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OnderzoekZernike (ZIAM)MBPVan Oijen Group

Publications

2014

Graham, TGW, Wang, X, Song, D, Etson, CM, van Oijen, AM, Rudner, DZ & Loparo, JJ 2014, 'ParB spreading requires DNA bridging' Genes & Development, vol 28, no. 11, pp. 1228-1238., 10.1101/gad.242206.114

Kusters, I, van Oijen, AM & Driessen, AJM 2014, 'Membrane-on-a-Chip: Microstructured Silicon/Silicon-Dioxide Chips for High-Throughput Screening of Membrane Transport and Viral Membrane Fusion' Acs Nano, vol 8, no. 4, pp. 3380-3392., 10.1021/nn405884a

Geertsema, HJ, Kulczyk, AW, Richardson, CC & van Oijen, AM 2014, 'Single-molecule studies of polymerase dynamics and stoichiometry at the bacteriophage T7 replication machinery' Proceedings of the National Academy of Science of the United States of America, vol 111, no. 11, pp. 4073-4078., 10.1073/pnas.1402010111

Duderstadt, KE, Reyes-Lamothe, R, van Oijen, AM & Sherratt, DJ 2014, 'Replication-Fork Dynamics' Cold spring harbor perspectives in biology, vol 6, no. 1, 010157., 10.1101/cshperspect.a010157

van Oijen, A & Mashaghitabari, S 2014, 'A versatile approach to the generation of fluid supported lipid bilayers and its applications' Biotechnology and Bioengineering, pp. 1-6.

Stratmann, SA & Oijen, AMV 2014, 'DNA replication at the single-molecule level' Chemical Society Reviews, vol 43, no. 4, pp. 1201-1220., 10.1039/c3cs60391a

Duderstadt, KE, Punter, CM, Kulczyk, AW, Richardson, CC & Oijen, AMV 2014, 'Simultaneous Imaging of Leading- and Lagging-Strand Synthesis Reveals Distinct Operational Modes of Single Replication Machines' Biophysical Journal, vol 106, no. 2, pp. 273a-273a., 10.1016/j.bpj.2013.11.1600

2013

Erkens, GB, Hänelt, I, Goudsmits, JMH, Slotboom, DJ & van Oijen, AM 2013, 'Unsynchronised subunit motion in single trimeric sodium-coupled aspartate transporters' Nature, vol 502, no. 7469, pp. 119-123., 10.1038/nature12538

Geertsema, HJ, van Oijen, AM, Chiu, W (ed.) & Wagner, G (ed.) 2013, 'A single-molecule view of DNA replication: the dynamic nature of multi-protein complexes revealed' Current Opinion in Structural Biology, vol 23, no. 5, pp. 788-793., 10.1016/j.sbi.2013.06.018

Kusters, I, Punter, M, Birkner, J-P, Tans, S, van Oijen, A & Driessen, AJ 2013, 'Single molecule observation of protein translocation' European biophysics journal with biophysics letters, vol 42, pp. S59-S59.

Jergic, S, Horan, NP, Elshenawy, MM, Mason, CE, Urathamakul, T, Ozawa, K, Robinson, A, Goudsmits, JMH, Wang, Y, Pan, X, Beck, JL, van Oijen, AM, Huber, T, Hamdan, SM & Dixon, NE 2013, 'A direct proofreader-clamp interaction stabilizes the Pol III replicase in the polymerization mode' EMBO Journal, vol 32, no. 9, pp. 1322-1333., 10.1038/emboj.2012.347

Robinson, A & van Oijen, AM 2013, 'Bacterial replication, transcription and translation: mechanistic insights from single-molecule biochemical studies' Nature Reviews Microbiology, vol 11, no. 5, pp. 303-315., 10.1038/nrmicro2994

Otterstrom, J & van Oijen, AM 2013, 'Visualization of Membrane Fusion, One Particle at a Time' Biochemistry, vol 52, no. 10, pp. 1654-1668., 10.1021/bi301573w

Birkner, JP, Kusters, I, Driessen, A & Oijen, AV 2013, 'Protein Translocation at the Single Molecule Level' Biophysical Journal, vol 104, no. 2, pp. 110a-110a., 10.1016/j.bpj.2012.11.640

Erkens, GB, Haenelt, I, Slotboom, DJ & Oijen, AMV 2013, 'Single-Molecule Dynamics of a Trimeric Aspartate Transporter' Biophysical Journal, vol 104, no. 2, pp. 384a-385a., 10.1016/j.bpj.2012.11.2143

Turkin, A, Mangel, WF & Oijen, AMV 2013, 'Single-Molecule Studies of Adenovirus Maturation' Biophysical Journal, vol 104, no. 2, pp. 178a-179a., 10.1016/j.bpj.2012.11.1004

Graham, TGW, Song, L, Wang, X, Etson, CM, Van Oijen, A, Rudner, DZ & Loparo, JJ 2013, 'Single-Molecule Studies of a ParB Family Chromosome Segregation Protein from Bacillussubtilis' Biophysical Journal, vol 104, no. 2, pp. 582A-583A.

Otterstrom, J, Juraszek, J, Tang, C, Koldijk, M, Vogels, R, Friesen, R, Brandenburg, B & van Oijen, A 2013, 'Stoichiometry of Influenza Hemagglutinin Neutralization by Broadly Acting Antibodies using Single Virus-Particle Visualization' Biophysical Journal, vol 104, no. 2, pp. 371A.

Ivanovic, T, Choi, JL, Whelan, SP, Oijen, AMV & Harrison, SC 2013, 'Influenza-virus membrane fusion by cooperative fold-back of stochastically induced hemagglutinin intermediates' eLife, vol 2, no. 2., 10.7554/elife.00333

Brandenburg, B, Koudstaal, W, Goudsmit, J, Klaren, V, Tang, C, Bujny, MV, Korse, HJWM, Kwaks, T, Otterstrom, JJ, Juraszek, J, Oijen, AMV, Vogels, R & Friesen, RHE 2013, 'Mechanisms of Hemagglutinin Targeted Influenza Virus Neutralization' PLoS ONE, vol 8, no. 12, pp. e80034-1-e80034-14., 10.1371/journal.pone.0080034

2012

Yardimci, H, Wang, X, Loveland, AB, Tappin, I, Rudner, DZ, Hurwitz, J, van Oijen, AM & Walter, JC 2012, 'Bypass of a protein barrier by a replicative DNA helicase' Nature, vol 492, no. 7428, pp. 205-+., 10.1038/nature11730

Quessada-Vial, A & van Oijen, AM 2012, 'How DNA-repair proteins find their targets' Proceedings of the National Academy of Sciences of the United States of America, vol 109, no. 45, pp. 18243-18244., 10.1073/pnas.1215845109

Leith, JS, Tafvizi, A, Huang, F, Uspal, WE, Doyle, PS, Fersht, AR, Mirny, LA, van Oijen, AM & Hammes, GG (ed.) 2012, 'Sequence-dependent sliding kinetics of p53' Proceedings of the National Academy of Sciences of the United States of America, vol 109, no. 41, pp. 16552-16557., 10.1073/pnas.1120452109

Quessada-Vial, A & van Oijen, AM 2012, 'Spotting the Mistakes, One Molecule at a Time' Structure, vol 20, no. 7, pp. 1130-1132., 10.1016/j.str.2012.06.007

Yardimci, H, Loveland, AB, van Oijen, AM, Walter, JC & Mechali, M (ed.) 2012, 'Single-molecule analysis of DNA replication in Xenopus egg extracts' Methods, vol 57, no. 2, pp. 179-186., 10.1016/j.ymeth.2012.03.033

Oijen, AMV 2012, 'A Single-Molecule Characterization of P53 Search on DNA' Biophysical Journal, vol 102, no. 3, pp. 1a-2a., 10.1016/j.bpj.2011.11.021

Otterstrom, J, Juraszek, J, Tang, C, Koldijk, M, Vogels, R, Friesen, R, Brandenburg, B & van Oijen, AM 2012, 'Watching Influenza get Hogtied' Biophysical Journal, vol 102, no. 3, pp. 605A-605A.

Loveland, AB, Habuchi, S, Walter, JC & Oijen, AMV 2012, 'A general approach to break the concentration barrier in single-molecule imaging' Nature Methods, vol 9, no. 10, pp. 987-992., 10.1038/nmeth.2174

Ivanovic, T, Rozendaal, R, Floyd, DL, Popovic, M, Oijen, AMV & Harrison, SC 2012, 'Kinetics of Proton Transport into Influenza Virions by the Viral M2 Channel' PLoS ONE, vol 7, no. 3, pp. e31566-1-e31566-9., 10.1371/journal.pone.0031566

2011

Williams, K, Grafe, B, Burke, KM, Tanner, N, van Oijen, AM, Loparo, J & Price, AC 2011, 'A single molecule DNA flow stretching microscope for undergraduates' American Journal of Physics, vol 79, no. 11, pp. 1112-1120., 10.1119/1.3620410

Akabayov, B, Kulczyk, AW, Akabayov, SR, Theile, C, McLaughlin, LW, Beauchamp, B, van Oijen, AM & Richardson, CC 2011, 'Pyrovanadolysis, a Pyrophosphorolysis-like Reaction Mediated by Pyrovanadate, Mn2+, and DNA Polymerase of Bacteriophage T7' Journal of Biological Chemistry, vol 286, no. 33, pp. 29146-29157., 10.1074/jbc.M111.250944

van Oijen, AM 2011, 'Single-molecule studies of DNA replication' European biophysics journal with biophysics letters, vol 40, pp. 99-100.

Tafvizi, A, Mirny, LA, van Oijen, AM, Huang, F, Fersht, AR & Fersht, AR (ed.) 2011, 'Dancing on DNA: Kinetic Aspects of Search Processes on DNA' Chemphyschem, vol 12, no. 8, pp. 1481-1489., 10.1002/cphc.201100112

Tanner, NA, Tolun, G, Loparo, JJ, Jergic, S, Griffith, JD, Dixon, NE & van Oijen, AM 2011, 'E. coli DNA replication in the absence of free beta clamps' EMBO Journal, vol 30, no. 9, pp. 1830-1840., 10.1038/emboj.2011.84

van Oijen, AM 2011, 'Single-molecule approaches to characterizing kinetics of biomolecular interactions' Current Opinion in Biotechnology, vol 22, no. 1, pp. 75-80., 10.1016/j.copbio.2010.10.002

Tafvizi, A, Huang, F, Fersht, AR, Mirny, LA & van Oijen, AM 2011, 'A single-molecule characterization of p53 search on DNA' Proceedings of the National Academy of Science of the United States of America, vol 108, no. 2, pp. 563-568., 10.1073/pnas.1016020107

Lebofsky, R, van Oijen, AM & Walter, JC 2011, 'DNA is a co-factor for its own replication in Xenopus egg extracts' Nucleic Acids Research, vol 39, no. 2, pp. 545-555., 10.1093/nar/gkq739

Tafvizi, A, Huang, F, Fersht, AR, Mirny, LA & Oijen, AMV 2011, 'A single-molecule characterization of p53 search on DNA' Proceedings of the National Academy of Sciences of the United States of America, vol 108, no. 2, pp. 563-568., 10.1002/cphc.201100112

Satapathy, AK, Kulczyk, AW, Ghosh, S, Oijen, AMV & Richardson, CC 2011, 'Coupling dTTP Hydrolysis with DNA Unwinding by the DNA Helicase of Bacteriophage T7' the Journal of Biological Chemistry, vol 286, no. 39, pp. 34468-34478., 10.1074/jbc.M111.283796

Fu, YV, Yardimci, H, Long, DT, Ho, TV, Guainazzi, A, Bermudez, VP, Hurwitz, J, Oijen, AV, Schärer, OD & Walter, JC 2011, 'Selective Bypass of a Lagging Strand Roadblock by the Eukaryotic Replicative DNA Helicase' Cell, vol 146, no. 6, pp. 931-941., 10.1016/j.cell.2011.07.045

Loparo, JJ, Kulczyk, AW, Richardson, CC & Oijen, AMV 2011, 'Simultaneous single-molecule measurements of phage T7 replisome composition and function reveal the mechanism of polymerase exchange' Proceedings of the National Academy of Sciences of the United States of America, vol 108, no. 9, pp. 3584-3589., 10.1073/pnas.1018824108

Yardimci, H, Oijen, AMV & Walter, JC 2011, 'Single-Molecule Studies of the Eukaryotic Replicative DNA Helicase MCM2-7' Biophysical Journal, vol 100, no. 3, pp. 239a-239a., 10.1016/j.bpj.2010.12.1521

2010

Yardimci, H, Loveland, AB, Habuchi, S, van Oijen, AM & Walter, JC 2010, 'Uncoupling of Sister Replisomes during Eukaryotic DNA Replication' Molecular Cell, vol 40, no. 5, pp. 834-840., 10.1016/j.molcel.2010.11.027

Elenko, MP, Szostak, JW & van Oijen, AM 2010, 'Single-molecule binding experiments on long time scales' Review of Scientific Instruments, vol 81, no. 8, 083705, pp. 083705-1-083705-9., 10.1063/1.3473936

Kulczyk, AW, Tanner, NA, Loparo, JJ, Richardson, CC & Oijen, AMV 2010, 'Direct observation of enzymes replicating DNA using a single-molecule DNA stretching assay' Journal of visualized experiments : JoVE, vol 44, no. 37., 10.3791/1689

Floyd, DL, Harrison, SC & Oijen, AMV 2010, 'Analysis of Kinetic Intermediates in Single-Particle Dwell-Time Distributions' Biophysical Journal, vol 99, no. 2, pp. 360-366., 10.1016/j.bpj.2010.04.049

Bassam, JA, Kim, H, Brouhard, G, Oijen, AV, Harrison, SC & Chang, F 2010, 'CLASP Promotes Microtubule Rescue by Recruiting Tubulin Dimers to the Microtubule' Developmental Cell, vol 19, no. 2, pp. 245-258., 10.1016/j.devcel.2010.07.016

Otterstrom, JJ, Floyd, DL, Skehel, JJ, Harrison, SC & Oijen, AMV 2010, 'Lipid Bilayer Rigidity Affects the Fusion Kinetics of Individually Observed Influenza Particles' Biophysical Journal, vol 98, no. 3, pp. 673a-673a., 10.1016/j.bpj.2009.12.3697

Etson, CM, Rudner, DZ & Oijen, AMV 2010, 'Nucleoprotein Complex Formation By Bacillus Subtilis Spo0J/ParB' Biophysical Journal, vol 98, no. 3, pp. 74a-74a., 10.1016/j.bpj.2009.12.418

Satapathy, AK, Kochaniak, AB, Mukherjee, S, Crampton, DJ, Oijen, AV & Richardson, CC (ed.) 2010, 'Residues in the central β-hairpin of the DNA helicase of bacteriophage T7 are important in DNA unwinding' Proceedings of the National Academy of Sciences of the United States of America, vol 107, no. 15, pp. 6782-6787., 10.1073/pnas.1002734107

Yardimci, H, Kochaniak, AB, Habuchi, S, Havens, CG, Walter, JC & Oijen, AV 2010, 'Single Molecule Studies of Eukaryotic Replisomes in Xenopus Egg Extracts' Biophysical Journal, vol 98, no. 3, pp. 437a-437a., 10.1016/j.bpj.2009.12.2371

Oijen, AMV & Loparo, JJ 2010, 'Single-Molecule Studies of the Replisome' Annual Review of Biophysics, vol 39, no. 1, pp. 429-448., 10.1146/annurev.biophys.093008.131327

Etson, CM, Hamdan, SM, Richardson, CC, Oijen, AMV & Richardson, CC (ed.) 2010, 'Thioredoxin suppresses microscopic hopping of T7 DNA polymerase on duplex DNA' Proceedings of the National Academy of Sciences of the United States of America, vol 107, no. 5, pp. 1900-1905., 10.1073/pnas.0912664107

Hamdan, SM & Oijen, AMV 2010, 'Timing, Coordination, and Rhythm: Acrobatics at the DNA Replication Fork' Journal of Biological Chemistry, vol 285, no. 25, pp. 18979-18983., 10.1074/jbc.R109.022939

Tanner, NA & van Oijen, AM 2010, 'VISUALIZING DNA REPLICATION AT THE SINGLE-MOLECULE LEVEL'. in NG Walter (ed.), METHODS IN ENZYMOLOGY, VOL 475: SINGLE MOLECULE TOOLS, PT B. Methods in Enzymology, vol. 475, Academic Press/Elsevier, SAN DIEGO, pp. 259-278., 10.1016/S0076-6879(10)75011-4

2009

Tanner, NA, Loparo, JJ & Oijen, AMV 2009, 'Visualizing Single-molecule DNA Replication with Fluorescence Microscopy' Journal of visualized experiments : JoVE, vol 44, no. 32, pp. e1529-1-e1529-4., 10.3791/1529

Floyd, DL, Harrison, SC & Oijen, AMV 2009, 'Method for measurement of viral fusion kinetics at the single particle level' Journal of visualized experiments : JoVE, vol 44, no. 31., 10.3791/1484

Hamdan, SM, Loparo, JJ, Takahashi, M, Richardson, CC & Oijen, AMV 2009, 'Dynamics of DNA replication loops reveal temporal control of lagging-strand synthesis' Nature, vol 457, no. 3, pp. 336-340., 10.1016/j.bpj.2008.12.3720

Otterstrom, JJ & Oijen, AMV 2009, 'Nudging Through a Nucleosome' Science, vol 325, no. 5940, pp. 547-548., 10.1126/science.1177311

Kochaniak, AB, Habuchi, S, Loparo, JJ, Chang, DJ, Cimprich, KA, Walter, JC & Oijen, AMV 2009, 'Proliferating Cell Nuclear Antigen Uses Two Distinct Modes to Move along DNA' the Journal of Biological Chemistry, vol 284, no. 26, pp. 17700-17710., 10.1074/jbc.M109.008706

Tanner, NA, Loparo, JJ, Hamdan, SM, Jergic, S, Dixon, NE & Oijen, AMV 2009, 'Real-time single-molecule observation of rolling-circle DNA replication' Nucleic Acids Research, vol 37, no. 4, pp. e27-1-e27-6., 10.1093/nar/gkp006

Leith, JS, Tafvizi, A, Huang, F, Fersht, AR, Mirny, LA & Oijen, AMV 2009, 'Sequence-Dependent Kinetics of One-Dimensional Diffusion of p53 on DNA' Biophysical Journal, vol 96, no. 3, pp. 416a-416a., 10.1016/j.bpj.2008.12.2125

Loparo, JJ & Oijen, AV 2009, 'Single-Molecule Enzymology'. in P Hinterdorfer & AV Oijen (eds), Handbook of Single-Molecule Biophysics. pp. 165-182.

Elenko, MP, Szostak, JW & Oijen, AMV 2009, 'Single-Molecule Imaging of an in Vitro-Evolved RNA Aptamer Reveals Homogeneous Ligand Binding Kinetics' Journal of the American Chemical Society, vol 131, no. 29, pp. 9866-9867., 10.1021/ja901880v

Tanner, NA & Oijen, AMV 2009, 'Single-Molecule Observation of Prokaryotic DNA Replication'. in JZ Dalgaard & S Vengrova (eds), DNA Replication. Methods and Protocols. 521 edn, Methods in Molecular Biology, no. 521, pp. 397-410.

Loparo, JJ, Hamdan, SM, Richardson, CC & Oijen, AMV 2009, 'Single-molecule Observations of Replisome Structure and Function' Biophysical Journal, vol 96, no. 3, pp. 556a-557a., 10.1016/j.bpj.2008.12.3655

Tafvizi, A, Leith, JS, Huang, F, Fersht, AR, Mirny, LA & Oijen, AMV 2009, 'Single-molecule Studies Of p53 Sliding Along DNA' Biophysical Journal, vol 96, no. 3, pp. 417a-417a., 10.1016/j.bpj.2008.12.2128

Elenko, M, Szostak, JW & Oijen, AMV 2009, 'Use Of Single-Molecule Imaging To Analyze The Distribution Of Binding Ability In RNA Aptamer Populations' Biophysical Journal, vol 96, no. 3, pp. 291a-291a., 10.1016/j.bpj.2008.12.1440

Floyd, D, Skehel, J, Harrison, S & Oijen, AV 2009, 'Visualizing Viral Fusion At The Single-particle Level' Biophysical Journal, vol 96, no. 3, pp. 358a-358a., 10.1016/j.bpj.2008.12.1806

2008

Oijen, AV 2008, 'A Singular Focus' The Scientist, vol 22, no. 5, pp. 50.

Oijen, AMV 2008, 'Cutting the forest to see a single tree?' Nature Chemical Biology, vol 4, no. 8, pp. 440-443., 10.1038/nchembio0808-440

Komazin-Meredith, G, Mirchev, R, Golan, DE, Oijen, AMV, Coen, DM & Richardson, CC (ed.) 2008, 'Hopping of a processivity factor on DNA revealed by single-molecule assays of diffusion' Proceedings of the National Academy of Sciences of the United States of America, vol 105, no. 31, pp. 10721-10726., 10.1073/pnas.0802676105

Tanner, NA, Hamdan, SM, Jergic, S, Loscha, KV, Schaeffer, PM, Dixon, NE & Oijen, AMV 2008, 'Single-molecule studies of fork dynamics in Escherichia coli DNA replication' Nature Structural & Molecular Biology, vol 15, no. 2, pp. 170-176., 10.1038/nsmb0908-998a

Floyd, DL, Ragains, JR, Skehel, JJ, Harrison, SC, Oijen, AMV & Harrison, SC (ed.) 2008, 'Single-particle kinetics of influenza virus membrane fusion' Proceedings of the National Academy of Sciences of the United States of America, vol 105, no. 40, pp. 15382-15387., 10.1073/pnas.0807771105

Tafvizi, A, Huang, F, Leith, JS, Fersht, AR, Mirny, LA, Oijen, AMV & Hall, KB (ed.) 2008, 'Tumor Suppressor p53 Slides on DNA with Low Friction and High Stability' Biophysical Journal: Biophysical Letters, vol 95, no. 1, pp. L01-L03., 10.1529/biophysj.108.134122

Habuchi, S, Tsutsui, H, Kochaniak, AB, Miyawaki, A & Oijen, AMV 2008, 'mKikGR, a Monomeric Photoswitchable Fluorescent Protein' PLoS ONE, vol 3, no. 12, pp. e3944-1-e3944-9., 10.1371/journal.pone.0003944

2007

Hamdan, SM, Johnson, DE, Tanner, NA, Lee, J-B, Qimron, U, Tabor, S, Oijen, AMV & Richardson, CC 2007, 'Dynamic DNA Helicase-DNA Polymerase Interactions Assure Processive Replication Fork Movement' Molecular Cell, vol 27, no. 4, pp. 539-549., 10.1016/j.molcel.2007.06.020

Oijen, AMV 2007, 'Honey, I Shrunk the DNA: DNA Length as a Probe for Nucleic-Acid Enzyme Activity' Biopolymers, vol 85, no. 2, pp. 144-153., 10.1002/bip.20624

Fujiyoshi, S, Fujiwara, M, Kim, C, Matsushita, M, Oijen, AMV & Schmidt, J 2007, 'Single-component reflecting objective for low-temperature spectroscopy in the entire visible region' Applied Physics Letters, vol 91, no. 5, pp. 051125-1-051125-3., 10.1063/1.2767778

Oijen, AMV 2007, 'Single-molecule studies of complex systems: the replisome' Molecular BioSystems, vol 3, no. 2, pp. 117-125., 10.1039/b612545j

2006

Blainey, PC, Oijen, AMV, Banerjee, A, Verdine, GL, Xie, XS & Hippel, PHV (ed.) 2006, 'A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA' Proceedings of the National Academy of Sciences of the United States of America, vol 103, no. 15, pp. 5752-5757., 10.1073/pnas.0509723103

Lee, J-B, Hite, RK, Hamdan, SM, Xie, XS, Richardson, CC & Oijen, AMV 2006, 'DNA primase acts as a molecular brake in DNA replication' Nature, vol 439, no. 7076, pp. 621-624., 10.1038/nature04317

English, BP, Min, W, Oijen, AMV, Lee, KT, Luo, G, Sun, H, Cherayil, BJ, Kou, SC & Xie, XS 2006, 'Ever-fluctuating single enzyme molecules: Michaelis-Menten equation revisited' Nature Chemical Biology, vol 2, no. 2, pp. 87-94., 10.1038/nchembio0306-168

2005

Kirchhausen, T, Boll, W, Oijen, AV & Ehrlich, M 2005, 'Single-molecule live-cell imaging of clathrin-based endocytosis'. in EPRINTS-BOOK-TITLE. 72 edn, Biochemical Society Symposium, no. 72, pp. 71-76.

Crampton, DJ, Mukherjee, S, Oijen, AV & Richardson, CC 2005, 'Unraveling the catalytic mechanism of the bacteriophage T7 gene 4 helicase' Febs Journal, pp. 334-334.

2004

Ehrlich, M, Boll, W, Oijen, AV, Hariharan, R, Chandran, K, Nibert, ML & Kirchhausen, T 2004, 'Endocytosis by Random Initiation and Stabilization of Clathrin-Coated Pits' Cell, vol 118, no. 5, pp. 591-605., 10.1016/j.cell.2004.08.017

2003

Oijen, AMV, Blainey, PC, Crampton, DJ, Richardson, CC, Ellenberger, T & Xie, XS 2003, 'Single-Molecule Kinetics of λ Exonuclease Reveal Base Dependence and Dynamic Disorder' Science, vol 301, no. 5637, pp. 1235-1238., 10.1126/science.1084387

2002

Verberk, R, Oijen, AMV & Orrit, M 2002, 'Simple model for the power-law blinking of single semiconductor nanocrystals' Physical Review B, vol 66, no. 23, pp. 233202-1-233202-4., 10.1103/PhysRevB.66.233202

2001

Oijen, AMV, Verberk, R, Durand, Y, Schmidt, J, Lingen, JNJV, Bol, AA & Meijerink, A 2001, 'Continuous-wave two-photon excitation of individual CdS nanocrystallites' Applied Physics Letters, vol 79, no. 6, pp. 830-832., 10.1063/1.1391231

Köhler, J, Oijen, AMV, Ketelaars, M, Hofmann, C, Matsushita, M, Aartsma, TJ & Schmidt, J 2001, 'Optical Spectroscopy of Individual Photosynthetic Pigment Protein Complexes' International Journal of Modern Physics B, vol 15, no. 28, pp. 3633-3636.

Ketelaars, M, Oijen, AMV, Matsushita, M, Köhler, J, Schmidt, J & Aartsma, TJ 2001, 'Spectroscopy on the B850 Band of Individual Light-Harvesting 2 Complexes of Rhodopseudomonas acidophila I. Experiments and Monte Carlo Simulations' Biophysical Journal, vol 80, no. 3, pp. 1591-1603.

Matsushita, M, Ketelaars, M, Oijen, AMV, Köhler, J, Aartsma, TJ & Schmidt, J 2001, 'Spectroscopy on the B850 Band of Individual Light-Harvesting 2 Complexes of Rhodopseudomonas acidophila II. Exciton States of an Elliptically Deformed Ring Aggregate' Biophysical Journal, vol 80, no. 3, pp. 1604-1614.

2000

Durand, Y, Bloeß, A, Oijen, AMV, Köhler, J, Groenen, EJJ & Schmidt, J 2000, 'An optical study of single pentacene molecules in n-tetradecane' Chemical Physics Letters, vol 317, pp. 232-237.

van Oijen, A & Ketelaars, M 2000, 'Een nieuwe kijk op fotosynthese' Nederlands Tijdschrift voor Natuurkunde, vol 66, pp. 38-41.

Oijen, AMV, Ketelaars, M, Köhler, J, Aartsma, TJ & Schmidt, J 2000, 'Spectroscopy of Individual Light-Harvesting 2 Complexes of Rhodopseudomonas acidophila: Diagonal Disorder, Intercomplex Heterogeneity, Spectral Diffusion, and Energy Transfer in the B800 Band' Biophysical Journal, vol 78, no. 3, pp. 1570-1577.

1999

Oijen, AMV, Köhler, J, Schmidt, J, Müller, M & Brakenhoff, GJ 1999, 'Far-field fluorescence microscopy beyond the diffraction limit' Journal of the Optical Society of America A, vol 16, no. 4, pp. 909-915.

Brouwer, ACJ, Köhler, J, Oijen, AMV, Groenen, EJJ & Schmidt, J 1999, 'Single-molecule fluorescence autocorrelation experiments on pentacene: The dependence of intersystem crossing on isotopic composition' Journal of Chemical Physics, vol 110, no. 18, pp. 9151-9159.

Oijen, AMV, Ketelaars, M, Köhler, J, Aartsma, TJ & Schmidt, J 1999, 'Spectroscopy of individual LH2 complexes of Rhodopseudomonas acidophila: localized excitations in the B800 band' Chemical Physics, vol 247, pp. 53-60.

Oijen, AMV, Ketelaars, M, Köhler, J, Aartsma, TJ & Schmidt, J 1999, 'Unraveling the Electronic Structure of Individual Photosynthetic Pigment-Protein Complexes' Science, vol 285, pp. 400-402.

1998

Oijen, AMV, Köhler, J, Schmidt, J, Müller, M & Brakenhoff, GJ 1998, '3-Dimensional super-resolution by spectrally selective imaging' Chemical Physics Letters, vol 292, pp. 183-187.

Oijen, AMV, Ketelaars, M, Köhler, J, Aartsma, TJ & Schmidt, J 1998, 'Spectroscopy of Single Light-Harvesting Complexes from Purple Photosynthetic Bacteria at 1.2 K' The Journal of Physical Chemistry B, vol 102, no. 47, pp. 9363-9366., 10.1021/jp9830629

Publications of Prof. dr. A.M. van Oijen in the Universities Research Database

2018

Bianchi, F., Syga, Ł., Moiset, G., Spakman, D., Schavemaker, P. E., Punter, C. M., ... Poolman, B. (2018). Steric exclusion and protein conformation determine the localization of plasma membrane transporters. Nature Communications, 9(1), [501]. DOI: 10.1038/s41467-018-02864-2

2017

Goudsmits, J. M. H., Slotboom, D. J., & van Oijen, A. M. (2017). Single-molecule visualization of conformational changes and substrate transport in the vitamin B-12 ABC importer BtuCD-F. Nature Communications, 8, [1652]. DOI: 10.1038/s41467-017-01815-7
Goudsmits, J. M. H., van Oijen, A. M., & Slotboom, D. J. (2017). Single-Molecule Fluorescence Studies of Membrane Transporters Using Total Internal Reflection Microscopy. Methods in Enzymology, 594, 101-121. DOI: 10.1016/bs.mie.2017.05.009

2016

van Gijtenbeek, L. A., Robinson, A., van Oijen , A., Poolman, B., & Kok, J. (2016). On the Spatial Organization of mRNA, Plasmids, and Ribosomes in a Bacterial Host Overexpressing Membrane Proteins. PLoS genetics, 12(12), 1-28. [e1006523]. DOI: 10.1371/journal.pgen.1006523
Duderstadt, K. E., Geertsema, H. J., Stratmann, S. A., Punter, C. M., Kulczyk, A. W., Richardson, C. C., & van Oijen, A. M. (2016). Simultaneous Real-Time Imaging of Leading and Lagging Strand Synthesis Reveals the Coordination Dynamics of Single Replisomes. Molecular Cell, 64(6), 1035-1047. DOI: 10.1016/j.molcel.2016.10.028
Blijleven, J. S., Boonstra, S., Onck, P. R., van der Giessen, E., & van Oijen, A. M. (2016). Mechanisms of influenza viral membrane fusion. Seminars in Cell & Developmental Biology, 60, 78-88. DOI: 10.1016/j.semcdb.2016.07.007
Koch, S., de Wit, J. G., Vos, I., Birkner, J. P., Gordiichuk, P., Herrmann, A., ... Driessen, A. J. M. (2016). Lipids activate SecA for high affinity binding to the SecYEG complex. The Journal of Biological Chemistry, 291(43), 22534-22543. DOI: 10.1074/jbc.M116.743831
Kalkman, G. A., Zhang, Y., Monachino, E., Mathwig, K., Kamminga, M. E., Pourhossein Aghbolagh, P., ... Chiechi, R. C. (2016). Bisecting Microfluidic Channels with Metallic Nanowires Fabricated by Nanoskiving. Acs Nano, 10(2), 2852–2859. DOI: 10.1021/acsnano.5b07996
Turkin, A., Zhang, L., Marcozzi, A., Mangel, W. F., Herrmann, A., & van Oijen, A. M. (2016). Speeding up biomolecular interactions by molecular sledding. Chemical Science, 7(2), 916-920. DOI: 10.1039/c5sc03063c
Åberg, C., Duderstadt, K. E., & van Oijen, A. M. (2016). Stability versus exchange: A paradox in DNA replication. Nucleic Acids Research, 44(10), 4846-4854. DOI: 10.1093/nar/gkw296

2015

van Duijl-Richter, M. K. S., Blijleven, J. S., van Oijen, A. M., & Smit, J. M. (2015). Chikungunya virus fusion properties elucidated by single-particle and bulk approaches. The Journal of general virology, 96, 2122-2132. DOI: 10.1099/vir.0.000144
Stratmann, S. A., Morrone, S. R., van Oijen, A. M., & Sohn, J. (2015). The innate immune sensor IFI16 recognizes foreign DNA in the nucleus by scanning along the duplex. eLife, 4, 1-13. DOI: 10.7554/eLife.11721

2014

Graham, T. G. W., Wang, X., Song, D., Etson, C. M., van Oijen, A. M., Rudner, D. Z., & Loparo, J. J. (2014). ParB spreading requires DNA bridging. Genes & Development, 28(11), 1228-1238. DOI: 10.1101/gad.242206.114
Kusters, I., van Oijen, A. M., & Driessen, A. J. M. (2014). Membrane-on-a-Chip: Microstructured Silicon/Silicon-Dioxide Chips for High-Throughput Screening of Membrane Transport and Viral Membrane Fusion. Acs Nano, 8(4), 3380-3392. DOI: 10.1021/nn405884a
Geertsema, H. J., Kulczyk, A. W., Richardson, C. C., & van Oijen, A. M. (2014). Single-molecule studies of polymerase dynamics and stoichiometry at the bacteriophage T7 replication machinery. Proceedings of the National Academy of Science of the United States of America, 111(11), 4073-4078. DOI: 10.1073/pnas.1402010111
Mangel, F. W., Blainey, P. C., Graziano, V., Herrmann, A., McGrath, W. J., van Oijen, A. M., & Xie, X. S. (2014). IPC No. C12N 15/ 11 A I. Molecular sleds comprising a positively -charged amino acid sequence and a molecular cargo and uses thereof (Patent No. WO2014012090.)
Duderstadt, K. E., Reyes-Lamothe, R., van Oijen, A. M., & Sherratt, D. J. (2014). Replication-Fork Dynamics. Cold Spring Harbor Perspectives in Biology, 6(1), [010157]. DOI: 10.1101/cshperspect.a010157
van Oijen, A., & Mashaghi, S. (2014). A versatile approach to the generation of fluid supported lipid bilayers and its applications. Biotechnology and Bioengineering, 1-6.
Stratmann, S. A., & Oijen, A. M. V. (2014). DNA replication at the single-molecule level. Chemical Society Reviews, 43(4), 1201-1220. DOI: 10.1039/c3cs60391a
Duderstadt, K. E., Punter, C. M., Kulczyk, A. W., Richardson, C. C., & Oijen, A. M. V. (2014). Simultaneous Imaging of Leading- and Lagging-Strand Synthesis Reveals Distinct Operational Modes of Single Replication Machines. Biophysical Journal, 106(2), 273a-273a. DOI: 10.1016/j.bpj.2013.11.1600

2012

Yardimci, H., Wang, X., Loveland, A. B., Tappin, I., Rudner, D. Z., Hurwitz, J., ... Walter, J. C. (2012). Bypass of a protein barrier by a replicative DNA helicase. Nature, 492(7428), 205-+. DOI: 10.1038/nature11730
Quessada-Vial, A., & van Oijen, A. M. (2012). How DNA-repair proteins find their targets. Proceedings of the National Academy of Sciences of the United States of America, 109(45), 18243-18244. DOI: 10.1073/pnas.1215845109
Leith, J. S., Tafvizi, A., Huang, F., Uspal, W. E., Doyle, P. S., Fersht, A. R., ... Hammes, G. G. (Ed.) (2012). Sequence-dependent sliding kinetics of p53. Proceedings of the National Academy of Sciences of the United States of America, 109(41), 16552-16557. DOI: 10.1073/pnas.1120452109
Quessada-Vial, A., & van Oijen, A. M. (2012). Spotting the Mistakes, One Molecule at a Time. Structure, 20(7), 1130-1132. DOI: 10.1016/j.str.2012.06.007
Yardimci, H., Loveland, A. B., van Oijen, A. M., & Walter, J. C. (2012). Single-molecule analysis of DNA replication in Xenopus egg extracts. Methods, 57(2), 179-186. DOI: 10.1016/j.ymeth.2012.03.033
Ivanovic, T., Rozendaal, R., Floyd, D. L., Popovic, M., Oijen, A. M. V., & Harrison, S. C. (2012). Kinetics of Proton Transport into Influenza Virions by the Viral M2 Channel. PLoS ONE, 7(3), [e31566]. DOI: 10.1371/journal.pone.0031566
Oijen, A. M. V. (2012). A Single-Molecule Characterization of P53 Search on DNA. Biophysical Journal, 102(3), 1a-2a. DOI: 10.1016/j.bpj.2011.11.021
Otterstrom, J., Juraszek, J., Tang, C., Koldijk, M., Vogels, R., Friesen, R., ... van Oijen, A. M. (2012). Watching Influenza get Hogtied. Biophysical Journal, 102(3), 605A.
Loveland, A. B., Habuchi, S., Walter, J. C., & Oijen, A. M. V. (2012). A general approach to break the concentration barrier in single-molecule imaging. Nature Methods, 9(10), 987-992. DOI: 10.1038/nmeth.2174

2013

Brandenburg, B., Koudstaal, W., Goudsmit, J., Klaren, V., Tang, C., Bujny, M. V., ... Friesen, R. H. E. (2013). Mechanisms of Hemagglutinin Targeted Influenza Virus Neutralization. PLoS ONE, 8(12), [e80034]. DOI: 10.1371/journal.pone.0080034
Erkens, G. B., Hänelt, I., Goudsmits, J. M. H., Slotboom, D. J., & van Oijen, A. M. (2013). Unsynchronised subunit motion in single trimeric sodium-coupled aspartate transporters. Nature, 502(7469), 119-123. DOI: 10.1038/nature12538
Geertsema, H. J., & van Oijen, A. M. (2013). A single-molecule view of DNA replication: the dynamic nature of multi-protein complexes revealed. Current Opinion in Structural Biology, 23(5), 788-793. DOI: 10.1016/j.sbi.2013.06.018
Kusters, I., Punter, M., Birkner, J. -P., Tans, S., van Oijen, A., & Driessen, A. J. (2013). Single molecule observation of protein translocation. European biophysics journal with biophysics letters, 42, S59-S59.
Jergic, S., Horan, N. P., Elshenawy, M. M., Mason, C. E., Urathamakul, T., Ozawa, K., ... Dixon, N. E. (2013). A direct proofreader-clamp interaction stabilizes the Pol III replicase in the polymerization mode. EMBO Journal, 32(9), 1322-1333. DOI: 10.1038/emboj.2012.347
Robinson, A., & van Oijen, A. M. (2013). Bacterial replication, transcription and translation: mechanistic insights from single-molecule biochemical studies. Nature Reviews Microbiology, 11(5), 303-315. DOI: 10.1038/nrmicro2994
Otterstrom, J., & van Oijen, A. M. (2013). Visualization of Membrane Fusion, One Particle at a Time. Biochemistry, 52(10), 1654-1668. DOI: 10.1021/bi301573w
Birkner, J. P., Kusters, I., Driessen, A., & Oijen, A. V. (2013). Protein Translocation at the Single Molecule Level. Biophysical Journal, 104(2), 110a-110a. DOI: 10.1016/j.bpj.2012.11.640
Turkin, A., Mangel, W. F., & Oijen, A. M. V. (2013). Single-Molecule Studies of Adenovirus Maturation. Biophysical Journal, 104(2), 178a-179a. DOI: 10.1016/j.bpj.2012.11.1004
Otterstrom, J., Juraszek, J., Tang, C., Koldijk, M., Vogels, R., Friesen, R., ... van Oijen, A. (2013). Stoichiometry of Influenza Hemagglutinin Neutralization by Broadly Acting Antibodies using Single Virus-Particle Visualization. Biophysical Journal, 104(2), 371A.
Graham, T. G. W., Song, L., Wang, X., Etson, C. M., Van Oijen, A., Rudner, D. Z., & Loparo, J. J. (2013). Single-Molecule Studies of a ParB Family Chromosome Segregation Protein from Bacillussubtilis. Biophysical Journal, 104(2), 582A-583A.
Ivanovic, T., Choi, J. L., Whelan, S. P., Oijen, A. M. V., & Harrison, S. C. (2013). Influenza-virus membrane fusion by cooperative fold-back of stochastically induced hemagglutinin intermediates. eLife, 2, [e00333]. DOI: 10.7554/elife.00333

2011

Williams, K., Grafe, B., Burke, K. M., Tanner, N., van Oijen, A. M., Loparo, J., & Price, A. C. (2011). A single molecule DNA flow stretching microscope for undergraduates. American Journal of Physics, 79(11), 1112-1120. DOI: 10.1119/1.3620410
Akabayov, B., Kulczyk, A. W., Akabayov, S. R., Theile, C., McLaughlin, L. W., Beauchamp, B., ... Richardson, C. C. (2011). Pyrovanadolysis, a Pyrophosphorolysis-like Reaction Mediated by Pyrovanadate, Mn2+, and DNA Polymerase of Bacteriophage T7. The Journal of Biological Chemistry, 286(33), 29146-29157. DOI: 10.1074/jbc.M111.250944
van Oijen, A. M. (2011). Single-molecule studies of DNA replication. European biophysics journal with biophysics letters, 40, 99-100.
Tafvizi, A., Mirny, L. A., & van Oijen, A. M. (2011). Dancing on DNA: Kinetic Aspects of Search Processes on DNA. Chemphyschem, 12(8), 1481-1489. DOI: 10.1002/cphc.201100112
Tanner, N. A., Tolun, G., Loparo, J. J., Jergic, S., Griffith, J. D., Dixon, N. E., & van Oijen, A. M. (2011). E. coli DNA replication in the absence of free beta clamps. EMBO Journal, 30(9), 1830-1840. DOI: 10.1038/emboj.2011.84
van Oijen, A. M. (2011). Single-molecule approaches to characterizing kinetics of biomolecular interactions. Current Opinion in Biotechnology, 22(1), 75-80. DOI: 10.1016/j.copbio.2010.10.002
Tafvizi, A., Huang, F., Fersht, A. R., Mirny, L. A., & van Oijen, A. M. (2011). A single-molecule characterization of p53 search on DNA. Proceedings of the National Academy of Science of the United States of America, 108(2), 563-568. DOI: 10.1073/pnas.1016020107
Lebofsky, R., van Oijen, A. M., & Walter, J. C. (2011). DNA is a co-factor for its own replication in Xenopus egg extracts. Nucleic Acids Research, 39(2), 545-555. DOI: 10.1093/nar/gkq739
Loparo, J. J., Kulczyk, A. W., Richardson, C. C., & Oijen, A. M. V. (2011). Simultaneous single-molecule measurements of phage T7 replisome composition and function reveal the mechanism of polymerase exchange. Proceedings of the National Academy of Sciences of the United States of America, 108(9), 3584-3589. DOI: 10.1073/pnas.1018824108
Satapathy, A. K., Kulczyk, A. W., Ghosh, S., Oijen, A. M. V., & Richardson, C. C. (2011). Coupling dTTP Hydrolysis with DNA Unwinding by the DNA Helicase of Bacteriophage T7. J. Biol. Chem., 286(39), 34468-34478. DOI: 10.1074/jbc.M111.283796
Yardimci, H., Oijen, A. M. V., & Walter, J. C. (2011). Single-Molecule Studies of the Eukaryotic Replicative DNA Helicase MCM2-7. Biophysical Journal, 100(3), 239a-239a. DOI: 10.1016/j.bpj.2010.12.1521
Fu, Y. V., Yardimci, H., Long, D. T., Ho, T. V., Guainazzi, A., Bermudez, V. P., ... Walter, J. C. (2011). Selective Bypass of a Lagging Strand Roadblock by the Eukaryotic Replicative DNA Helicase. Cell, 146(6), 931-941. DOI: 10.1016/j.cell.2011.07.045

2010

Yardimci, H., Loveland, A. B., Habuchi, S., van Oijen, A. M., & Walter, J. C. (2010). Uncoupling of Sister Replisomes during Eukaryotic DNA Replication. Molecular Cell, 40(5), 834-840. DOI: 10.1016/j.molcel.2010.11.027
Elenko, M. P., Szostak, J. W., & van Oijen, A. M. (2010). Single-molecule binding experiments on long time scales. Review of Scientific Instruments, 81(8), 083705-1-083705-9. [083705]. DOI: 10.1063/1.3473936
Kulczyk, A. W., Tanner, N. A., Loparo, J. J., Richardson, C. C., & Oijen, A. M. V. (2010). Direct observation of enzymes replicating DNA using a single-molecule DNA stretching assay. Journal of visualized experiments : JoVE, 44(37). DOI: 10.3791/1689
Etson, C. M., Hamdan, S. M., Richardson, C. C., & Oijen, A. M. V. (2010). Thioredoxin suppresses microscopic hopping of T7 DNA polymerase on duplex DNA. Proceedings of the National Academy of Sciences of the United States of America, 107(5), 1900-1905. DOI: 10.1073/pnas.0912664107
Satapathy, A. K., Kochaniak, A. B., Mukherjee, S., Crampton, D. J., Oijen, A. V., & Richardson, C. C. (Ed.) (2010). Residues in the central β-hairpin of the DNA helicase of bacteriophage T7 are important in DNA unwinding. Proceedings of the National Academy of Sciences of the United States of America, 107(15), 6782-6787. DOI: 10.1073/pnas.1002734107
Oijen, A. M. V., & Loparo, J. J. (2010). Single-Molecule Studies of the Replisome. Annual Review of Biophysics, 39(1), 429-448. DOI: 10.1146/annurev.biophys.093008.131327
Etson, C. M., Rudner, D. Z., & Oijen, A. M. V. (2010). Nucleoprotein Complex Formation By Bacillus Subtilis Spo0J/ParB. Biophysical Journal, 98(3), 74a-74a. DOI: 10.1016/j.bpj.2009.12.418
Floyd, D. L., Harrison, S. C., & Oijen, A. M. V. (2010). Analysis of Kinetic Intermediates in Single-Particle Dwell-Time Distributions. Biophysical Journal, 99(2), 360-366. DOI: 10.1016/j.bpj.2010.04.049
Otterstrom, J. J., Floyd, D. L., Skehel, J. J., Harrison, S. C., & Oijen, A. M. V. (2010). Lipid Bilayer Rigidity Affects the Fusion Kinetics of Individually Observed Influenza Particles. Biophysical Journal, 98(3), 673a-673a. DOI: 10.1016/j.bpj.2009.12.3697
Yardimci, H., Kochaniak, A. B., Habuchi, S., Havens, C. G., Walter, J. C., & Oijen, A. V. (2010). Single Molecule Studies of Eukaryotic Replisomes in Xenopus Egg Extracts. Biophysical Journal, 98(3), 437a-437a. DOI: 10.1016/j.bpj.2009.12.2371
Hamdan, S. M., & Oijen, A. M. V. (2010). Timing, Coordination, and Rhythm: Acrobatics at the DNA Replication Fork. The Journal of Biological Chemistry, 285(25), 18979-18983. DOI: 10.1074/jbc.R109.022939
Bassam, J. A., Kim, H., Brouhard, G., Oijen, A. V., Harrison, S. C., & Chang, F. (2010). CLASP Promotes Microtubule Rescue by Recruiting Tubulin Dimers to the Microtubule. Developmental Cell, 19(2), 245-258. DOI: 10.1016/j.devcel.2010.07.016
Tanner, N. A., & van Oijen, A. M. (2010). Visualizing DNA Replication at the Single-Molecule Level. In N. G. Walter (Ed.), Methods in Enzymology (37 ed., Vol. 475, pp. 259-278). (Methods in Enzymology; Vol. 475). San Diego: Academic Press. Methods in Enzymology, DOI: 10.1016/S0076-6879(10)75011-4

2009

Tanner, N. A., Loparo, J. J., & Oijen, A. M. V. (2009). Visualizing Single-molecule DNA Replication with Fluorescence Microscopy. Journal of visualized experiments : JoVE, 44(32), e1529-1-e1529-4. DOI: 10.3791/1529
Floyd, D. L., Harrison, S. C., & Oijen, A. M. V. (2009). Method for measurement of viral fusion kinetics at the single particle level. Journal of visualized experiments : JoVE, 44(31). DOI: 10.3791/1484
Kochaniak, A. B., Habuchi, S., Loparo, J. J., Chang, D. J., Cimprich, K. A., Walter, J. C., & Oijen, A. M. V. (2009). Proliferating Cell Nuclear Antigen Uses Two Distinct Modes to Move along DNA. J. Biol. Chem., 284(26), 17700-17710. DOI: 10.1074/jbc.M109.008706
Elenko, M., Szostak, J. W., & Oijen, A. M. V. (2009). Use Of Single-Molecule Imaging To Analyze The Distribution Of Binding Ability In RNA Aptamer Populations. Biophysical Journal, 96(3), 291a-291a. DOI: 10.1016/j.bpj.2008.12.1440
Floyd, D., Skehel, J., Harrison, S., & Oijen, A. V. (2009). Visualizing Viral Fusion At The Single-particle Level. Biophysical Journal, 96(3), 358a-358a. DOI: 10.1016/j.bpj.2008.12.1806
Leith, J. S., Tafvizi, A., Huang, F., Fersht, A. R., Mirny, L. A., & Oijen, A. M. V. (2009). Sequence-Dependent Kinetics of One-Dimensional Diffusion of p53 on DNA. Biophysical Journal, 96(3), 416a-416a. DOI: 10.1016/j.bpj.2008.12.2125
Loparo, J. J., Hamdan, S. M., Richardson, C. C., & Oijen, A. M. V. (2009). Single-molecule Observations of Replisome Structure and Function. Biophysical Journal, 96(3), 556a-557a. DOI: 10.1016/j.bpj.2008.12.3655
Tafvizi, A., Leith, J. S., Huang, F., Fersht, A. R., Mirny, L. A., & Oijen, A. M. V. (2009). Single-molecule Studies Of p53 Sliding Along DNA. Biophysical Journal, 96(3), 417a-417a. DOI: 10.1016/j.bpj.2008.12.2128
Elenko, M. P., Szostak, J. W., & Oijen, A. M. V. (2009). Single-Molecule Imaging of an in Vitro-Evolved RNA Aptamer Reveals Homogeneous Ligand Binding Kinetics. Journal of the American Chemical Society, 131(29), 9866-9867. DOI: 10.1021/ja901880v
Hamdan, S. M., Loparo, J. J., Takahashi, M., Richardson, C. C., & Oijen, A. M. V. (2009). Dynamics of DNA replication loops reveal temporal control of lagging-strand synthesis. Nature, 457(3), 336-340. DOI: 10.1016/j.bpj.2008.12.3720
Tanner, N. A., Loparo, J. J., Hamdan, S. M., Jergic, S., Dixon, N. E., & Oijen, A. M. V. (2009). Real-time single-molecule observation of rolling-circle DNA replication. Nucleic Acids Research, 37(4), e27-1-e27-6. DOI: 10.1093/nar/gkp006
Otterstrom, J. J., & Oijen, A. M. V. (2009). Nudging Through a Nucleosome. Science, 325(5940), 547-548. DOI: 10.1126/science.1177311
Tanner, N. A., & Oijen, A. M. V. (2009). Single-Molecule Observation of Prokaryotic DNA Replication. In J. Z. Dalgaard, & S. Vengrova (Eds.), DNA Replication. Methods and Protocols (521 ed., pp. 397-410). (Methods in Molecular Biology; No. 521).
Loparo, J. J., & Oijen, A. V. (2009). Single-Molecule Enzymology. In P. Hinterdorfer, & A. V. Oijen (Eds.), Handbook of Single-Molecule Biophysics (pp. 165-182)

2008

Habuchi, S., Tsutsui, H., Kochaniak, A. B., Miyawaki, A., & Oijen, A. M. V. (2008). mKikGR, a Monomeric Photoswitchable Fluorescent Protein. PLoS ONE, 3(12), [3944]. DOI: 10.1371/journal.pone.0003944
Floyd, D. L., Ragains, J. R., Skehel, J. J., Harrison, S. C., & Oijen, A. M. V. (2008). Single-particle kinetics of influenza virus membrane fusion. Proceedings of the National Academy of Sciences of the United States of America, 105(40), 15382-15387. DOI: 10.1073/pnas.0807771105
Komazin-Meredith, G., Mirchev, R., Golan, D. E., Oijen, A. M. V., Coen, D. M., & Richardson, C. C. (Ed.) (2008). Hopping of a processivity factor on DNA revealed by single-molecule assays of diffusion. Proceedings of the National Academy of Sciences of the United States of America, 105(31), 10721-10726. DOI: 10.1073/pnas.0802676105
Tafvizi, A., Huang, F., Leith, J. S., Fersht, A. R., Mirny, L. A., & Oijen, A. M. V. (2008). Tumor Suppressor p53 Slides on DNA with Low Friction and High Stability. Biophysical Journal: Biophysical Letters, 95(1), L01-L03. DOI: 10.1529/biophysj.108.134122
Oijen, A. M. V. (2008). Cutting the forest to see a single tree? Nature Chemical Biology, 4(8), 440-443. DOI: 10.1038/nchembio0808-440
Tanner, N. A., Hamdan, S. M., Jergic, S., Loscha, K. V., Schaeffer, P. M., Dixon, N. E., & Oijen, A. M. V. (2008). Single-molecule studies of fork dynamics in Escherichia coli DNA replication. Nature Structural & Molecular Biology, 15(2), 170-176. DOI: 10.1038/nsmb0908-998a
Oijen, A. V. (2008). A Singular Focus. The Scientist, 22(5), 50.

2007

Fujiyoshi, S., Fujiwara, M., Kim, C., Matsushita, M., Oijen, A. M. V., & Schmidt, J. (2007). Single-component reflecting objective for low-temperature spectroscopy in the entire visible region. Applied Physics Letters, 91(5), 051125-1-051125-3. DOI: 10.1063/1.2767778
Oijen, A. M. V. (2007). Honey, I Shrunk the DNA: DNA Length as a Probe for Nucleic-Acid Enzyme Activity. Biopolymers, 85(2), 144-153. DOI: 10.1002/bip.20624
Oijen, A. M. V. (2007). Single-molecule studies of complex systems: the replisome. Molecular BioSystems, 3(2), 117-125. DOI: 10.1039/b612545j
Hamdan, S. M., Johnson, D. E., Tanner, N. A., Lee, J-B., Qimron, U., Tabor, S., ... Richardson, C. C. (2007). Dynamic DNA Helicase-DNA Polymerase Interactions Assure Processive Replication Fork Movement. Molecular Cell, 27(4), 539-549. DOI: 10.1016/j.molcel.2007.06.020

2006

Blainey, P. C., van Oijen, A. M., Banerjee, A., Verdine, G. L., & Sunney Xie, X. (2006). A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA. Proceedings of the National Academy of Sciences of the United States of America, 103(15), 5752-5757. DOI: 10.1073/pnas.0509723103
English, B. P., Min, W., Oijen, A. M. V., Lee, K. T., Luo, G., Sun, H., ... Xie, X. S. (2006). Ever-fluctuating single enzyme molecules: Michaelis-Menten equation revisited. Nature Chemical Biology, 2(2), 87-94. DOI: 10.1038/nchembio0306-168
Lee, J-B., Hite, R. K., Hamdan, S. M., Xie, X. S., Richardson, C. C., & Oijen, A. M. V. (2006). DNA primase acts as a molecular brake in DNA replication. Nature, 439(7076), 621-624. DOI: 10.1038/nature04317

2005

Crampton, D. J., Mukherjee, S., Oijen, A. V., & Richardson, C. C. (2005). Unraveling the catalytic mechanism of the bacteriophage T7 gene 4 helicase. Febs Journal, 334-334.
Kirchhausen, T., Boll, W., Oijen, A. V., & Ehrlich, M. (2005). Single-molecule live-cell imaging of clathrin-based endocytosis. In EPRINTS-BOOK-TITLE (72 ed., pp. 71-76). (Biochemical Society Symposium; No. 72).

2004

Ehrlich, M., Boll, W., Oijen, A. V., Hariharan, R., Chandran, K., Nibert, M. L., & Kirchhausen, T. (2004). Endocytosis by Random Initiation and Stabilization of Clathrin-Coated Pits. Cell, 118(5), 591-605. DOI: 10.1016/j.cell.2004.08.017

2003

Oijen, A. M. V., Blainey, P. C., Crampton, D. J., Richardson, C. C., Ellenberger, T., & Xie, X. S. (2003). Single-Molecule Kinetics of λ Exonuclease Reveal Base Dependence and Dynamic Disorder. Science, 301(5637), 1235-1238. DOI: 10.1126/science.1084387

2002

Verberk, R., Oijen, A. M. V., & Orrit, M. (2002). Simple model for the power-law blinking of single semiconductor nanocrystals. Physical Review B, 66(23), 233202-1-233202-4. DOI: 10.1103/PhysRevB.66.233202

2001

Köhler, J., Oijen, A. M. V., Ketelaars, M., Hofmann, C., Matsushita, M., Aartsma, T. J., & Schmidt, J. (2001). Optical Spectroscopy of Individual Photosynthetic Pigment Protein Complexes. International Journal of Modern Physics B, 15(28), 3633-3636.
van Oijen, A. M., Verberk, R., Durand, Y., Schmidt, J., van Lingen, J. N. J., Bol, A. A., & Meijerink, A. (2001). Continuous-wave two-photon excitation of individual CdS nanocrystallites. Applied Physics Letters, 79(6), 830-832. DOI: 10.1063/1.1391231
Ketelaars, M., Oijen, A. M. V., Matsushita, M., Köhler, J., Schmidt, J., & Aartsma, T. J. (2001). Spectroscopy on the B850 Band of Individual Light-Harvesting 2 Complexes of Rhodopseudomonas acidophila I. Experiments and Monte Carlo Simulations. Biophysical Journal, 80(3), 1591-1603.
Matsushita, M., Ketelaars, M., Oijen, A. M. V., Köhler, J., Aartsma, T. J., & Schmidt, J. (2001). Spectroscopy on the B850 Band of Individual Light-Harvesting 2 Complexes of Rhodopseudomonas acidophila II. Exciton States of an Elliptically Deformed Ring Aggregate. Biophysical Journal, 80(3), 1604-1614.

2000

van Oijen, A., & Ketelaars, M. (2000). Een nieuwe kijk op fotosynthese. Nederlands Tijdschrift voor Natuurkunde, 66, 38-41.
Oijen, A. M. V., Ketelaars, M., Köhler, J., Aartsma, T. J., & Schmidt, J. (2000). Spectroscopy of Individual Light-Harvesting 2 Complexes of Rhodopseudomonas acidophila: Diagonal Disorder, Intercomplex Heterogeneity, Spectral Diffusion, and Energy Transfer in the B800 Band. Biophysical Journal, 78(3), 1570-1577.
Durand, Y., Bloeß, A., Oijen, A. M. V., Köhler, J., Groenen, E. J. J., & Schmidt, J. (2000). An optical study of single pentacene molecules in n-tetradecane. Chemical Physics Letters, 317, 232-237.

1999

Oijen, A. M. V., Köhler, J., Schmidt, J., Müller, M., & Brakenhoff, G. J. (1999). Far-field fluorescence microscopy beyond the diffraction limit. Journal of the Optical Society of America A, 16(4), 909-915.
Oijen, A. M. V., Ketelaars, M., Köhler, J., Aartsma, T. J., & Schmidt, J. (1999). Unraveling the Electronic Structure of Individual Photosynthetic Pigment-Protein Complexes. Science, 285, 400-402.
Oijen, A. M. V., Ketelaars, M., Köhler, J., Aartsma, T. J., & Schmidt, J. (1999). Spectroscopy of individual LH2 complexes of Rhodopseudomonas acidophila: localized excitations in the B800 band. Chemical Physics, 247, 53-60.
Brouwer, A. C. J., Köhler, J., Oijen, A. M. V., Groenen, E. J. J., & Schmidt, J. (1999). Single-molecule fluorescence autocorrelation experiments on pentacene: The dependence of intersystem crossing on isotopic composition. Journal of Chemical Physics, 110(18), 9151-9159.

1998

Oijen, A. M. V., Köhler, J., Schmidt, J., Müller, M., & Brakenhoff, G. J. (1998). 3-Dimensional super-resolution by spectrally selective imaging. Chemical Physics Letters, 292, 183-187.
Oijen, A. M. V., Ketelaars, M., Köhler, J., Aartsma, T. J., & Schmidt, J. (1998). Spectroscopy of Single Light-Harvesting Complexes from Purple Photosynthetic Bacteria at 1.2 K. The Journal of Physical Chemistry B, 102(47), 9363-9366. DOI: 10.1021/jp9830629
Last modified:16 February 2016 1.18 p.m.