van Oijen, Antoine M.

Top Publications

Year	Title
2020	A Primase-Induced Conformational Switch Controls the Stability of the Bacterial Replisome Published in Molecular Cell
2020	Single-molecule imaging reveals molecular coupling between transcription and DNA repair machinery in live cells Published in Nature Communications
2020	Single-molecule live-cell imaging visualizes parallel pathways of prokaryotic nucleotide excision repair Published in Nature Communications
2020	Tunability of DNA Polymerase Stability during Eukaryotic DNA Replication Published in Molecular Cell
2019	Spatial and temporal organization of RecA in the Escherichia coli DNA-damage response Published in eLife
2018	The transcription-repair coupling factor Mfd associates with RNA polymerase in the absence of exogenous damage Published in Nature Communications
2017	Single-molecule visualization of conformational changes and substrate transport in the vitamin B12ABC importer BtuCD-F Published in Nature Communications
2017	Single-molecule visualization of fast polymerase turnover in the bacterial replisome Published in eLife
2013	Bacterial replication, transcription and translation: mechanistic insights from single-molecule biochemical studies Published in Nature Reviews Microbiology
2013	Unsynchronised subunit motion in single trimeric sodium-coupled aspartate transporters Published in Nature
2012	A general approach to break the concentration barrier in single-molecule imaging Published in Nature Methods
2009	Dynamics of DNA replication loops reveal temporal control of lagging-strand synthesis Published in Nature

Research Areas

Research Overview

Antoine van Oijen obtained his BSc and PhD degrees in the Netherlands, where he was trained as a physicist. A growing fascination for biology resulted in him moving to the USA and establishing a research group at Harvard Medical School. Subsequently, he was appointed as full professor at Groningen University in the Netherlands where he established a thriving biophysics research program focused on the development of single-molecule visualisation techniques and their applications in basic and applied science. In 2014, he moved to the UOW and was awarded a prestigious Laureate Fellowship by the Australian Research Council to further develop biophysical approaches to visualise the molecular processes that define life. He is currently Director of Molecular Horizons and an NHMRC Leadership Fellow.

Selected Publications

Journal Article

Year	Title
2020	A Primase-Induced Conformational Switch Controls the Stability of the Bacterial Replisome Published In Molecular Cell
2020	A mechanism for the extension and unfolding of parallel telomeric G-quadruplexes by human telomerase at single-molecule resolution Published In eLife
2020	CHD4 slides nucleosomes by decoupling entry- and exit-side DNA translocation Published In Nature Communications
2020	Community perspectives on the benefits and risks of technologically enhanced communicable disease surveillance systems: A report on four community juries Published In BMC Medical Ethics
2020	Design of customizable long linear DNA substrates with controlled end modifications for single-molecule studies Published In Analytical Biochemistry
2020	Development of a single-stranded DNA-binding protein fluorescent fusion toolbox Published In Nucleic Acids Research
2020	Frequent template switching in postreplication gaps: suppression of deleterious consequences by the Escherichia coli Uup and RadD proteins Published In Nucleic Acids Research
2020	Resolving Toxic DNA repair intermediates in every E. coli replication cycle: critical roles for RecG, Uup and RadD Published In Nucleic Acids Research
2020	Single-molecule imaging reveals molecular coupling between transcription and DNA repair machinery in live cells Published In Nature Communications
2020	Single-molecule live-cell imaging reveals RecB-dependent function of DNA polymerase IV in double strand break repair Published In Nucleic Acids Research
2020	Single-molecule live-cell imaging visualizes parallel pathways of prokaryotic nucleotide excision repair Published In Nature Communications
2020	Tunability of DNA Polymerase Stability during Eukaryotic DNA Replication Published In Molecular Cell
2019	Identification of Multiple Kinetic Populations of DNA-Binding Proteins in Live Cells Published In Biophysical Journal
2019	Nuclease dead Cas9 is a programmable roadblock for DNA replication Published In Scientific Reports
2019	RecFOR epistasis group: RecF and RecO have distinct localizations and functions in Escherichia coli Published In Nucleic Acids Research
2019	Recycling of single-stranded DNA-binding protein by the bacterial replisome Published In Nucleic Acids Research
2019	Role of RNase H enzymes in maintaining genome stability in Escherichia coli expressing a steric-gate mutant of pol VICE391 Published In DNA Repair
2019	Shining a spotlight on DNA: Single-molecule methods to visualise DNA Published In Molecules
2019	Spatial and temporal organization of RecA in the Escherichia coli DNA-damage response Published In eLife
2019	Spy-ing on Cas9: Single-molecule tools reveal the enzymology of Cas9 Published In Current Opinion in Biomedical Engineering
2019	The drivers of antibiotic use and misuse: the development and investigation of a theory driven community measure Published In BMC Public Health
2019	When proteins play tag: the dynamic nature of the replisome Published In Biophysical Reviews
2018	Anisotropic functionalization of upconversion nanoparticles Published In Chemical Science
2018	DNA polymerase IV primarily operates outside of DNA replication forks in Escherichia coli Published In PLoS Genetics
2018	Design of DNA rolling-circle templates with controlled fork topology to study mechanisms of DNA replication Published In Analytical Biochemistry
2018	Detection of kinetic change points in piece-wise linear single molecule motion Published In Journal of Chemical Physics
2018	Nanoparticles for super-resolution microscopy and single-molecule tracking Published In Nature Methods
2018	Quantification of ligand density and stoichiometry on the surface of liposomes using single-molecule fluorescence imaging Published In Journal of Controlled Release
2018	Single-molecule live-cell imaging of bacterial DNA repair and damage tolerance Published In Biochemical Society Transactions
2018	Single-particle fusion of influenza viruses reveals complex interactions with target membranes Published In Journal of Physics: Condensed Matter
2018	Special Issue on Cell Biophysics Published In Biophysical Journal
2018	Specialised DNA polymerases in Escherichia coli: roles within multiple pathways Published In Current Genetics: lower eukaryotes and organelles
2018	The small heat shock protein Hsp27 binds α-synuclein fibrils, preventing elongation and cytotoxicity Published In Journal of Biological Chemistry
2018	The transcription-repair coupling factor Mfd associates with RNA polymerase in the absence of exogenous damage Published In Nature Communications
2018	Using single-molecule approaches to understand the molecular mechanisms of heat-shock protein chaperone function Published In American Journal of Molecular Biology
2017	Architecture of the Nucleosome Remodeling and Deacetylase (NuRD) Complex Published In The FASEB Journal
2017	Diatrack particle tracking software: Review of applications and performance evaluation Published In Traffic
2017	Mechanism of membrane fusion induced by vesicular stomatitis virus G protein Published In Proceedings of the National Academy of Sciences of USA
2017	Single-Molecule Fluorescence Studies of Membrane Transporters Using Total Internal Reflection Microscopy Published In Methods in Enzymology
2017	Single-molecule visualization of Saccharomyces cerevisiae leading-strand synthesis reveals dynamic interaction between MTC and the replisome Published In Proceedings of the National Academy of Sciences of USA
2017	Single-molecule visualization of conformational changes and substrate transport in the vitamin B12ABC importer BtuCD-F Published In Nature Communications
2017	Single-molecule visualization of fast polymerase turnover in the bacterial replisome Published In eLife
2017	The more the merrier: high-throughput single-molecule techniques Published In Biochemical Society Transactions
2017	Watching cellular machinery in action, one molecule at a time Published In The Journal of Cell Biology
2016	A tool for alignment and averaging of sparse fluorescence signals in rod-shaped bacteria Published In Biophysical Journal
2016	Bisecting Microfluidic Channels with Metallic Nanowires Fabricated by Nanoskiving Published In ACS Nano
2016	Droplet microfluidics for kinetic studies of viral fusion Published In Biomicrofluidics
2016	Droplet microfluidics: a tool for biology, chemistry and nanotechnology Published In Trends in Analytical Chemistry
2016	Lipids activate SecA for high affinity binding to the SecYEG complex Published In Journal of Biological Chemistry
2016	Mechanisms of influenza viral membrane fusion Published In Seminars in Cell and Developmental Biology
2016	Mutations for worse or better: low-fidelity DNA Synthesis by SOS DNA polymerase v is a tightly regulated double-edged sword Published In Biochemistry
2016	On the spatial organization of mRNA, plasmids, and ribosomes in a bacterial host overexpressing membrane proteins Published In PLoS Genetics
2016	Simultaneous real-time imaging of leading and lagging strand synthesis reveals the coordination dynamics of single replisomes Published In Molecular Cell
2016	Single-molecule specific mislocalization of red fluorescent proteins in live Escherichia coli Published In Biophysical Journal
2016	Speeding up biomolecular interactions by molecular sledding Published In Chemical Science
2016	Stability versus exchange: a paradox in DNA replication Published In Nucleic Acids Research
2015	Chikungunya virus fusion properties elucidated by single-particle and bulk approaches Published In Journal of General Virology
2015	External control of reactions in microdroplets Published In Scientific Reports
2015	ISBatch: a batch-processing platform for data analysis and exploration of live-cell single-molecule microscopy images and other hierarchical datasets Published In Molecular Biosystems
2015	In vivo single-molecule studies of DNA repair in E. Coli Published In The FASEB Journal
2015	Probing molecular choreography through single-molecule biochemistry Published In Nature Structural and Molecular Biology
2015	Regulation of mutagenic DNA polymerase V activation in space and time Published In PLoS Genetics
2015	Single-molecule imaging at high fluorophore concentrations by local activation of dye Published In Biophysical Journal
2015	Single-molecule observation of prokaryotic DNA replication Published In Methods in Molecular Biology
2015	The innate immune sensor IFI16 recognizes foreign DNA in the nucleus by scanning along the duplex Published In eLife
2015	Theory of bimolecular reactions in a solution with linear traps: application to the problem of target search on DNA Published In Physical Review E: Statistical, Nonlinear, and Soft Matter Physics
2014	A versatile approach to the generation of fluid supported lipid bilayers and its applications Published In Biotechnology and Bioengineering
2014	DNA replication at the single-molecule level Published In Chemical Society Reviews
2014	Membrane-on-a-Chip: Microstructured Silicon/Silicon-Dioxide Chips for High-Throughput Screening of Membrane Transport and Viral Membrane Fusion Published In ACS Nano
2014	ParB spreading requires DNA bridging Published In Genes and Development
2014	Relating influenza virus membrane fusion kinetics to stoichiometry of neutralizing antibodies at the single-particle level Published In Proceedings of the National Academy of Sciences of USA
2014	Single-molecule studies of polymerase dynamics and stoichiometry at the bacteriophage T7 replication machinery Published In Proceedings of the National Academy of Sciences of USA
2013	A direct proofreader-clamp interaction stabilizes the Pol III replicase in the polymerization mode Published In The EMBO Journal
2013	A single-molecule view of DNA replication: the dynamic nature of multi-protein complexes revealed Published In Current Opinion in Structural Biology
2013	Bacterial replication, transcription and translation: mechanistic insights from single-molecule biochemical studies Published In Nature Reviews Microbiology
2013	Influenza-virus membrane fusion by cooperative fold-back of stochastically induced hemagglutinin intermediates Published In eLife
2013	Mechanisms of hemagglutinin targeted influenza virus neutralization Published In PLoS One
2013	Unsynchronised subunit motion in single trimeric sodium-coupled aspartate transporters Published In Nature
2013	Visualization of membrane fusion, one particle at a time Published In Biochemistry
2012	A general approach to break the concentration barrier in single-molecule imaging Published In Nature Methods
2012	Bypass of a protein barrier by a replicative DNA helicase Published In Nature
2012	How DNA-repair proteins find their targets Published In Proceedings of the National Academy of Sciences of USA
2012	Kinetics of proton transport into influenza virions by the viral M2 channel Published In PLoS One
2012	Sequence-dependent sliding kinetics of p53 Published In Proceedings of the National Academy of Sciences of USA
2012	Single-molecule analysis of DNA replication in Xenopus egg extracts Published In Methods
2012	Spotting the mistakes, one molecule at a time Published In Structure
2011	A single molecule DNA flow stretching microscope for undergraduates Published In American Journal of Physics
2011	A single-molecule characterization of p53 search on DNA Published In Proceedings of the National Academy of Sciences of USA
2011	Coupling dTTP hydrolysis with DNA unwinding by the DNA helicase of bacteriophage T7 Published In Journal of Biological Chemistry
2011	DNA is a co-factor for its own replication in Xenopus egg extracts Published In Nucleic Acids Research
2011	Dancing on DNA: kinetic aspects of search processes on DNA Published In ChemPhysChem: a European journal of chemical physics and physical chemistry
2011	E. coli DNA replication in the absence of free β clamps Published In The EMBO Journal
2011	Pyrovanadolysis, a pyrophosphorolysis-like reaction mediated by pyrovanadate, Mn2+, and DNA polymerase of bacteriophage T7 Published In Journal of Biological Chemistry
2011	Selective bypass of a lagging strand roadblock by the eukaryotic replicative DNA helicase Published In Cell
2011	Simultaneous single-molecule measurements of phage T7 replisome composition and function reveal the mechanism of polymerase exchange Published In Proceedings of the National Academy of Sciences of USA
2011	Single-molecule approaches to characterizing kinetics of biomolecular interactions Published In Current Opinion in Biotechnology
2010	Analysis of kinetic intermediates in single-particle dwell-Time distributions Published In Biophysical Journal
2010	CLASP promotes microtubule rescue by recruiting tubulin dimers to the microtubule Published In Developmental Cell
2010	Direct observation of enzymes replicating DNA using a single-molecule DNA stretching assay Published In Journal of Visualized Experiments
2010	Residues in the central β-hairpin of the DNA helicase of bacteriophage T7 are important in DNA unwinding Published In Proceedings of the National Academy of Sciences of USA
2010	Single-molecule binding experiments on long time scales Published In Review of Scientific Instruments
2010	Single-molecule studies of the replisome Published In Annual Review of Biophysics
2010	Thioredoxin suppresses microscopic hopping of T7 DNA polymerase on duplex DNA Published In Proceedings of the National Academy of Sciences of USA
2010	Timing, coordination, and rhythm: acrobatics at the DNA replication fork Published In Journal of Biological Chemistry
2010	Uncoupling of sister replisomes during eukaryotic DNA replication Published In Molecular Cell
2010	Visualizing DNA replication at the single-molecule level Published In Methods in Enzymology
2009	Dynamics of DNA replication loops reveal temporal control of lagging-strand synthesis Published In Nature
2009	Method for measurement of viral fusion kinetics at the single particle level Published In Journal of Visualized Experiments
2009	Nudging through a nucleosome Published In Science
2009	Proliferating cell nuclear antigen uses two distinct modes to move along DNA Published In Journal of Biological Chemistry
2009	Real-time single-molecule observation of rolling-circle DNA replication Published In Nucleic Acids Research
2009	Single-molecule imaging of an in vitro-evolved RNA aptamer reveals homogeneous ligand binding kinetics Published In Journal of the American Chemical Society
2009	Single-molecule observation of prokaryotic DNA replication Published In Methods in Molecular Biology
2009	Visualizing single-molecule DNA replication with fluorescence microscopy Published In Journal of Visualized Experiments
2008	Cutting the forest to see a single tree? Published In Nature Chemical Biology
2008	Hopping of a processivity factor on DNA revealed by single-molecule assays of diffusion Published In Proceedings of the National Academy of Sciences of USA
2008	Single-molecule studies of fork dynamics in Escherichia coli DNA replication Published In Nature Structural and Molecular Biology
2008	Single-particle kinetics of influenza virus membrane fusion Published In Proceedings of the National Academy of Sciences of USA
2008	Tumor suppressor p53 slides on DNA with low friction and high stability Published In Biophysical Journal
2008	mKikGR, a monomeric photoswitchable fluorescent protein Published In PLoS One

Chapter

Year	Title
2013	Replication-fork dynamics Published In DNA Replication: a Subject Collection from Cold Spring Harbor Perspectives in Biology Publisher New York
2009	Single molecule studies of nucleic acid enzymes Published In Single Molecule Biology
2009	Single-molecule enzymology Published In Handbook of Single-Molecule Biophysics Publisher Dordrecht

Editor Of

Book
- Handbook of Single-Molecule Biophysics. Dordrecht. 2009

Investigator On

Year	Title
2021 - 2026	ARC Training Centre for Cryo-electron microscopy of membrane proteins for drug discovery - CCEMMP Awarded by: Australian Research Council (ARC) Funding Scheme: Industrial Transformation Training Centres
2021 - 2025	Roadblocks to DNA replication and implications for antimicrobial resistance Awarded by: National Health and Medical Research Council (NHMRC) Funding Scheme: Investigator Grants
2020 - 2022	Electron Microscopy Centre and Cryo-EM University of Wollongong Awarded by: Microscopy Australia Funding Scheme: Linked Labs Program
2020 - 2022	Revealing the molecular mechanistic details of viral DNA recombination towards developing novel anti-viral drugs Awarded by: National Health and Medical Research Council (NHMRC) Funding Scheme: Ideas Grant
2017 - 2022	Structure and function of a cancer-linked co-regulator complex Awarded by: National Health and Medical Research Council (NHMRC) Funding Scheme: Project Grant
2021	Cryo-Focused Ion Beam Facility: From soft to hard materials Awarded by: Australian Research Council (ARC) Funding Scheme: Linkage Infrastructure Equipment & Facilities (LIEF)
2021	High-throughput camera system for biological cryo-electron microscopy Awarded by: Australian Research Council (ARC) Funding Scheme: Linkage Infrastructure Equipment & Facilities (LIEF)
2021	Roadblocks in DNA replication Awarded by: Australian Research Council (ARC) Funding Scheme: Discovery Projects
2019 - 2021	Antibiotic resistance: combining microscopy, microfluidics and genomics to target bacterial DNA repair pathways Awarded by: National Health and Medical Research Council (NHMRC) Funding Scheme: Project Grant
2019 - 2021	Creation and Repair of Postreplicative DNA Gaps Awarded by: National Institute of Health (NIH) Funding Scheme: Grant
2020	Antoine van Oijen Nomination Awarded by: Office of the NSW Chief Scientist and Engineer Funding Scheme: NSW Premier's Prizes
2020	High-throughput single-molecule evolution Awarded by: Human Frontier Science Program Funding Scheme: Program Grant
2015 - 2020	Under the hood: single-molecule studies of multi-protein machines Awarded by: Australian Research Council (ARC) Funding Scheme: Australian Laureate Fellowships
2019	Antimicrobial Research Taskforce Awarded by: NUW Alliance Funding Scheme: Grant
2019	Use of disruptive technologies to trace, track and tackle antibiotic resistance Awarded by: Medical Research Future Fund (MRFF) Funding Scheme: Frontier Health and Medical Research initiative
2019	Volumetric Imaging Facility: Observing the Cell in its Native Environment Awarded by: Australian Research Council (ARC) Funding Scheme: Linkage Infrastructure Equipment & Facilities (LIEF)
2018	High-throughput portable and wearable device fabrication facility Awarded by: Australian Research Council (ARC) Funding Scheme: Linkage Infrastructure Equipment & Facilities (LIEF)
2018	Pushing the Limits of Fluorescence Microscopy with Adaptive Optics Awarded by: Australian Research Council (ARC) Funding Scheme: Linkage Infrastructure Equipment & Facilities (LIEF)
2016 - 2018	Formin' actin filaments associated with cancer Awarded by: National Health and Medical Research Council (NHMRC) Funding Scheme: Project Grant
2017	Australia-China Joint Research Centre for Point-of-Care Testing Awarded by: Department of Innovation, Industry, Science and Research (DIISR) Funding Scheme: Australia-China Science and Research Fund
2016	Superresolution fluorescence imaging in microbiology Awarded by: Australian Research Council (ARC) Funding Scheme: Linkage Infrastructure Equipment & Facilities (LIEF)
2015	Functional dissection of the bacterial replisome Awarded by: Australian Research Council (ARC) Funding Scheme: Discovery Projects
2015	Rescuing Stalled Replisomes by Accessory Helicases at the Single-Molecule Level Awarded by: KAUST - King Abdullah University of Science and Technology Funding Scheme: Competitive Research Grant Scheme (CRG)
2015	Single molecule imaging laboratory Awarded by: Australian Research Council (ARC) Funding Scheme: Linkage Infrastructure Equipment & Facilities (LIEF)
2008	Functional Dissection of the Bacterial Replisome Awarded by: Australian Research Council (ARC) Funding Scheme: Discovery Projects
2008	Mass Spectrometric Investigations of Conformation and Dynamics of Biological Complexes Awarded by: Australian Research Council (ARC) Funding Scheme: Linkage International
	A functional dissection of the bacterial replisome Awarded by: Australian Research Council (ARC) Funding Scheme: Discovery Projects

Advisees

Graduate Advising Relationship

Degree	Research Title	Advisee
Doctor of Philosophy	Functional Implications of RarA at the Escherichia Coli Replication Fork
Doctor of Philosophy	Single-molecule studies of Saccharomyces cerevisiae DNA replication	Natarajan, Varsha
Doctor of Philosophy	Studying the Chaperone Function of Small Heat-Shock Proteins Using Single-Molecule Fluorescence Microscopy	Johnston, Caitlin
Doctor of Philosophy	The role of translesion DNA synthesis in the development of antibiotic resistance	Cherry, Megan
Doctor of Philosophy	The development of a protein folding-sensor to study molecular chaperones at the single-molecule level	Marzano, Nicholas
Doctor of Philosophy	Exploring Helicase Dynamics in Bacterial DNA Replication: A Single-Molecule Approach	Spinks, Richard
Doctor of Philosophy	Single-molecule studies of the bacterial replisome	Mueller, Stefan
Doctor of Philosophy	Visualising Single-Strand Gap Repair in Live Escherichia Coli Cells	Armstrong, Thomas
Doctor of Philosophy	Dynamic Iinteractions of E. coli Accessory Helicases Rep and UvrD with Stalled Replication Forks	Whinn, Kelsey
Doctor of Philosophy	Antibiotic-induced evolution: combining microscopy, microfluidics and genomics to study resistance in individual bacterial cells	Ripandelli, Remy
Doctor of Philosophy	Roles of Bacterial DNA Repair Pathways in Antibiotic Resistance	Wright, Elizabeth
Doctor of Philosophy	Developing Single-Molecule Approaches to Investigate Interactions Between Alpha-Synuclein and Heat Shock Protein Molecular Chaperones	Rice, Lauren
Doctor of Philosophy	Single-molecule Imaging Analysis of Postreplicative Gap Formation and Repair in Escherichia coli	Belhaffef, Ouraida Amira
Doctor of Philosophy	Conquering chronic pain: an investigation into the structural and functional effects of the a-conotoxin Vc1.1 on GABA(B) receptor mediated G-protein signalling.	Steele, Maddie
Doctor of Philosophy	Investigating the role of recombination mediator proteins in the formation and resolution of single-strand gaps during the E. coli DNA damage response using single molecule live cell imaging. Studying replication-transcription conflicts at the singl...	Sharma, Nischal

Awards And Honors

Biochemistry and Molecular Biology Award , conferred by Dutch Society, 2011
C.J. Kok Prize, conferred by Leiden University, 2002
Starting Grant , conferred by European Research Council, 2012 - 2017
Vici Award, conferred by Dutch Science Foundation, 2011 - 2016
NSF CAREER Award, conferred by National Science Foundation, 2006 - 2011
Searle Scholar, 2005 - 2008
Armenise-Harvard Junior Faculty Award, conferred by Armenise-Harvard Foundation, 2005 - 2007
Long-term postdoctoral fellowship , conferred by Human Frontier Science Program, 2002 - 2004
Postdoctoral fellowship, conferred by Niels Stensen Foundation, 2000 - 2002
Australian Research Council Laureate Fellow, conferred by Australian Research Council, 2015 -

Top Publications

Year	Title
2020	A Primase-Induced Conformational Switch Controls the Stability of the Bacterial Replisome Published in Molecular Cell
2020	Single-molecule imaging reveals molecular coupling between transcription and DNA repair machinery in live cells Published in Nature Communications
2020	Single-molecule live-cell imaging visualizes parallel pathways of prokaryotic nucleotide excision repair Published in Nature Communications
2020	Tunability of DNA Polymerase Stability during Eukaryotic DNA Replication Published in Molecular Cell
2019	Spatial and temporal organization of RecA in the Escherichia coli DNA-damage response Published in eLife
2018	The transcription-repair coupling factor Mfd associates with RNA polymerase in the absence of exogenous damage Published in Nature Communications
2017	Single-molecule visualization of conformational changes and substrate transport in the vitamin B12ABC importer BtuCD-F Published in Nature Communications
2017	Single-molecule visualization of fast polymerase turnover in the bacterial replisome Published in eLife
2013	Bacterial replication, transcription and translation: mechanistic insights from single-molecule biochemical studies Published in Nature Reviews Microbiology
2013	Unsynchronised subunit motion in single trimeric sodium-coupled aspartate transporters Published in Nature
2012	A general approach to break the concentration barrier in single-molecule imaging Published in Nature Methods
2009	Dynamics of DNA replication loops reveal temporal control of lagging-strand synthesis Published in Nature

Research Areas

Research Overview

Antoine van Oijen obtained his BSc and PhD degrees in the Netherlands, where he was trained as a physicist. A growing fascination for biology resulted in him moving to the USA and establishing a research group at Harvard Medical School. Subsequently, he was appointed as full professor at Groningen University in the Netherlands where he established a thriving biophysics research program focused on the development of single-molecule visualisation techniques and their applications in basic and applied science. In 2014, he moved to the UOW and was awarded a prestigious Laureate Fellowship by the Australian Research Council to further develop biophysical approaches to visualise the molecular processes that define life. He is currently Director of Molecular Horizons and an NHMRC Leadership Fellow.

Selected Publications

Journal Article

Year	Title
2020	A Primase-Induced Conformational Switch Controls the Stability of the Bacterial Replisome Published In Molecular Cell
2020	A mechanism for the extension and unfolding of parallel telomeric G-quadruplexes by human telomerase at single-molecule resolution Published In eLife
2020	CHD4 slides nucleosomes by decoupling entry- and exit-side DNA translocation Published In Nature Communications
2020	Community perspectives on the benefits and risks of technologically enhanced communicable disease surveillance systems: A report on four community juries Published In BMC Medical Ethics
2020	Design of customizable long linear DNA substrates with controlled end modifications for single-molecule studies Published In Analytical Biochemistry
2020	Development of a single-stranded DNA-binding protein fluorescent fusion toolbox Published In Nucleic Acids Research
2020	Frequent template switching in postreplication gaps: suppression of deleterious consequences by the Escherichia coli Uup and RadD proteins Published In Nucleic Acids Research
2020	Resolving Toxic DNA repair intermediates in every E. coli replication cycle: critical roles for RecG, Uup and RadD Published In Nucleic Acids Research
2020	Single-molecule imaging reveals molecular coupling between transcription and DNA repair machinery in live cells Published In Nature Communications
2020	Single-molecule live-cell imaging reveals RecB-dependent function of DNA polymerase IV in double strand break repair Published In Nucleic Acids Research
2020	Single-molecule live-cell imaging visualizes parallel pathways of prokaryotic nucleotide excision repair Published In Nature Communications
2020	Tunability of DNA Polymerase Stability during Eukaryotic DNA Replication Published In Molecular Cell
2019	Identification of Multiple Kinetic Populations of DNA-Binding Proteins in Live Cells Published In Biophysical Journal
2019	Nuclease dead Cas9 is a programmable roadblock for DNA replication Published In Scientific Reports
2019	RecFOR epistasis group: RecF and RecO have distinct localizations and functions in Escherichia coli Published In Nucleic Acids Research
2019	Recycling of single-stranded DNA-binding protein by the bacterial replisome Published In Nucleic Acids Research
2019	Role of RNase H enzymes in maintaining genome stability in Escherichia coli expressing a steric-gate mutant of pol VICE391 Published In DNA Repair
2019	Shining a spotlight on DNA: Single-molecule methods to visualise DNA Published In Molecules
2019	Spatial and temporal organization of RecA in the Escherichia coli DNA-damage response Published In eLife
2019	Spy-ing on Cas9: Single-molecule tools reveal the enzymology of Cas9 Published In Current Opinion in Biomedical Engineering
2019	The drivers of antibiotic use and misuse: the development and investigation of a theory driven community measure Published In BMC Public Health
2019	When proteins play tag: the dynamic nature of the replisome Published In Biophysical Reviews
2018	Anisotropic functionalization of upconversion nanoparticles Published In Chemical Science
2018	DNA polymerase IV primarily operates outside of DNA replication forks in Escherichia coli Published In PLoS Genetics
2018	Design of DNA rolling-circle templates with controlled fork topology to study mechanisms of DNA replication Published In Analytical Biochemistry
2018	Detection of kinetic change points in piece-wise linear single molecule motion Published In Journal of Chemical Physics
2018	Nanoparticles for super-resolution microscopy and single-molecule tracking Published In Nature Methods
2018	Quantification of ligand density and stoichiometry on the surface of liposomes using single-molecule fluorescence imaging Published In Journal of Controlled Release
2018	Single-molecule live-cell imaging of bacterial DNA repair and damage tolerance Published In Biochemical Society Transactions
2018	Single-particle fusion of influenza viruses reveals complex interactions with target membranes Published In Journal of Physics: Condensed Matter
2018	Special Issue on Cell Biophysics Published In Biophysical Journal
2018	Specialised DNA polymerases in Escherichia coli: roles within multiple pathways Published In Current Genetics: lower eukaryotes and organelles
2018	The small heat shock protein Hsp27 binds α-synuclein fibrils, preventing elongation and cytotoxicity Published In Journal of Biological Chemistry
2018	The transcription-repair coupling factor Mfd associates with RNA polymerase in the absence of exogenous damage Published In Nature Communications
2018	Using single-molecule approaches to understand the molecular mechanisms of heat-shock protein chaperone function Published In American Journal of Molecular Biology
2017	Architecture of the Nucleosome Remodeling and Deacetylase (NuRD) Complex Published In The FASEB Journal
2017	Diatrack particle tracking software: Review of applications and performance evaluation Published In Traffic
2017	Mechanism of membrane fusion induced by vesicular stomatitis virus G protein Published In Proceedings of the National Academy of Sciences of USA
2017	Single-Molecule Fluorescence Studies of Membrane Transporters Using Total Internal Reflection Microscopy Published In Methods in Enzymology
2017	Single-molecule visualization of Saccharomyces cerevisiae leading-strand synthesis reveals dynamic interaction between MTC and the replisome Published In Proceedings of the National Academy of Sciences of USA
2017	Single-molecule visualization of conformational changes and substrate transport in the vitamin B12ABC importer BtuCD-F Published In Nature Communications
2017	Single-molecule visualization of fast polymerase turnover in the bacterial replisome Published In eLife
2017	The more the merrier: high-throughput single-molecule techniques Published In Biochemical Society Transactions
2017	Watching cellular machinery in action, one molecule at a time Published In The Journal of Cell Biology
2016	A tool for alignment and averaging of sparse fluorescence signals in rod-shaped bacteria Published In Biophysical Journal
2016	Bisecting Microfluidic Channels with Metallic Nanowires Fabricated by Nanoskiving Published In ACS Nano
2016	Droplet microfluidics for kinetic studies of viral fusion Published In Biomicrofluidics
2016	Droplet microfluidics: a tool for biology, chemistry and nanotechnology Published In Trends in Analytical Chemistry
2016	Lipids activate SecA for high affinity binding to the SecYEG complex Published In Journal of Biological Chemistry
2016	Mechanisms of influenza viral membrane fusion Published In Seminars in Cell and Developmental Biology
2016	Mutations for worse or better: low-fidelity DNA Synthesis by SOS DNA polymerase v is a tightly regulated double-edged sword Published In Biochemistry
2016	On the spatial organization of mRNA, plasmids, and ribosomes in a bacterial host overexpressing membrane proteins Published In PLoS Genetics
2016	Simultaneous real-time imaging of leading and lagging strand synthesis reveals the coordination dynamics of single replisomes Published In Molecular Cell
2016	Single-molecule specific mislocalization of red fluorescent proteins in live Escherichia coli Published In Biophysical Journal
2016	Speeding up biomolecular interactions by molecular sledding Published In Chemical Science
2016	Stability versus exchange: a paradox in DNA replication Published In Nucleic Acids Research
2015	Chikungunya virus fusion properties elucidated by single-particle and bulk approaches Published In Journal of General Virology
2015	External control of reactions in microdroplets Published In Scientific Reports
2015	ISBatch: a batch-processing platform for data analysis and exploration of live-cell single-molecule microscopy images and other hierarchical datasets Published In Molecular Biosystems
2015	In vivo single-molecule studies of DNA repair in E. Coli Published In The FASEB Journal
2015	Probing molecular choreography through single-molecule biochemistry Published In Nature Structural and Molecular Biology
2015	Regulation of mutagenic DNA polymerase V activation in space and time Published In PLoS Genetics
2015	Single-molecule imaging at high fluorophore concentrations by local activation of dye Published In Biophysical Journal
2015	Single-molecule observation of prokaryotic DNA replication Published In Methods in Molecular Biology
2015	The innate immune sensor IFI16 recognizes foreign DNA in the nucleus by scanning along the duplex Published In eLife
2015	Theory of bimolecular reactions in a solution with linear traps: application to the problem of target search on DNA Published In Physical Review E: Statistical, Nonlinear, and Soft Matter Physics
2014	A versatile approach to the generation of fluid supported lipid bilayers and its applications Published In Biotechnology and Bioengineering
2014	DNA replication at the single-molecule level Published In Chemical Society Reviews
2014	Membrane-on-a-Chip: Microstructured Silicon/Silicon-Dioxide Chips for High-Throughput Screening of Membrane Transport and Viral Membrane Fusion Published In ACS Nano
2014	ParB spreading requires DNA bridging Published In Genes and Development
2014	Relating influenza virus membrane fusion kinetics to stoichiometry of neutralizing antibodies at the single-particle level Published In Proceedings of the National Academy of Sciences of USA
2014	Single-molecule studies of polymerase dynamics and stoichiometry at the bacteriophage T7 replication machinery Published In Proceedings of the National Academy of Sciences of USA
2013	A direct proofreader-clamp interaction stabilizes the Pol III replicase in the polymerization mode Published In The EMBO Journal
2013	A single-molecule view of DNA replication: the dynamic nature of multi-protein complexes revealed Published In Current Opinion in Structural Biology
2013	Bacterial replication, transcription and translation: mechanistic insights from single-molecule biochemical studies Published In Nature Reviews Microbiology
2013	Influenza-virus membrane fusion by cooperative fold-back of stochastically induced hemagglutinin intermediates Published In eLife
2013	Mechanisms of hemagglutinin targeted influenza virus neutralization Published In PLoS One
2013	Unsynchronised subunit motion in single trimeric sodium-coupled aspartate transporters Published In Nature
2013	Visualization of membrane fusion, one particle at a time Published In Biochemistry
2012	A general approach to break the concentration barrier in single-molecule imaging Published In Nature Methods
2012	Bypass of a protein barrier by a replicative DNA helicase Published In Nature
2012	How DNA-repair proteins find their targets Published In Proceedings of the National Academy of Sciences of USA
2012	Kinetics of proton transport into influenza virions by the viral M2 channel Published In PLoS One
2012	Sequence-dependent sliding kinetics of p53 Published In Proceedings of the National Academy of Sciences of USA
2012	Single-molecule analysis of DNA replication in Xenopus egg extracts Published In Methods
2012	Spotting the mistakes, one molecule at a time Published In Structure
2011	A single molecule DNA flow stretching microscope for undergraduates Published In American Journal of Physics
2011	A single-molecule characterization of p53 search on DNA Published In Proceedings of the National Academy of Sciences of USA
2011	Coupling dTTP hydrolysis with DNA unwinding by the DNA helicase of bacteriophage T7 Published In Journal of Biological Chemistry
2011	DNA is a co-factor for its own replication in Xenopus egg extracts Published In Nucleic Acids Research
2011	Dancing on DNA: kinetic aspects of search processes on DNA Published In ChemPhysChem: a European journal of chemical physics and physical chemistry
2011	E. coli DNA replication in the absence of free β clamps Published In The EMBO Journal
2011	Pyrovanadolysis, a pyrophosphorolysis-like reaction mediated by pyrovanadate, Mn2+, and DNA polymerase of bacteriophage T7 Published In Journal of Biological Chemistry
2011	Selective bypass of a lagging strand roadblock by the eukaryotic replicative DNA helicase Published In Cell
2011	Simultaneous single-molecule measurements of phage T7 replisome composition and function reveal the mechanism of polymerase exchange Published In Proceedings of the National Academy of Sciences of USA
2011	Single-molecule approaches to characterizing kinetics of biomolecular interactions Published In Current Opinion in Biotechnology
2010	Analysis of kinetic intermediates in single-particle dwell-Time distributions Published In Biophysical Journal
2010	CLASP promotes microtubule rescue by recruiting tubulin dimers to the microtubule Published In Developmental Cell
2010	Direct observation of enzymes replicating DNA using a single-molecule DNA stretching assay Published In Journal of Visualized Experiments
2010	Residues in the central β-hairpin of the DNA helicase of bacteriophage T7 are important in DNA unwinding Published In Proceedings of the National Academy of Sciences of USA
2010	Single-molecule binding experiments on long time scales Published In Review of Scientific Instruments
2010	Single-molecule studies of the replisome Published In Annual Review of Biophysics
2010	Thioredoxin suppresses microscopic hopping of T7 DNA polymerase on duplex DNA Published In Proceedings of the National Academy of Sciences of USA
2010	Timing, coordination, and rhythm: acrobatics at the DNA replication fork Published In Journal of Biological Chemistry
2010	Uncoupling of sister replisomes during eukaryotic DNA replication Published In Molecular Cell
2010	Visualizing DNA replication at the single-molecule level Published In Methods in Enzymology
2009	Dynamics of DNA replication loops reveal temporal control of lagging-strand synthesis Published In Nature
2009	Method for measurement of viral fusion kinetics at the single particle level Published In Journal of Visualized Experiments
2009	Nudging through a nucleosome Published In Science
2009	Proliferating cell nuclear antigen uses two distinct modes to move along DNA Published In Journal of Biological Chemistry
2009	Real-time single-molecule observation of rolling-circle DNA replication Published In Nucleic Acids Research
2009	Single-molecule imaging of an in vitro-evolved RNA aptamer reveals homogeneous ligand binding kinetics Published In Journal of the American Chemical Society
2009	Single-molecule observation of prokaryotic DNA replication Published In Methods in Molecular Biology
2009	Visualizing single-molecule DNA replication with fluorescence microscopy Published In Journal of Visualized Experiments
2008	Cutting the forest to see a single tree? Published In Nature Chemical Biology
2008	Hopping of a processivity factor on DNA revealed by single-molecule assays of diffusion Published In Proceedings of the National Academy of Sciences of USA
2008	Single-molecule studies of fork dynamics in Escherichia coli DNA replication Published In Nature Structural and Molecular Biology
2008	Single-particle kinetics of influenza virus membrane fusion Published In Proceedings of the National Academy of Sciences of USA
2008	Tumor suppressor p53 slides on DNA with low friction and high stability Published In Biophysical Journal
2008	mKikGR, a monomeric photoswitchable fluorescent protein Published In PLoS One

Chapter

Year	Title
2013	Replication-fork dynamics Published In DNA Replication: a Subject Collection from Cold Spring Harbor Perspectives in Biology Publisher New York
2009	Single molecule studies of nucleic acid enzymes Published In Single Molecule Biology
2009	Single-molecule enzymology Published In Handbook of Single-Molecule Biophysics Publisher Dordrecht

Editor Of

Book
- Handbook of Single-Molecule Biophysics. Dordrecht. 2009

Investigator On

Year	Title
2021 - 2026	ARC Training Centre for Cryo-electron microscopy of membrane proteins for drug discovery - CCEMMP Awarded by: Australian Research Council (ARC) Funding Scheme: Industrial Transformation Training Centres
2021 - 2025	Roadblocks to DNA replication and implications for antimicrobial resistance Awarded by: National Health and Medical Research Council (NHMRC) Funding Scheme: Investigator Grants
2020 - 2022	Electron Microscopy Centre and Cryo-EM University of Wollongong Awarded by: Microscopy Australia Funding Scheme: Linked Labs Program
2020 - 2022	Revealing the molecular mechanistic details of viral DNA recombination towards developing novel anti-viral drugs Awarded by: National Health and Medical Research Council (NHMRC) Funding Scheme: Ideas Grant
2017 - 2022	Structure and function of a cancer-linked co-regulator complex Awarded by: National Health and Medical Research Council (NHMRC) Funding Scheme: Project Grant
2021	Cryo-Focused Ion Beam Facility: From soft to hard materials Awarded by: Australian Research Council (ARC) Funding Scheme: Linkage Infrastructure Equipment & Facilities (LIEF)
2021	High-throughput camera system for biological cryo-electron microscopy Awarded by: Australian Research Council (ARC) Funding Scheme: Linkage Infrastructure Equipment & Facilities (LIEF)
2021	Roadblocks in DNA replication Awarded by: Australian Research Council (ARC) Funding Scheme: Discovery Projects
2019 - 2021	Antibiotic resistance: combining microscopy, microfluidics and genomics to target bacterial DNA repair pathways Awarded by: National Health and Medical Research Council (NHMRC) Funding Scheme: Project Grant
2019 - 2021	Creation and Repair of Postreplicative DNA Gaps Awarded by: National Institute of Health (NIH) Funding Scheme: Grant
2020	Antoine van Oijen Nomination Awarded by: Office of the NSW Chief Scientist and Engineer Funding Scheme: NSW Premier's Prizes
2020	High-throughput single-molecule evolution Awarded by: Human Frontier Science Program Funding Scheme: Program Grant
2015 - 2020	Under the hood: single-molecule studies of multi-protein machines Awarded by: Australian Research Council (ARC) Funding Scheme: Australian Laureate Fellowships
2019	Antimicrobial Research Taskforce Awarded by: NUW Alliance Funding Scheme: Grant
2019	Use of disruptive technologies to trace, track and tackle antibiotic resistance Awarded by: Medical Research Future Fund (MRFF) Funding Scheme: Frontier Health and Medical Research initiative
2019	Volumetric Imaging Facility: Observing the Cell in its Native Environment Awarded by: Australian Research Council (ARC) Funding Scheme: Linkage Infrastructure Equipment & Facilities (LIEF)
2018	High-throughput portable and wearable device fabrication facility Awarded by: Australian Research Council (ARC) Funding Scheme: Linkage Infrastructure Equipment & Facilities (LIEF)
2018	Pushing the Limits of Fluorescence Microscopy with Adaptive Optics Awarded by: Australian Research Council (ARC) Funding Scheme: Linkage Infrastructure Equipment & Facilities (LIEF)
2016 - 2018	Formin' actin filaments associated with cancer Awarded by: National Health and Medical Research Council (NHMRC) Funding Scheme: Project Grant
2017	Australia-China Joint Research Centre for Point-of-Care Testing Awarded by: Department of Innovation, Industry, Science and Research (DIISR) Funding Scheme: Australia-China Science and Research Fund
2016	Superresolution fluorescence imaging in microbiology Awarded by: Australian Research Council (ARC) Funding Scheme: Linkage Infrastructure Equipment & Facilities (LIEF)
2015	Functional dissection of the bacterial replisome Awarded by: Australian Research Council (ARC) Funding Scheme: Discovery Projects
2015	Rescuing Stalled Replisomes by Accessory Helicases at the Single-Molecule Level Awarded by: KAUST - King Abdullah University of Science and Technology Funding Scheme: Competitive Research Grant Scheme (CRG)
2015	Single molecule imaging laboratory Awarded by: Australian Research Council (ARC) Funding Scheme: Linkage Infrastructure Equipment & Facilities (LIEF)
2008	Functional Dissection of the Bacterial Replisome Awarded by: Australian Research Council (ARC) Funding Scheme: Discovery Projects
2008	Mass Spectrometric Investigations of Conformation and Dynamics of Biological Complexes Awarded by: Australian Research Council (ARC) Funding Scheme: Linkage International
	A functional dissection of the bacterial replisome Awarded by: Australian Research Council (ARC) Funding Scheme: Discovery Projects

Advisees

Graduate Advising Relationship

Degree	Research Title	Advisee
Doctor of Philosophy	Functional Implications of RarA at the Escherichia Coli Replication Fork
Doctor of Philosophy	Single-molecule studies of Saccharomyces cerevisiae DNA replication	Natarajan, Varsha
Doctor of Philosophy	Studying the Chaperone Function of Small Heat-Shock Proteins Using Single-Molecule Fluorescence Microscopy	Johnston, Caitlin
Doctor of Philosophy	The role of translesion DNA synthesis in the development of antibiotic resistance	Cherry, Megan
Doctor of Philosophy	The development of a protein folding-sensor to study molecular chaperones at the single-molecule level	Marzano, Nicholas
Doctor of Philosophy	Exploring Helicase Dynamics in Bacterial DNA Replication: A Single-Molecule Approach	Spinks, Richard
Doctor of Philosophy	Single-molecule studies of the bacterial replisome	Mueller, Stefan
Doctor of Philosophy	Visualising Single-Strand Gap Repair in Live Escherichia Coli Cells	Armstrong, Thomas
Doctor of Philosophy	Dynamic Iinteractions of E. coli Accessory Helicases Rep and UvrD with Stalled Replication Forks	Whinn, Kelsey
Doctor of Philosophy	Antibiotic-induced evolution: combining microscopy, microfluidics and genomics to study resistance in individual bacterial cells	Ripandelli, Remy
Doctor of Philosophy	Roles of Bacterial DNA Repair Pathways in Antibiotic Resistance	Wright, Elizabeth
Doctor of Philosophy	Developing Single-Molecule Approaches to Investigate Interactions Between Alpha-Synuclein and Heat Shock Protein Molecular Chaperones	Rice, Lauren
Doctor of Philosophy	Single-molecule Imaging Analysis of Postreplicative Gap Formation and Repair in Escherichia coli	Belhaffef, Ouraida Amira
Doctor of Philosophy	Conquering chronic pain: an investigation into the structural and functional effects of the a-conotoxin Vc1.1 on GABA(B) receptor mediated G-protein signalling.	Steele, Maddie
Doctor of Philosophy	Investigating the role of recombination mediator proteins in the formation and resolution of single-strand gaps during the E. coli DNA damage response using single molecule live cell imaging. Studying replication-transcription conflicts at the singl...	Sharma, Nischal

Awards And Honors

Biochemistry and Molecular Biology Award , conferred by Dutch Society, 2011
C.J. Kok Prize, conferred by Leiden University, 2002
Starting Grant , conferred by European Research Council, 2012 - 2017
Vici Award, conferred by Dutch Science Foundation, 2011 - 2016
NSF CAREER Award, conferred by National Science Foundation, 2006 - 2011
Searle Scholar, 2005 - 2008
Armenise-Harvard Junior Faculty Award, conferred by Armenise-Harvard Foundation, 2005 - 2007
Long-term postdoctoral fellowship , conferred by Human Frontier Science Program, 2002 - 2004
Postdoctoral fellowship, conferred by Niels Stensen Foundation, 2000 - 2002
Australian Research Council Laureate Fellow, conferred by Australian Research Council, 2015 -

van Oijen, Antoine M. Distinguished Professor

Director Molecular Horizons

Overview

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Research Overview

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Selected Publications

Journal Article

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Editor Of

Book

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Investigator On

Supervision

Advisees

Graduate Advising Relationship

Background

Awards And Honors

Overview

Top Publications

Research Areas

Research Overview

Publications

Selected Publications

Journal Article

Chapter

Editor Of

Book

Funding

Investigator On

Supervision

Advisees

Graduate Advising Relationship

Background

Awards And Honors

Visualisations

Research Areas