM, Gmeiner WH, Chu E, Schmitz JC. Development of modified siRNA molecules incorporating 5-fluoro-2′-deoxyuridine residues to enhance cytotoxicity. Nucleic Acids Research 2013, 41: 4650-4659. PMID: 23449220, PMCID: PMC3632118, DOI: 10.1093/nar/gkt120.Peer-Reviewed Original ResearchConceptsTS proteinMultiple DNA damage repairCovalent inhibitory ternary complexNovel drug development approachDNA damage repairInhibitory ternary complexRNA stabilityDamage repairApoptotic pathwayHuman diseasesWatson-Crick base pairingPrecise fateSiRNAsControl siRNAsBase pairingTernary complexRNA expressionThymidylate synthaseMessenger RNA expressionDrug development approachesCytotoxic nucleosidesInhibitor compoundsNucleotidesSiRNAProtein
2012
The Hexameric Helicase DnaB Adopts a Nonplanar Conformation during Translocation
Itsathitphaisarn O, Wing RA, Eliason WK, Wang J, Steitz TA. The Hexameric Helicase DnaB Adopts a Nonplanar Conformation during Translocation. Cell 2012, 151: 267-277. PMID: 23022319, PMCID: PMC3597440, DOI: 10.1016/j.cell.2012.09.014.Peer-Reviewed Original ResearchConceptsTranslocation mechanismParental duplex DNAReplicative DNA helicaseNucleotides of ssDNAC-terminal domainDNA helicaseDnaB hexamerHelicase DnaBNTP hydrolysisNascent DNAStructural insightsQuaternary structureDNA templateDuplex DNADNA polymeraseDnaBTranslocationSequential hydrolysisSubunitsUnwindingNucleotidesDNASsDNAHelicasesHelicase
2011
Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement
Isaacs FJ, Carr PA, Wang HH, Lajoie MJ, Sterling B, Kraal L, Tolonen AC, Gianoulis TA, Goodman DB, Reppas NB, Emig CJ, Bang D, Hwang SJ, Jewett MC, Jacobson JM, Church GM. Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement. Science 2011, 333: 348-353. PMID: 21764749, PMCID: PMC5472332, DOI: 10.1126/science.1205822.Peer-Reviewed Original ResearchConceptsGenome engineeringSynonymous codon substitutionsGenome engineering technologiesSynthetic lethal effectMegabase scaleCodon replacementsTAA codonCodon substitutionsRecombination frequencyCodon modificationGenetic landscapeEscherichia coliGenomeChromosomesCodonPrecise changesLethal effectsPrecise manipulationEngineering technologyNucleotidesColiPhenotypeTagsModification
2009
U2504 Determines the Species Specificity of the A-Site Cleft Antibiotics: The Structures of Tiamulin, Homoharringtonine, and Bruceantin Bound to the Ribosome
Gürel G, Blaha G, Moore PB, Steitz TA. U2504 Determines the Species Specificity of the A-Site Cleft Antibiotics: The Structures of Tiamulin, Homoharringtonine, and Bruceantin Bound to the Ribosome. Journal Of Molecular Biology 2009, 389: 146-156. PMID: 19362093, PMCID: PMC2682339, DOI: 10.1016/j.jmb.2009.04.005.Peer-Reviewed Original ResearchConceptsSpecies specificityLarge ribosomal subunitPeptidyl transferase centerAmino acid side chainsHaloarcula marismortuiRibosomal subunitAcid side chainsSingle nucleotideNeighboring nucleotidesProtein synthesisRibosomesNucleotidesSide chainsMarismortuiInhibitorsSubunitsSpecificityInteractionComplexesA-siteHomoharringtonine
This site is protected by hCaptcha and its Privacy Policy and Terms of Service apply