2024
Channel width modulates the permeability of DNA origami–based nuclear pore mimics
Feng Q, Saladin M, Wu C, Cao E, Zheng W, Zhang A, Bhardwaj P, Li X, Shen Q, Kapinos L, Kozai T, Mariappan M, Lusk C, Xiong Y, Lim R, Lin C. Channel width modulates the permeability of DNA origami–based nuclear pore mimics. Science Advances 2024, 10: eadq8773. PMID: 39536094, PMCID: PMC11559598, DOI: 10.1126/sciadv.adq8773.Peer-Reviewed Original ResearchDNA-Based Molecular Clamp for Probing Protein Interactions and Structure under Force
Chung M, Zhou K, Powell J, Lin C, Schwartz M. DNA-Based Molecular Clamp for Probing Protein Interactions and Structure under Force. ACS Nano 2024, 18: 27590-27596. PMID: 39344156, PMCID: PMC11518680, DOI: 10.1021/acsnano.4c08663.Peer-Reviewed Original ResearchConceptsTalin rod domainNegative-stain electron microscopyDouble-stranded DNADNA clampProtein functionRod domainCryptic sitesProtein interactionsMolecular clampCellular mechanotransductionStudy proteinsBiochemical studiesCell biologyAdult physiologyProtein conformationTalinProteinBiochemical scaleMultiple diseasesDNAARPC5LVinculinStructural analysisEmbryogenesisDNA-based devicesDNA nanoswitches pack an anti-cancer punch
Zhou K, Lin C. DNA nanoswitches pack an anti-cancer punch. Nature Nanotechnology 2024, 1-2. PMID: 39209995, DOI: 10.1038/s41565-024-01749-4.Commentaries, Editorials and LettersLipid osmosis, membrane tension, and other mechanochemical driving forces of lipid flow
Zhang Y, Lin C. Lipid osmosis, membrane tension, and other mechanochemical driving forces of lipid flow. Current Opinion In Cell Biology 2024, 88: 102377. PMID: 38823338, PMCID: PMC11193448, DOI: 10.1016/j.ceb.2024.102377.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsMembrane tensionLipid transportNonvesicular lipid transportLipid transfer proteinsOrganelle biogenesisLipid transferMembrane proteinsMembrane domainsLipid homeostasisBiological functionsLipid flowMembrane protein densityTransfer proteinMembrane regionsProtein densityProteinMembraneLipidBiogenesisOrganelles
2023
Recent Advances in DNA Origami-Engineered Nanomaterials and Applications
Zhan P, Peil A, Jiang Q, Wang D, Mousavi S, Xiong Q, Shen Q, Shang Y, Ding B, Lin C, Ke Y, Liu N. Recent Advances in DNA Origami-Engineered Nanomaterials and Applications. Chemical Reviews 2023, 123: 3976-4050. PMID: 36990451, PMCID: PMC10103138, DOI: 10.1021/acs.chemrev.3c00028.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsDNA origami techniquePaul RothemundDNA nanotechnologyOrigami techniqueExciting achievementsNanomaterialsMaterials scienceRecent progressRecent advancesNanotechnologyUseful applicationsApplicationsRothemundSignificant advancesUnexplored research avenuesOriginal proposalFieldPhysicsMathematicsEngineeringAdvancesUnique fieldThe capsid lattice engages a bipartite NUP153 motif to mediate nuclear entry of HIV-1 cores
Shen Q, Kumari S, Xu C, Jang S, Shi J, Burdick R, Levintov L, Xiong Q, Wu C, Devarkar S, Tian T, Tripler T, Hu Y, Yuan S, Temple J, Feng Q, Lusk C, Aiken C, Engelman A, Perilla J, Pathak V, Lin C, Xiong Y. The capsid lattice engages a bipartite NUP153 motif to mediate nuclear entry of HIV-1 cores. Proceedings Of The National Academy Of Sciences Of The United States Of America 2023, 120: e2202815120. PMID: 36943880, PMCID: PMC10068764, DOI: 10.1073/pnas.2202815120.Peer-Reviewed Original ResearchConceptsHIV-1 capsidC-terminal tail regionTriple arginine motifNuclear pore complexPhenylalanine-glycine motifsBipartite motifNuclear importPore complexNuclear poresNuclear entryNup153Capsid latticeInteraction moduleProtein latticeCA assemblyCA hexamersIntact capsidsNucleoporinsHIV-1 coreMotifCapsidTail regionIntact formInfection studiesMechanistic evidenceModeling HIV-1 nuclear entry with nucleoporin-gated DNA-origami channels
Shen Q, Feng Q, Wu C, Xiong Q, Tian T, Yuan S, Shi J, Bedwell G, Yang R, Aiken C, Engelman A, Lusk C, Lin C, Xiong Y. Modeling HIV-1 nuclear entry with nucleoporin-gated DNA-origami channels. Nature Structural & Molecular Biology 2023, 30: 425-435. PMID: 36807645, PMCID: PMC10121901, DOI: 10.1038/s41594-023-00925-9.Peer-Reviewed Original ResearchConceptsNuclear pore complexHIV-1 nuclear entryNuclear entryNuclear importNPC central channelPore complexHost nucleusCapsid dockingVirus genomeAffinity gradientNup153Central channelMechanistic insightsMolecular interactionsCapsidNucleoporinsNup358Nup62GenomeNucleusVirusDockingVirus-1 infectionImportComplexesCLASP2 recognizes tubulins exposed at the microtubule plus-end in a nucleotide state–sensitive manner
Luo W, Demidov V, Shen Q, Girão H, Chakraborty M, Maiorov A, Ataullakhanov F, Lin C, Maiato H, Grishchuk E. CLASP2 recognizes tubulins exposed at the microtubule plus-end in a nucleotide state–sensitive manner. Science Advances 2023, 9: eabq5404. PMID: 36598991, PMCID: PMC9812398, DOI: 10.1126/sciadv.abq5404.Peer-Reviewed Original Research
2022
Functionalized DNA-Origami-Protein Nanopores Generate Large Transmembrane Channels with Programmable Size-Selectivity
Shen Q, Xiong Q, Zhou K, Feng Q, Liu L, Tian T, Wu C, Xiong Y, Melia T, Lusk C, Lin C. Functionalized DNA-Origami-Protein Nanopores Generate Large Transmembrane Channels with Programmable Size-Selectivity. Journal Of The American Chemical Society 2022, 145: 1292-1300. PMID: 36577119, PMCID: PMC9852090, DOI: 10.1021/jacs.2c11226.Peer-Reviewed Original ResearchConceptsExchange of macromoleculesCholesterol-rich membranesHybrid nanoporesSynthetic biologyBiophysical toolsSynthetic cellsTransmembrane channelsTransmembrane nanoporesDNA ringsProtein nanoporeCell membraneBacterial toxinsDNA origami techniqueLipid membranesAnalytical chemistryMacromolecule sizeDNA origamiMembraneProgrammable sizeNanoporesSized poresNucleoporinsAverage inner diameterCellsPneumolysinActuating tension-loaded DNA clamps drives membrane tubulation
Liu L, Xiong Q, Xie C, Pincet F, Lin C. Actuating tension-loaded DNA clamps drives membrane tubulation. Science Advances 2022, 8: eadd1830. PMID: 36223466, PMCID: PMC9555772, DOI: 10.1126/sciadv.add1830.Peer-Reviewed Original ResearchConceptsDNA clampMembrane tubulationMembrane dynamicsMembrane-remodeling eventsVesicle tubulationConformational changesSpatiotemporal controlDNA signalsCell membraneDNA nanostructuresTubulationMembrane deformationClosed stateOpen stateSelf-assembled DNA nanostructuresOrganismsProteinMembrane tubeArtificial systemsTube widthMembraneDynamicsFrame-Guided Assembly of Amphiphiles
Dong Y, Yang Y, Lin C, Liu D. Frame-Guided Assembly of Amphiphiles. Accounts Of Chemical Research 2022, 55: 1938-1948. PMID: 35786832, DOI: 10.1021/acs.accounts.2c00234.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsFrame-guided assemblyMolecular structureAssembly of amphiphilesArrangement of moleculesTraditional chemical industryMembrane protein incorporationProtein-lipid bilayerAmphiphilic assembliesAssembly morphologyAmphiphile assembliesFunctional nanomaterialsVersatile strategyAqueous environmentHydrophobic groupsHydrophobic moleculesFull surface areaHydrophobic interactionsAmphiphilesDrug deliveryMembrane proteinsFunctional complexAmphiphile concentrationAssembly strategyEPR effectNanomaterialsOmicron-specific mRNA vaccination alone and as a heterologous booster against SARS-CoV-2
Fang Z, Peng L, Filler R, Suzuki K, McNamara A, Lin Q, Renauer PA, Yang L, Menasche B, Sanchez A, Ren P, Xiong Q, Strine M, Clark P, Lin C, Ko AI, Grubaugh ND, Wilen CB, Chen S. Omicron-specific mRNA vaccination alone and as a heterologous booster against SARS-CoV-2. Nature Communications 2022, 13: 3250. PMID: 35668119, PMCID: PMC9169595, DOI: 10.1038/s41467-022-30878-4.Peer-Reviewed Original ResearchConceptsHeterologous boosterSARS-CoV-2Antibody responseMRNA vaccinesMRNA vaccinationDelta variantOmicron variantType of vaccinationStrong antibody responseMRNA vaccine candidatesVaccine candidatesNeutralization potencyImmune evasionSARS-CoV.Two weeksComparable titersVaccinationVaccineTiters 10MiceOmicronWeeksWA-1LNP-mRNABoosterFluorogenic DNA-PAINT for faster, low-background super-resolution imaging
Chung KKH, Zhang Z, Kidd P, Zhang Y, Williams ND, Rollins B, Yang Y, Lin C, Baddeley D, Bewersdorf J. Fluorogenic DNA-PAINT for faster, low-background super-resolution imaging. Nature Methods 2022, 19: 554-559. PMID: 35501386, PMCID: PMC9133131, DOI: 10.1038/s41592-022-01464-9.Peer-Reviewed Original ResearchConceptsSlow imaging speedSuper-resolution imagingSuper-resolution microscopy methodsDNA-PAINTOptical sectioningImaging speedFast imagingNanometer resolutionDNA-based points accumulationHigh-fidelity imagesUnbound fluorophoresMicroscopy methodsDocking strandsHigh backgroundPoint accumulationNanoscale topographyProbeVariant-specific vaccination induces systems immune responses and potent in vivo protection against SARS-CoV-2
Peng L, Renauer PA, Ökten A, Fang Z, Park JJ, Zhou X, Lin Q, Dong MB, Filler R, Xiong Q, Clark P, Lin C, Wilen CB, Chen S. Variant-specific vaccination induces systems immune responses and potent in vivo protection against SARS-CoV-2. Cell Reports Medicine 2022, 3: 100634. PMID: 35561673, PMCID: PMC9040489, DOI: 10.1016/j.xcrm.2022.100634.Peer-Reviewed Original ResearchConceptsImmune responseImmune cell populationsSARS-CoV-2 spikeAssessment of efficacySARS-CoV-2LNP-mRNABreakthrough infectionsCD8 TImmune profilingMRNA vaccinesPotent protectionT lymphocytesNeutralization activityDelta variantAnimal modelsPotent antibodiesRepertoire diversityCell responsesAuthentic virusSystemic increaseVariant lineagesClonal expansionCell populationsCOVID-19Vaccination
2021
DNA-Origami NanoTrap for Studying the Selective Barriers Formed by Phenylalanine-Glycine-Rich Nucleoporins
Shen Q, Tian T, Xiong Q, Fisher P, Xiong Y, Melia TJ, Lusk CP, Lin C. DNA-Origami NanoTrap for Studying the Selective Barriers Formed by Phenylalanine-Glycine-Rich Nucleoporins. Journal Of The American Chemical Society 2021, 143: 12294-12303. PMID: 34324340, PMCID: PMC8363578, DOI: 10.1021/jacs.1c05550.Peer-Reviewed Original ResearchConceptsNuclear pore complexFundamental biological activitiesRich nucleoporinsNuclear transport receptorsSelective barrierPhenylalanine-GlycineStructure-function relationshipsPore complexNuclear transportTransport receptorsProtein assembliesFG-NupsMolecular trafficFG interactionsFG networkBiomolecular machinesNucleoporinsCritical determinantDNA nanotechnologyBiomimetic constructsBiological activityDiffusion barrierModel cargoNanotrapsSpatial arrangementFisB relies on homo-oligomerization and lipid binding to catalyze membrane fission in bacteria
Landajuela A, Braun M, Rodrigues CDA, Martínez-Calvo A, Doan T, Horenkamp F, Andronicos A, Shteyn V, Williams ND, Lin C, Wingreen NS, Rudner DZ, Karatekin E. FisB relies on homo-oligomerization and lipid binding to catalyze membrane fission in bacteria. PLOS Biology 2021, 19: e3001314. PMID: 34185788, PMCID: PMC8274934, DOI: 10.1371/journal.pbio.3001314.Peer-Reviewed Original ResearchConceptsMembrane fissionMembrane fission machineryMother cell membraneNegative-curvature lipidsMother cell cytoplasmUnique membrane topologyFission machineryMembrane scissionMembrane topologyLipid microdomainsMembrane necksFission proteinsLipid bindingMembrane curvatureFilamentous cellsBacillus subtilisFisBProtein BCell cytoplasmAcidic lipidsCell membraneCurvature sensingImmobile clustersIntrinsic abilityBacteriaSorting sub-150-nm liposomes of distinct sizes by DNA-brick-assisted centrifugation
Yang Y, Wu Z, Wang L, Zhou K, Xia K, Xiong Q, Liu L, Zhang Z, Chapman ER, Xiong Y, Melia TJ, Karatekin E, Gu H, Lin C. Sorting sub-150-nm liposomes of distinct sizes by DNA-brick-assisted centrifugation. Nature Chemistry 2021, 13: 335-342. PMID: 33785892, PMCID: PMC8049973, DOI: 10.1038/s41557-021-00667-5.Peer-Reviewed Original ResearchDNA origami
Dey S, Fan C, Gothelf K, Li J, Lin C, Liu L, Liu N, Nijenhuis M, Saccà B, Simmel F, Yan H, Zhan P. DNA origami. Nature Reviews Methods Primers 2021, 1: 13. DOI: 10.1038/s43586-020-00009-8.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsDNA origami technologyOrigami technologyDNA origami techniqueNear-atomic precisionDNA nanotechnologyOrigami techniqueDNA origamiDrug deliveryOrigami structuresMolecular machinesOrigami designBiological materialsLiving cellsSynthesisVivo synthesisNanophotonicsNanotechnologyNanofabricationNanostructuresNanoelectronicsBioimagingScale of productionFabricationTechnologyFunctionalization
2020
DNA-Origami-Based Fluorescence Brightness Standards for Convenient and Fast Protein Counting in Live Cells
Williams ND, Landajuela A, Kasula RK, Zhou W, Powell JT, Xi Z, Isaacs FJ, Berro J, Toomre D, Karatekin E, Lin C. DNA-Origami-Based Fluorescence Brightness Standards for Convenient and Fast Protein Counting in Live Cells. Nano Letters 2020, 20: 8890-8896. PMID: 33164530, PMCID: PMC7726105, DOI: 10.1021/acs.nanolett.0c03925.Peer-Reviewed Original ResearchConceptsCopies of proteinsBrightness standardsFluorescence microscopyProtein countingMammalian cellsFluorescent proteinCopy numberLive cellsConventional quantification techniquesBiological LaboratoryFluorescence microscopeProteinDNA origamiVersatile toolCellsBiologyCurrent quantification methodsCopiesOrganic dyesRNA returns to the fold
Shen Q, Lin C. RNA returns to the fold. Nature Chemistry 2020, 12: 221-222. PMID: 32108762, DOI: 10.1038/s41557-020-0432-5.Commentaries, Editorials and Letters