Home

Publications

2014 2013 2012 2011 2010 2009 2008

2014

T.G. Graham, X. Wang, D. Song, C.M. Etson, A.M. van Oijen, D.Z. Rudner, J.J. Loparo
ParB spreading requires DNA bridging
Genes Dev. (2014) 28(11):1228-38 (pdf)

S. Mashaghi, A.M. van Oijen
A versatile approach to the generation of fluid supported lipid bilayers and its applications
Biotechnol Bioeng. (2014) (pdf)

I. Kusters, A.M. van Oijen, A.J. Driessen
Membrane-on-a-chip: microstructured silicon/silicon-dioxide chips for high-throughput screening of membrane transport and viral membrane fusion
ACS Nano (2014) 8(4):3380-92 (pdf)

H.J. Geertsema, A.W. Kulczyk, C.C. Richardson, A.M. van Oijen
Single-molecule studies of polymerase dynamics and stoichiometry at the bacteriophage T7 replication machinery
Proc Natl Acad Sci U S A. (2014) 111(11):4073-8 (pdf)

S.A. Stratmann, A.M. van Oijen
DNA replication at the single-molecule level
Soc Rev. (2014) 43(4):1201-20 (pdf)

K.E. Duderstadt, R. Reyes-Lamothe, A.M. van Oijen, D.J. Sherratt
Replication-fork dynamics
Cold Spring Harb Perspect Biol. (2014) 6(1) (pdf)

2013

B. Brandenburg, W. Koudstaal, J. Goudsmit, V. Klaren, C. Tang, M.V. Bujny, H.J. Korse, T. Kwaks, J.J. Otterstrom, J. Juraszek, A.M. van Oijen, R. Vogels, R.H. Friesen
Mechanisms of hemagglutinin targeted influenza virus neutralization
PLoS One (2013) 8(12) (pdf)

G.B. Erkens, I. Hänelt, J.M.H. Goudsmits, D.J. Slotboom, A.M. van Oijen
Unsynchronised subunit motion in single trimeric sodium-coupled aspartate transporters
Nature (2013) 502: 119-23 (pdf)

H.J. Geertsema, A.M. van Oijen
A single-molecule view of DNA replication: the dynamic nature of multi-protein complexes revealed
Curr Opin Struct Biol. (2013) 788-93 (pdf)

T. Ivanovic, J.L. Choi, S.P. Whelan, A.M. van Oijen, S.C. Harrison
Influenza-virus membrane fusion by cooperative fold-back of stochastically induced hemagglutinin intermediates
Elife (2013) 2:e00333. doi: 10.7554/eLife.00333 (pdf)

A. Robinson, A.M. van Oijen
Bacterial replication, transcription and translation: mechanistic insights from single-molecule biochemical studies
Nature Rev Microbiol. (2013) 11:303-15 (pdf)

S. Jergic, N.P. Horan, M.M. Elshenawy, C.E. Mason, T. Urathamakul, K. Ozawa, A. Robinson, J.M. Goudsmits, Y. Wang, X. Pan, J.L. Beck, A.M. van Oijen, T. Huber, S.M. Hamdan, N.E. Dixon
A direct proofreader-clamp interaction stabilizes the Pol III replicase in the polymerization mode.
EMBO Journal (2013) doi: 10.1038/emboj.2012.347 (pdf)

J. Otterstrom, A.M. van Oijen
Visualization of Membrane Fusion, One Particle at a Time.
Biochemistry (2013) Feb 19. [Epub ahead of print] (pdf)

2012

H. Yardimci, X. Wang, A.B. Loveland, I. Tappin, D.Z. Rudner, J. Hurwitz, A.M. van Oijen, J.C. Walter
Bypass of a protein barrier by a replicative helicase
Nature (2012) 492: 205-9 (pdf)

J.S. Leith, A. Tafvizi, F. Huang, W.E. Uspal, P.S. Doyle, A.R. Fersht, L.A. Mirny, A.M. van Oijen
Sequence-dependent sliding kinetics of p53
Proc. Natl. Acad. Sci. USA (2012) 109(41): 16552-7 (pdf)

A.B. Loveland, S. Habuchi, J.C. Walter, A.M. van Oijen
A general approach to break the concentration barrier in single-molecule imaging
Nature Methods (2012) 9(10): 987-92 (pdf)

A. Quessada-Vial, A.M. van Oijen
Spotting the mistakes, one molecule at a time
Structure (2012) 20(7): 1130-2 (pdf)

H. Yardimci, A.B. Loveland, A.M. van Oijen, J.C. Walter
Single-molecule analysis of DNA replication in Xenopus egg extracts
Methods (2012) 57(2): 179-86 (pdf)

T. Ivanovic, R. Rozendaal, D.L. Floyd, M. Popovic, A.M. van Oijen, S.C. Harrison
Kinetics of proton transport into influenza virions by the viral M2 channel
PLoS One (2012) 7(3): e31566 (pdf)

2011

A.K. Satapathy, A.W. Kulczyk, S. Ghosh, A.M. van Oijen, C.C. Richardson
Coupling dTTP hydrolysis with DNA unwinding by the DNA helicase of bacteriophage T7
J. Biol. Chem. (2011) 286(39): 34468-78 (pdf)

B. Akabayov, A.W. Kulczyk, S.R. Akabayov, C. Theile, L.W. McLaughlin, B. Beauchamp, A.M. van Oijen, C.C. Richardson
Pyrovanadolysis, a pyrophosphorolysis-like reaction mediated by pyrovanadate, Mn2+, and DNA polymerase of bacteriophage T7
J. Biol. Chem. (2011) 286(33): 29146-57 (pdf)

A. Tafvizi, L.A. Mirny, A.M. van Oijen
Dancing on DNA: kinetic aspects of search processes on DNA
Chemphyschem (2011) 12(8): 1481-9 (pdf)

N.A. Tanner, G. Tolun, J.J. Loparo, S. Jergic, J.D. Griffith, N.E. Dixon, A.M. van Oijen
E. coli DNA replication in the absence of free β clamps
EMBO J. (2011) 30(9): 1830-40 (pdf)

A.M. van Oijen
Single-molecule approaches to characterizing kinetics of biomolecular interactions
Curr. Opin. Biotechnol. (2011) 22(1): 75-80 (pdf)

J.J. Loparo, A.W. Kulczyk, C.C. Richardson, A.M. van Oijen
Simultaneous single-molecule measurements of phage T7 replisome composition and function reveal the mechanism of polymerase exchange
Proc. Natl. Acad. Sci. USA(2011): Epub ahead of print (pdf)

A. Tafvizi, F. Huang, A.R. Fersht, L.A. Mirny, A.M. van Oijen
A single-molecule characterization of p53 search on DNA
Proc. Natl. Acad. Sci. USA(2011) 108: 563-8 (pdf)

2010

H. Yardimci, A.B. Loveland, S. Habuchi, A.M. van Oijen, J.C. Walter
Uncoupling of sister replisomes during eukaryotic DNA replication
Mol. Cell (2010)40: 834-40 (pdf) (Discussed in: DNA replication: Making two forks from one prepreplication complex; Botchan and Berger; Mol. Cell (2010) 40: 860-1) (pdf)

R. Lebofsky, A.M. van Oijen, J.C. Walter
DNA is a co-factor for its own replication in Xenopus egg extracts
Nucleic Acids Res.(2011) 39: 545-55 (pdf)

A.M. van Oijen
Single-molecule approaches to characterizing kinetics of biomolecular interactions
Curr. Opin. Biotechnol.(2010): Epub ahead of print (pdf)

M.P. Elenko, J.W. Szostak, A.M. van Oijen
Single-molecule binding experiments on long time scales
Rev. Sci. Instrum.(2010) 81:083705 (pdf)

A.M. van Oijen, J.J. Loparo
Single-molecule studies of the replisome
Annu. Rev. Biophys.(2010) 39:429-48 (pdf)

A.K. Satapathy, A.B. Kochaniak, S. Mukherjee, D.J. Crampton, A. van Oijen, C.C. Richardson
Residues in the central beta-hairpin of the DNA helicase of bacteriophage T7 are important in DNA unwinding
Proc. Natl. Acad. Sci. USA(2010) 107: 6782-7 (pdf)

N.A. Tanner, A.M. van Oijen
Visualizing DNA replication at the single-molecule level
Methods Enzymology(2010) 475: 259-78 (pdf)

D.L. Floyd, S.C. Harrison, A.M. van Oijen
Analysis of kinetic intermediates in single-particle dwell-time distributions
Biophys. Jrnl.(2010) 99: 360-6 (pdf)

J. Al-Bassam, H. Kim, G. Brouhard, A. van Oijen, S.C. Harrison, F. Chang
CLASP promotes microtubule rescue by recruiting tubulin dimmers to the microtubule
Dev. Cell(2010) 19: 245-58 (pdf)

S.M. Hamdan, A.M. van Oijen
Timing, coordination, and rhythm: acrobatics at the DNA replication fork
J. Biol. Chem.(2010) 285:18979-83 (pdf)

A.W. Kulczyk, N.A. Tanner, J.J. Loparo, C.C. Richardson, A.M. van Oijen
Direct observation of enzymes replicating DNA using a single-molecule DNA stretching assay
J. Vis. Exp.(2010) Mar. 23;(37). pii: 168 (link)

C.M. Etson, S.M. Hamdan, C.C. Richardson, A.M. van Oijen
Thioredoxin suppresses microscopic hopping of T7 DNA polymerase on duplex DNA
Proc. Natl. Acad. Sci.(2010) 107(5):1900-5 (pdf)

2009

N.A. Tanner, J.J. Loparo, A.M. van Oijen
Visualizing single-molecule DNA replication with fluorescence microscopy
J. Vis. Exp.(2009) Oct. 9;(32). pii: 1529 (link)

D.L. Floyd, S.C. Harrison, A.M. van Oijen
Method for measurement of viral fusion kinetics at the single particle level
J. Vis. Exp.(2009) Sep. 7;(31). pii: 1484 (link)

J.J. Otterstrom, A.M. van Oijen
Nudging through a nucleosome
Science(2009) 325(5940):547-8 (pdf)

M.P. Elenko, J.W. Szostak, A.M. van Oijen
Single-molecule imaging of an in vitro-evolved RNA aptamer reveals homogeneous ligand binding kinetics
J. Am. Chem. Soc.(2009) 131(29):9866-7 (pdf)

N.A. Tanner, A.M. van Oijen
Single-molecule observation of prokaryotic DNA replication
Methods Mol. Biol.(2009) 521:397-410

S.M. Hamdan, J.J. Loparo, M. Takahashi, C.C. Richardson, A.M. van Oijen
Dynamics of individual DNA replication loops reveal temporal control of lagging-strand synthesis
Nature (2009) 457(7227):336-9 (pdf)

2008

D.L. Floyd, J. Ragains, J.J. Skehel, S.C. Harrison, A.M. van Oijen
Single-particle kinetics of influenza membrane fusion
Proc. Natl. Acad. Sci. USA (2008) 105(40):15382-7 (pdf)

A.M. van Oijen
Cutting down the forest to see a single tree
Nature Chemical Biology(2008) 4:440-3 (pdf)

G. Komazin-Meredith, R. Mirchev, P.W. Yacono, D.E. Golan, A.M. van Oijen, D.M. Coen
Hopping of a processivity factor on DNA revealed by single-molecule assays of diffusion
Proc. Natl. Acad. Sci. USA(2008) 105:10721-6 (pdf)

A. Tafvizi, F. Huang, J.S. Leith, A.R. Fersht, L.A. Mirny, A.M. van Oijen
Tumor suppressor p53 slides on DNA with low friction and high stability
Biophys. Jrnl.(2008) 95:L01-L03 (pdf)

N.A. Tanner, S.M. Hamdan, J. Slobodan, K.V. Loscha, P.M. Schaeffer, N.E. Dixon, A.M. van Oijen
Single-molecule studies of fork dynamics in Escherichia coli DNA replication
Nature Structure & Molecular Biology (2008) 15:170-5 (pdf)
(Discussed in: Understanding how the replisome works, Kenneth J. Marians, Nature Struct.&Mol.Biol. (2008) 15:125-7 (pdf))

2007

A.M. van Oijen
Honey, I shrunk the DNA: DNA length as a probe for nucleic-acid enzyme activity
Biopolymers (2007) 144-53 (pdf)

S.M. Hamdan, D.E. Johnson, N.A. Tanner, J.-B. Lee, U. Qimron, S. Tabor, A.M. van Oijen, C.C. Richardson
DNA helicase-DNA polymerase interactions assure processive replication fork movement
Molecular Cell(2007) 27:539-49 (pdf)

A.M. van Oijen
Single-molecule studies of complex systems: The replisome
Mol. Biosystems(2007) 3:117-25 (pdf)

S. Fujiyoshi, M. Fujiwara, C. Kim, M. Matsushita, A.M. van Oijen, J. Schmidt
Single-component reflective objective for low-temperature spectroscopy in the entire visible region
Appl. Phys. Lett. (2007) 051125 (pdf)

2006

P.C. Blainey, A.M. van Oijen, A. Banerjee, G.L. Verdine, X.S. Xie
A base-excision DNA-repair protein searches for intrahelical lesions by fast sliding along DNA
Proc. Natl. Acad. Sci. USA(2006), 103:5752-7 (pdf)

J.B. Lee, R.K. Hite, S.M. Hamdan, X.S. Xie, C.C. Richardson, A.M. van Oijen
DNA primase acts as a molecular brake in DNA replication
Nature(2006) 439:621-4 (pdf)
(Discussed in: Prime-time progress, Stephen D. Bell, Nature (2006) 439:542-3 (pdf)
The double helix unzipped, Arianne Heinrichs, Nature Reviews Molecular Cell Biology (2006) 7:158-9 (pdf)
Tortoise puts brake on hare, Journal of Cell Biology (2006) 172:640 (pdf)
DNA copier component found to be real drag, Courtney Humphries, Focus (Harvard Medical School), Feb 24 2006 (link))

Brian P. English, Wei Min, Antoine M. van Oijen, Kang Taek Lee, Guobin Luo, Hongye Sun, Binny J Cherayil, S.C. Kou, X. Sunney Xie
Ever-fluctuating single enzyme molecules: Michaelis-Menten equation revisited
Nature Chemical Biology(2006) 2:87-94 (pdf)
(Discussed in: Michaelis-Menten is dead, long live Michaelis-Menten!, Nils G. Walter, Nature Chem. Biol. (2006) 2:66-7 (pdf)
Michaelis-Menten for single molecule, Allison Doerr, Nature Methods (2006) 3:158 (pdf))

2004

Marcelo Ehrlich, Werner Boll, Antoine van Oijen, Ramesh Hariharan, Kartik Chandran, Max L. Nibert, Tomas Kirchhausen
Endocytosis by Random Initiation and Stabilization of Clathrin-Coated Pits
Cell(2004) 118:591-605 (pdf)
(Discussed in: Light on Pits, Elizabeth Smythe, Nature 431 (2003) 641-642) (pdf)

2003

A.M. van Oijen, P.C. Blainey, D.J. Crampton, C.C. Richardson, T. Ellenberger, X.S. Xie
Single-molecule kinetics reveal base dependence and dynamic disorder of lambda exonuclease
Science(2003) 301:1235-1238 (pdf)
(Discussed in: Breakthrough of the year: The Runners-up, News and Editorial Staff, Science 302 (2003) 2039-2045) (pdf)

2002

R. Verberk, A.M.van Oijen, M. Orrit
A simple model for the power-law blinking of single semiconductor nanocrystals
Phys. Rev. B(2002) 66(233202):1-4 (pdf)

2001

J. Wrachtrup, T.J. Aartsma, J. Köhler, M. Ketelaars, A.M. van Oijen, M. Matsushita, J. Schmidt, C. Tietz, F. Jelezko
Fluorescence-excitation spectroscopy on individual light-harvesting 2 complexes of Rhodopseudomonas acidophila
Single-Molecule Detection in Solution; Methods and Applications (Eds. Ch. Zander, J. Enderlein, R.A. Keller, R.R. Keller; published 2002 by John Wiley & Sons)

A.M. van Oijen, R. Verberk, Y. Durand, J. Schmidt, J.N.J. van Lingen, A.A. Bol, A. Meijerink
Continuous-wave two-photon excitation of individual CdS nanocrystallites
Appl. Phys. Lett.(2001) 79:830-832

M. Matsushita, M. Ketelaars, A.M. van Oijen, J. Köhler, T.J. Aartsma, J.Schmidt
Spectroscopy on the B850 band of individual light-harvesting 2 complexes of Rhodopseudomonas acidophila; II. Exciton states of an elliptically deformed ring aggregate
Biophys. Jrnl.(2001) 80:1604-1614

M. Ketelaars, A.M. van Oijen, M. Matsushita, J. Köhler, J. Schmidt, T.J. Aartsma
Spectroscopy on the B850 band of individual light-harvesting 2 complexes of Rhodopseudomonas acidophila; I. Experiments and Monte-Carlo simulations
Biophys. Jrnl.(2001) 80:1591-1603

A.M. van Oijen, M. Ketelaars, C. Hofmann, M. Matsushita, T.J. Aartsma, J. Schmidt
Optical spectroscopy of individual photosynthetic pigment protein complexes
International Journal of Modern Physics B(2001) 15:3633-3636

A.M. van Oijen, M. Ketelaars, J. Köhler, T.J. Aartsma, J. Schmidt
The electronic structure of single photosynthetic pigment-protein complexes
Springer Series in Chemical Physics(2001) 67:62-81 J. Köhler,

2000

Y. Durand, A. Bloeß, A.M. van Oijen, E.J.J. Groenen, J. Schmidt
Pentacene: a suitable molecule to investigate the Sphol’skii effect at a molecular level?
Chem. Phys. Lett.(2000) 317:232-237

A.M. van Oijen, M. Ketelaars, J. Köhler, T.J. Aartsma, J. Schmidt
Spectroscopy of individual LH2 complexes of Rhodopseudomonas acidophila: diagonal disorder, sample heterogeneity, spectral diffusion and energy transfer in the B 800 band
Biophys. Jrnl.(2000) 78:1570-1577

1999

A.M. van Oijen, M. Ketelaars, J. Köhler, T.J. Aartsma, J. Schmidt
Spectroscopy of individual LH2 complexes of Rhodopseudomonas acidophila: Localized excitations in the B800 band
Chem. Phys. (1999) 247:53-60

A.M. van Oijen, M. Ketelaars, J. Köhler, T.J. Aartsma, J. Schmidt
Unraveling the electronic structure of individual photosynthetic pigment-protein complexes
Science (1999) 285:400-402
(Discussed in: Coherent excitation in the antennacomplex, Michel Orrit, Science (1999) 285:5426, and Electronic structure of light-harvesting complex unraveled, Chemical & Engineering News, July 19, 1999)

A.C.J. Brouwer, J. Köhler, A.M. van Oijen, E.J.J. Groenen, J. Schmidt
Single-molecule fluorescence autocorrelation experiments on pentacene. The dependence of intersystem crossing on isotopic composition
J. Chem. Phys.(1999) 110:9151-9159

A.M. van Oijen, M. Ketelaars
Een nieuwe kijk op fotosynthese
Nederlands Tijdschrift voor Natuurkunde(2000) 66:38-41

A.M. van Oijen, J. Köhler, J. Schmidt, M. Müller, G.J. Brakenhoff
Far-field fluorescence microscopy beyond the diffraction limit
J. Opt. Soc. Am. A(1999) 16:909-915

1998

A.M. van Oijen, M. Ketelaars, J. Köhler, T.J. Aartsma, J. Schmidt
Spectroscopy of Single Light-Harvesting Complexes from Purple Photosynthetic Bacteria at 1.2 K
J. Phys. Chem. B(1998) 102:9363-9366

A.M. van Oijen, J. Köhler, J. Schmidt, M. Müller, G.J. Brakenhoff
3-Dimensional super-resolution by spectrally selective imaging
Chem. Phys. Lett.(1998) 292:183-187
(Discussed in: Molecular Imaging Beats Limits of Light, Rob van den Berg, Science 281 (1998) 629)