2025
Cellular determinants influence the red blood cell adsorption efficiency of poly(amine-co-ester) nanoparticles
Binns T, Eaton D, Akiki D, Deschenes E, Piotrowski-Daspit A, Bracaglia L, Hendrickson J, Saltzman W. Cellular determinants influence the red blood cell adsorption efficiency of poly(amine-co-ester) nanoparticles. Science Advances 2025, 11: eadt8637. PMID: 40315323, PMCID: PMC12047439, DOI: 10.1126/sciadv.adt8637.Peer-Reviewed Original ResearchConceptsRed blood cellsDelivery of nucleic acidsOptimized adsorption protocolNanoparticle biodistributionIntravenous administrationPulmonary tissueNanoparticle platformClinical translationCellular determinantsBlood cellsVascular infusionPoly(amine-co-esterDrug delivery vehiclesAdsorption efficiencyDelivery vehiclesMembrane stiffnessStudy designAdsorption protocolNanoparticlesAdministrationNucleic acidsTissueDelivery
2024
Identifying the minimal sets of distance restraints for FRET‐assisted protein structural modeling
Liu Z, Grigas A, Sumner J, Knab E, Davis C, O'Hern C. Identifying the minimal sets of distance restraints for FRET‐assisted protein structural modeling. Protein Science 2024, 33: e5219. PMID: 39548730, PMCID: PMC11568256, DOI: 10.1002/pro.5219.Peer-Reviewed Original ResearchConceptsForster resonance energy transferProtein structure determination techniquesCellular environmentProtein structure modelingAmino acid pairsConformational changesProteins in vivoForster resonance energy transfer studiesCrowded cellular environmentStructure determination techniquesDynamics in vivoStructures in vivoInduce conformational changesProtein structureResonance energy transferRoot-mean-square deviationAcid pairsInter-residue restraintsStructural ensemblesAmino acidsNon-physiological environmentsProteinDistance restraintsNucleic acidsAminoMass Spectrometry Analysis of Nucleic Acid Modifications: From Beginning to Future
Xie Y, Brás‐Costa C, Lin Z, Garcia B. Mass Spectrometry Analysis of Nucleic Acid Modifications: From Beginning to Future. Mass Spectrometry Reviews 2024 PMID: 39308031, PMCID: PMC11928337, DOI: 10.1002/mas.21907.Peer-Reviewed Original ResearchMass spectrometryRegulate gene expressionMS-based methodsNucleic acidsNucleic acid structuresGenomic methodsTranscriptome researchModification statusGenetic informationNucleic acid modificationsProtein translationNucleic acid sample preparationBiological functionsGene expressionMS analysisSample preparationAcid structuresBiological moleculesModified speciesHigh-throughputDiverse modificationsLiving organismsAccurate quantitative informationAcid modificationGenomeIdentifying the minimal sets of distance restraints for FRET‐assisted protein structural modeling
Liu Z, Grigas A, Sumner J, Knab E, Davis C, O'Hern C. Identifying the minimal sets of distance restraints for FRET‐assisted protein structural modeling. Protein Science 2024, 33 PMID: 38800659, PMCID: PMC11118665, DOI: 10.1002/pro.5219.Peer-Reviewed Original ResearchForster resonance energy transferProtein structure determination techniquesCellular environmentProtein structure modelingAmino acid pairsConformational changesForster resonance energy transfer studiesCrowded cellular environmentStructure determination techniquesInduce conformational changesProtein structureResonance energy transferRoot-mean-square deviationAcid pairsInter-residue restraintsStructural ensemblesAmino acidsNon-physiological environmentsProteinDistance restraintsNucleic acidsAminoMD simulationsFRET pairsOrganellesPeptide Nucleic Acid-Mediated Regulation of CRISPR-Cas9 Specificity
Carufe K, Economos N, Glazer P. Peptide Nucleic Acid-Mediated Regulation of CRISPR-Cas9 Specificity. Nucleic Acid Therapeutics 2024, 34: 245-256. PMID: 39037032, PMCID: PMC11564683, DOI: 10.1089/nat.2024.0007.Peer-Reviewed Original ResearchPeptide nucleic acidProtospacer adjacent motifAllele-specific mannerDegree of homologyWild-type sequencePAM-proximal regionSynthetic peptide nucleic acidOff-target sitesSpacer sequencesAdjacent motifMutant allelesCas9 cuttingBase pairsCas9 activityCRISPR technologyAutosomal dominant diseaseGRNACRISPR applicationsNucleic acidsBinding positionDominant diseaseSequenceDeliberate mismatchGene therapyBiology of Exfoliation of Plasma Membrane-Derived Vesicles and the Radiation Response: Historical Background, Applications in Biodosimetry and Cell-Free Therapeutics, and Quantal Mechanisms for Their Release and Function with Implications for Space Travel
Dainiak N. Biology of Exfoliation of Plasma Membrane-Derived Vesicles and the Radiation Response: Historical Background, Applications in Biodosimetry and Cell-Free Therapeutics, and Quantal Mechanisms for Their Release and Function with Implications for Space Travel. Radiation Research 2024, 202: 328-354. PMID: 38981604, DOI: 10.1667/rade-24-00078.1.Peer-Reviewed Original ResearchCell-free therapeuticsPlasma membrane-derived vesiclesExtracellular vesiclesExposure to ionizing radiationIndividual radiation dosesMembrane-derived vesiclesExposure to radiationProperties of extracellular vesiclesPathogenesis of diseaseSpace travelDeep spaceRadiation doseInhibitory moleculesSignal traffickingHuman cellsClinical disordersQuantal mechanismRadiation responseMembrane turnoverVesiclesNucleic acidsVesicle surfaceBiophysical propertiesCell-FreeRadiationThe West Nile virus genome harbors essential riboregulatory elements with conserved and host-specific functional roles
Huston N, Tsao L, Brackney D, Pyle A. The West Nile virus genome harbors essential riboregulatory elements with conserved and host-specific functional roles. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 121: e2312080121. PMID: 38985757, PMCID: PMC11260092, DOI: 10.1073/pnas.2312080121.Peer-Reviewed Original ResearchConceptsWest Nile virus genomeWest Nile virusPositive-sense RNA virusesFunctional roleArthropod cell linesRiboregulatory elementsGenome foldingFlaviviral genomeRNA genomeIncreasing global threatVirus genomeGenomeRNA virusesStructural homologyHost-dependentSecondary structureLack of effective therapeuticsFunctional validationLocked nucleic acidStructural insightsRNA drugsCell linesArthropod-borneNucleic acidsAntisense locked nucleic acidA method for sampling the living wood microbiome
Arnold W, Gewirtzman J, Raymond P, Bradford M, Butler C, Peccia J. A method for sampling the living wood microbiome. Methods In Ecology And Evolution 2024, 15: 1084-1096. DOI: 10.1111/2041-210x.14311.Peer-Reviewed Original ResearchGlobal microbial ecologyExtraction of nucleic acidsGlobal biogeochemical cyclesTree microbiomeUnique taxaEndophytic microbiomeDiverse taxaDownstream analysisTree speciesMicrobiomeBiogeochemical cyclesMicrobial lifeTaxaDiverse environmentsNucleic acidsMicrobial analysisEcosystem healthSpeciesMethane cycleTreesEndophytesWoodNicheLeavesEcosystemPhotosensitive Nanoprobes for Rapid High Purity Isolation and Size‐Specific Enrichment of Synthetic and Extracellular Vesicle Subpopulations
Weerakkody J, Tseng T, Topper M, Thoduvayil S, Radhakrishnan A, Pincet F, Kyriakides T, Gunasekara R, Ramakrishnan S. Photosensitive Nanoprobes for Rapid High Purity Isolation and Size‐Specific Enrichment of Synthetic and Extracellular Vesicle Subpopulations. Advanced Functional Materials 2024, 34 PMID: 39372670, PMCID: PMC11452007, DOI: 10.1002/adfm.202400390.Peer-Reviewed Original ResearchExtracellular vesicle subpopulationsVesicle subpopulationsIsolation of vesiclesPurity extracellular vesiclesRelease of vesiclesAnalysis of nucleic acidsNear-native formLarge-scale isolationLipid nanoprobesDownstream analysisPurity isolationEfficient isolationVesiclesSynthetic vesiclesNucleic acidsExtracellular vesiclesIsolation methodIsolatesBiomarker discoveryExposure to lightSubpopulationsEnrichmentProteinComplex biological mediaCleavage
2023
Actin and Microtubules Position Stress Granules
Böddeker T, Rusch A, Leeners K, Murrell M, Dufresne E. Actin and Microtubules Position Stress Granules. PRX Life 2023, 1: 023010. DOI: 10.1103/prxlife.1.023010.Peer-Reviewed Original ResearchIntegrative analysis reveals a conserved role for the amyloid precursor protein in proteostasis during aging
Nithianandam V, Bukhari H, Leventhal M, Battaglia R, Dong X, Fraenkel E, Feany M. Integrative analysis reveals a conserved role for the amyloid precursor protein in proteostasis during aging. Nature Communications 2023, 14: 7034. PMID: 37923712, PMCID: PMC10624868, DOI: 10.1038/s41467-023-42822-1.Peer-Reviewed Original ResearchConceptsAmyloid precursor proteinPrecursor proteinNormal function of APPFunction of amyloid precursor proteinPathogenesis of Alzheimer's diseaseRelevant to Alzheimer's diseaseAlzheimer's diseaseDrosophila orthologMutant fliesTauopathy modelGenetic screeningAB peptideCellular signalingCellular pathwaysProteomic studiesMitochondrial functionProteostasisNeurodegenerative diseasesIntegrated analysisLipid metabolismRegulating autophagyNucleic acidsSingle cellsAmyloidTGFB signalingHead-to-head comparison of in vitro and in vivo efficacy of pHLIP-conjugated anti-seed gamma peptide nucleic acids
Dhuri K, Duran T, Chaudhuri B, Slack F, Vikram A, Glazer P, Bahal R. Head-to-head comparison of in vitro and in vivo efficacy of pHLIP-conjugated anti-seed gamma peptide nucleic acids. Cell Reports Physical Science 2023, 4: 101584. PMID: 38144419, PMCID: PMC10745205, DOI: 10.1016/j.xcrp.2023.101584.Peer-Reviewed Original ResearchBiomarkers and biosensors for early cancer diagnosis, monitoring and prognosis
Wahab M, Palaniyandi T, Ravi M, viswanathan S, Baskar G, Surendran H, Gangadharan S, Rajendran B. Biomarkers and biosensors for early cancer diagnosis, monitoring and prognosis. Pathology - Research And Practice 2023, 250: 154812. PMID: 37741139, DOI: 10.1016/j.prp.2023.154812.Peer-Reviewed Original ResearchEarly cancer diagnosisBiosensorEarly cancer detectionCancer biomarkersChip modelSuch biomarkersEngineering technologyBiological samplesCancer typesRecent advancementsEarly detectionNucleic acidsEarly diagnostic markerCancer detectionDevelopment of technologyGlobal socioeconomic impactTumor cell DNAProstate cancerMajor challengeBiomedical engineering technologyTherapeutic outcomesDetectionDiagnostic markerTechnologyParticular cancer typesDigital assay for rapid electronic quantification of clinical pathogens using DNA nanoballs
Tayyab M, Barrett D, van Riel G, Liu S, Reinius B, Scharfe C, Griffin P, Steinmetz L, Javanmard M, Pelechano V. Digital assay for rapid electronic quantification of clinical pathogens using DNA nanoballs. Science Advances 2023, 9: eadi4997. PMID: 37672583, PMCID: PMC10482329, DOI: 10.1126/sciadv.adi4997.Peer-Reviewed Original ResearchConceptsMicrofluidic impedance cytometerDNA nanoballsLabel-free assayColorimetric readoutImpedance cytometerDigital assaysLoop-mediated isothermal amplificationCapillary-driven flowNanoballsDNA detectionStandalone deviceDNA/RNAIsothermal amplificationCompact systemNucleic acidsClinical pathogensPathogen identificationAccurate detectionRapid testReadoutDetectionNovel methodImpedanceSmall interfering RNA-based nanotherapeutics for treating skin-related diseases
Chang Y, Huang T, Alalaiwe A, Hwang E, Fang J. Small interfering RNA-based nanotherapeutics for treating skin-related diseases. Expert Opinion On Drug Delivery 2023, 20: 757-772. PMID: 37088710, DOI: 10.1080/17425247.2023.2206646.Peer-Reviewed Original ResearchConceptsDifferent nanoparticle typesMechanism of RNAiRNA interferenceSkin delivery systemsLarge-scale productionNanoparticle productsSiRNA deliveryNanoparticle typesSiRNA applicationCutaneous targetingSkin targetingSkin disease managementSkin deliveryPotential applicationsDelivery systemGreat potentialNanocarriersNanotherapeuticsSkin-related diseasesSkin therapySkin penetrationNucleic acidsImproved targetingNanoparticlesTargetingStress promotes RNA G-quadruplex folding in human cells
Kharel P, Fay M, Manasova E, Anderson P, Kurkin A, Guo J, Ivanov P. Stress promotes RNA G-quadruplex folding in human cells. Nature Communications 2023, 14: 205. PMID: 36639366, PMCID: PMC9839774, DOI: 10.1038/s41467-023-35811-x.Peer-Reviewed Original ResearchConceptsHuman cellsMRNA stabilityCellular stress responseRG4 structuresG-quadruplex structuresRNA G4sDynamic regulationG-quadruplex foldingRich nucleic acidsStress responsePermissive conditionsRG4FoldingStress removalRegulatory impactNucleic acidsCellsDimethylsulfateRNAMotifGuanineMRNARegulationStressSequence
2022
Nanoparticle‐mediated genome editing in single‐cell embryos via peptide nucleic acids
Putman R, Ricciardi A, Carufe K, Quijano E, Bahal R, Glazer P, Saltzman W. Nanoparticle‐mediated genome editing in single‐cell embryos via peptide nucleic acids. Bioengineering & Translational Medicine 2022, 8: e10458. PMID: 37206203, PMCID: PMC10189434, DOI: 10.1002/btm2.10458.Peer-Reviewed Original ResearchSingle-cell embryosPeptide nucleic acidGene editingNucleic acidsNanoparticlesGross developmental abnormalitiesGenome editingNormal physiological developmentOff-target effectsDonor DNAGenetic diseasesConcept workEmbryosGenomic effectsDevelopmental abnormalitiesNormal growthEmbryogenesisPhysiological developmentEditingUnderlying mutationPreimplantation genetic diagnosisDisease pathogenesisGenetic diagnosisNormal morphologyAcidUS-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes
Zhang C, Shine M, Pyle AM, Zhang Y. US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes. Nature Methods 2022, 19: 1109-1115. PMID: 36038728, DOI: 10.1038/s41592-022-01585-1.Peer-Reviewed Original ResearchConceptsStructure comparisonStructural biology studiesStructure alignmentDNA dockingMacromolecular complexesBiology studiesMultiple structure alignmentNucleic acidsDifferent moleculesRNAProteinFundamental importanceDNAComplex structureDockingUniversal protocolAlignmentExtensive optimizationFunctionComplexesAn ELISA-based platform for rapid identification of structure-dependent nucleic acid–protein interactions detects novel DNA triplex interactors
Economos NG, Thapar U, Balasubramanian N, Karras GI, Glazer PM. An ELISA-based platform for rapid identification of structure-dependent nucleic acid–protein interactions detects novel DNA triplex interactors. Journal Of Biological Chemistry 2022, 298: 102398. PMID: 35988651, PMCID: PMC9493393, DOI: 10.1016/j.jbc.2022.102398.Peer-Reviewed Original ResearchConceptsNucleic acid structuresNucleic acid-protein interactionsNucleotide excision repairSingle-strand annealing repairDouble-strand break intermediatesUnusual nucleic acid structuresNovel interactorNucleic acid interactionsHigh-throughput platformCellular processesFactor localizationAcid structureExcision repairRelevant lociHuman cellsGene editingAcid interactionsInteractorsTherapeutic gene editingNucleic acidsDNA triplexesRapid identificationComparative approachGenomeTriplexesChapter Three Monitoring functional RNA binding of RNA-dependent ATPase enzymes such as SF2 helicases using RNA dependent ATPase assays: A RIG-I case study
Guo R, Pyle AM. Chapter Three Monitoring functional RNA binding of RNA-dependent ATPase enzymes such as SF2 helicases using RNA dependent ATPase assays: A RIG-I case study. Methods In Enzymology 2022, 673: 39-52. PMID: 35965013, DOI: 10.1016/bs.mie.2022.03.064.Peer-Reviewed Original ResearchConceptsEnzymatic ATPase activitySuperfamily 1Nucleic acid-dependent ATPasesATPase activityRNA-dependent ATPaseSimple reporter systemNucleic acid bindingNucleic acid ligandsNucleic acidsATPase enzymeSF2 helicaseAcid ligandsKinetic parametersRNA associationSF2 helicasesRNA bindingMultitude of processesMotor proteinsBiological functionsSF1 helicasesReporter systemFunctional bindingConformational changesDirect binding assaysAcid binding
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