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Items: 1 to 50 of 114

1.

Identification of Multiple Kinetic Populations of DNA-Binding Proteins in Live Cells.

Ho HN, Zalami D, Köhler J, van Oijen AM, Ghodke H.

Biophys J. 2019 Jul 19. pii: S0006-3495(19)30583-1. doi: 10.1016/j.bpj.2019.07.015. [Epub ahead of print]

PMID:
31383358
2.

When proteins play tag: the dynamic nature of the replisome.

Mueller SH, Spenkelink LM, van Oijen AM.

Biophys Rev. 2019 Jul 4:641-651. doi: 10.1007/s12551-019-00569-4. [Epub ahead of print] Review.

3.

Recycling of single-stranded DNA-binding protein by the bacterial replisome.

Spenkelink LM, Lewis JS, Jergic S, Xu ZQ, Robinson A, Dixon NE, van Oijen AM.

Nucleic Acids Res. 2019 May 7;47(8):4111-4123. doi: 10.1093/nar/gkz090.

4.

Spatial and temporal organization of RecA in the Escherichia coli DNA-damage response.

Ghodke H, Paudel BP, Lewis JS, Jergic S, Gopal K, Romero ZJ, Wood EA, Woodgate R, Cox MM, van Oijen AM.

Elife. 2019 Feb 5;8. pii: e42761. doi: 10.7554/eLife.42761.

5.

Shining a Spotlight on DNA: Single-Molecule Methods to Visualise DNA.

Kaur G, Lewis JS, van Oijen AM.

Molecules. 2019 Jan 30;24(3). pii: E491. doi: 10.3390/molecules24030491. Review.

6.

RecFOR epistasis group: RecF and RecO have distinct localizations and functions in Escherichia coli.

Henrikus SS, Henry C, Ghodke H, Wood EA, Mbele N, Saxena R, Basu U, van Oijen AM, Cox MM, Robinson A.

Nucleic Acids Res. 2019 Apr 8;47(6):2946-2965. doi: 10.1093/nar/gkz003.

7.

Plasticity of Multi-Protein Complexes.

van Oijen AM, Duderstadt KE, Xiao J, Fishel R.

J Mol Biol. 2018 Oct 26;430(22):4441-4442. doi: 10.1016/j.jmb.2018.08.008. Epub 2018 Aug 10. No abstract available.

PMID:
30102893
8.

Design of DNA rolling-circle templates with controlled fork topology to study mechanisms of DNA replication.

Monachino E, Ghodke H, Spinks RR, Hoatson BS, Jergic S, Xu ZQ, Dixon NE, van Oijen AM.

Anal Biochem. 2018 Sep 15;557:42-45. doi: 10.1016/j.ab.2018.07.008. Epub 2018 Jul 18.

PMID:
30016625
9.

Special Issue on Cell Biophysics.

van Oijen AM.

Biophys J. 2018 Jul 17;115(2):E1-E2. doi: 10.1016/j.bpj.2018.06.017. Epub 2018 Jun 27. No abstract available.

10.

Nanoparticles for super-resolution microscopy and single-molecule tracking.

Jin D, Xi P, Wang B, Zhang L, Enderlein J, van Oijen AM.

Nat Methods. 2018 Jun;15(6):415-423. doi: 10.1038/s41592-018-0012-4. Epub 2018 May 28. Review.

PMID:
29808018
11.

Using Single-Molecule Approaches to Understand the Molecular Mechanisms of Heat-Shock Protein Chaperone Function.

Johnston CL, Marzano NR, van Oijen AM, Ecroyd H.

J Mol Biol. 2018 Oct 26;430(22):4525-4546. doi: 10.1016/j.jmb.2018.05.021. Epub 2018 May 19. Review.

PMID:
29787765
12.

Anisotropic functionalization of upconversion nanoparticles.

Ren W, Wen S, Tawfik SA, Su QP, Lin G, Ju LA, Ford MJ, Ghodke H, van Oijen AM, Jin D.

Chem Sci. 2018 Apr 23;9(18):4352-4358. doi: 10.1039/c8sc01023d. eCollection 2018 May 14.

13.

Specialised DNA polymerases in Escherichia coli: roles within multiple pathways.

Henrikus SS, van Oijen AM, Robinson A.

Curr Genet. 2018 Dec;64(6):1189-1196. doi: 10.1007/s00294-018-0840-x. Epub 2018 Apr 26. Review.

PMID:
29700578
14.

The transcription-repair coupling factor Mfd associates with RNA polymerase in the absence of exogenous damage.

Ho HN, van Oijen AM, Ghodke H.

Nat Commun. 2018 Apr 20;9(1):1570. doi: 10.1038/s41467-018-03790-z.

15.

Single-particle fusion of influenza viruses reveals complex interactions with target membranes.

van der Borg G, Braddock S, Blijleven JS, van Oijen AM, Roos WH.

J Phys Condens Matter. 2018 May 23;30(20):204005. doi: 10.1088/1361-648X/aabc21. Epub 2018 Apr 6.

PMID:
29623903
16.

Detection of kinetic change points in piece-wise linear single molecule motion.

Hill FR, van Oijen AM, Duderstadt KE.

J Chem Phys. 2018 Mar 28;148(12):123317. doi: 10.1063/1.5009387.

PMID:
29604840
17.

Quantification of ligand density and stoichiometry on the surface of liposomes using single-molecule fluorescence imaging.

Belfiore L, Spenkelink LM, Ranson M, van Oijen AM, Vine KL.

J Control Release. 2018 May 28;278:80-86. doi: 10.1016/j.jconrel.2018.03.022. Epub 2018 Mar 22.

PMID:
29577949
18.

Hemagglutinin-Mediated Membrane Fusion: A Biophysical Perspective.

Boonstra S, Blijleven JS, Roos WH, Onck PR, van der Giessen E, van Oijen AM.

Annu Rev Biophys. 2018 May 20;47:153-173. doi: 10.1146/annurev-biophys-070317-033018. Epub 2018 Mar 1. Review.

PMID:
29494252
19.

Steric exclusion and protein conformation determine the localization of plasma membrane transporters.

Bianchi F, Syga Ł, Moiset G, Spakman D, Schavemaker PE, Punter CM, Seinen AB, van Oijen AM, Robinson A, Poolman B.

Nat Commun. 2018 Feb 5;9(1):501. doi: 10.1038/s41467-018-02864-2.

20.

The small heat shock protein Hsp27 binds α-synuclein fibrils, preventing elongation and cytotoxicity.

Cox D, Whiten DR, Brown JWP, Horrocks MH, San Gil R, Dobson CM, Klenerman D, van Oijen AM, Ecroyd H.

J Biol Chem. 2018 Mar 23;293(12):4486-4497. doi: 10.1074/jbc.M117.813865. Epub 2018 Jan 30.

21.

DNA polymerase IV primarily operates outside of DNA replication forks in Escherichia coli.

Henrikus SS, Wood EA, McDonald JP, Cox MM, Woodgate R, Goodman MF, van Oijen AM, Robinson A.

PLoS Genet. 2018 Jan 19;14(1):e1007161. doi: 10.1371/journal.pgen.1007161. eCollection 2018 Jan.

22.

Resolving the Gordian Knot: Srs2 Strips Intermediates Formed during Homologous Recombination.

Ghodke H, Lewis JS, van Oijen AM.

Trends Biochem Sci. 2018 Mar;43(3):149-151. doi: 10.1016/j.tibs.2017.12.004. Epub 2017 Dec 28.

PMID:
29290471
23.

Single-molecule live-cell imaging of bacterial DNA repair and damage tolerance.

Ghodke H, Ho H, van Oijen AM.

Biochem Soc Trans. 2018 Feb 19;46(1):23-35. doi: 10.1042/BST20170055. Epub 2017 Dec 1. Review.

PMID:
29196610
24.

Single-molecule visualization of conformational changes and substrate transport in the vitamin B12 ABC importer BtuCD-F.

Goudsmits JMH, Slotboom DJ, van Oijen AM.

Nat Commun. 2017 Nov 21;8(1):1652. doi: 10.1038/s41467-017-01815-7.

25.

Diatrack particle tracking software: Review of applications and performance evaluation.

Vallotton P, van Oijen AM, Whitchurch CB, Gelfand V, Yeo L, Tsiavaliaris G, Heinrich S, Dultz E, Weis K, Grünwald D.

Traffic. 2017 Dec;18(12):840-852. doi: 10.1111/tra.12530. Epub 2017 Oct 23. Review.

26.

Single-molecule visualization of Saccharomyces cerevisiae leading-strand synthesis reveals dynamic interaction between MTC and the replisome.

Lewis JS, Spenkelink LM, Schauer GD, Hill FR, Georgescu RE, O'Donnell ME, van Oijen AM.

Proc Natl Acad Sci U S A. 2017 Oct 3;114(40):10630-10635. doi: 10.1073/pnas.1711291114. Epub 2017 Sep 18.

27.

Single-Molecule Fluorescence Studies of Membrane Transporters Using Total Internal Reflection Microscopy.

Goudsmits JMH, van Oijen AM, Slotboom DJ.

Methods Enzymol. 2017;594:101-121. doi: 10.1016/bs.mie.2017.05.009. Epub 2017 Jul 18.

PMID:
28779837
28.

The more the merrier: high-throughput single-molecule techniques.

Hill FR, Monachino E, van Oijen AM.

Biochem Soc Trans. 2017 Jun 15;45(3):759-769. doi: 10.1042/BST20160137. Review.

PMID:
28620037
29.

Single-molecule visualization of fast polymerase turnover in the bacterial replisome.

Lewis JS, Spenkelink LM, Jergic S, Wood EA, Monachino E, Horan NP, Duderstadt KE, Cox MM, Robinson A, Dixon NE, van Oijen AM.

Elife. 2017 Apr 22;6. pii: e23932. doi: 10.7554/eLife.23932.

30.

Watching cellular machinery in action, one molecule at a time.

Monachino E, Spenkelink LM, van Oijen AM.

J Cell Biol. 2017 Jan 2;216(1):41-51. doi: 10.1083/jcb.201610025. Epub 2016 Dec 15. Review.

31.

On the Spatial Organization of mRNA, Plasmids, and Ribosomes in a Bacterial Host Overexpressing Membrane Proteins.

van Gijtenbeek LA, Robinson A, van Oijen AM, Poolman B, Kok J.

PLoS Genet. 2016 Dec 15;12(12):e1006523. doi: 10.1371/journal.pgen.1006523. eCollection 2016 Dec.

32.

Mechanism of membrane fusion induced by vesicular stomatitis virus G protein.

Kim IS, Jenni S, Stanifer ML, Roth E, Whelan SP, van Oijen AM, Harrison SC.

Proc Natl Acad Sci U S A. 2017 Jan 3;114(1):E28-E36. doi: 10.1073/pnas.1618883114. Epub 2016 Dec 14.

33.

Simultaneous Real-Time Imaging of Leading and Lagging Strand Synthesis Reveals the Coordination Dynamics of Single Replisomes.

Duderstadt KE, Geertsema HJ, Stratmann SA, Punter CM, Kulczyk AW, Richardson CC, van Oijen AM.

Mol Cell. 2016 Dec 15;64(6):1035-1047. doi: 10.1016/j.molcel.2016.10.028. Epub 2016 Nov 23.

34.

Lipids Activate SecA for High Affinity Binding to the SecYEG Complex.

Koch S, de Wit JG, Vos I, Birkner JP, Gordiichuk P, Herrmann A, van Oijen AM, Driessen AJ.

J Biol Chem. 2016 Oct 21;291(43):22534-22543. Epub 2016 Sep 9.

35.

Mechanisms of influenza viral membrane fusion.

Blijleven JS, Boonstra S, Onck PR, van der Giessen E, van Oijen AM.

Semin Cell Dev Biol. 2016 Dec;60:78-88. doi: 10.1016/j.semcdb.2016.07.007. Epub 2016 Jul 9. Review.

PMID:
27401120
36.

Single-Molecule Specific Mislocalization of Red Fluorescent Proteins in Live Escherichia coli.

Ghodke H, Caldas VE, Punter CM, van Oijen AM, Robinson A.

Biophys J. 2016 Jul 12;111(1):25-7. doi: 10.1016/j.bpj.2016.05.047. Epub 2016 Jun 20.

37.

A Tool for Alignment and Averaging of Sparse Fluorescence Signals in Rod-Shaped Bacteria.

Goudsmits JMH, van Oijen AM, Robinson A.

Biophys J. 2016 Apr 26;110(8):1708-1715. doi: 10.1016/j.bpj.2016.02.039.

38.

Stability versus exchange: a paradox in DNA replication.

Åberg C, Duderstadt KE, van Oijen AM.

Nucleic Acids Res. 2016 Jun 2;44(10):4846-54. doi: 10.1093/nar/gkw296. Epub 2016 Apr 25.

39.

Mutations for Worse or Better: Low-Fidelity DNA Synthesis by SOS DNA Polymerase V Is a Tightly Regulated Double-Edged Sword.

Jaszczur M, Bertram JG, Robinson A, van Oijen AM, Woodgate R, Cox MM, Goodman MF.

Biochemistry. 2016 Apr 26;55(16):2309-18. doi: 10.1021/acs.biochem.6b00117. Epub 2016 Apr 12. Review.

40.

Droplet microfluidics for kinetic studies of viral fusion.

Mashaghi S, van Oijen AM.

Biomicrofluidics. 2016 Mar 2;10(2):024102. doi: 10.1063/1.4943126. eCollection 2016 Mar.

41.

Speeding up biomolecular interactions by molecular sledding.

Turkin A, Zhang L, Marcozzi A, Mangel WF, Herrmann A, van Oijen AM.

Chem Sci. 2016 Feb 1;7(2):916-920. Epub 2015 Oct 7.

42.

Bisecting Microfluidic Channels with Metallic Nanowires Fabricated by Nanoskiving.

Kalkman GA, Zhang Y, Monachino E, Mathwig K, Kamminga ME, Pourhossein P, Oomen PE, Stratmann SA, Zhao Z, van Oijen AM, Verpoorte E, Chiechi RC.

ACS Nano. 2016 Feb 23;10(2):2852-9. doi: 10.1021/acsnano.5b07996. Epub 2016 Feb 5.

PMID:
26836373
43.

The innate immune sensor IFI16 recognizes foreign DNA in the nucleus by scanning along the duplex.

Stratmann SA, Morrone SR, van Oijen AM, Sohn J.

Elife. 2015 Dec 16;4:e11721. doi: 10.7554/eLife.11721.

44.

Theory of bimolecular reactions in a solution with linear traps: Application to the problem of target search on DNA.

Turkin A, van Oijen AM, Turkin AA.

Phys Rev E Stat Nonlin Soft Matter Phys. 2015;92(5):052703. doi: 10.1103/PhysRevE.92.052703. Epub 2015 Nov 3.

PMID:
26651719
45.

Probing molecular choreography through single-molecule biochemistry.

van Oijen AM, Dixon NE.

Nat Struct Mol Biol. 2015 Dec;22(12):948-52. doi: 10.1038/nsmb.3119.

PMID:
26643847
46.

Regulation of Mutagenic DNA Polymerase V Activation in Space and Time.

Robinson A, McDonald JP, Caldas VE, Patel M, Wood EA, Punter CM, Ghodke H, Cox MM, Woodgate R, Goodman MF, van Oijen AM.

PLoS Genet. 2015 Aug 28;11(8):e1005482. doi: 10.1371/journal.pgen.1005482. eCollection 2015 Aug.

47.

iSBatch: a batch-processing platform for data analysis and exploration of live-cell single-molecule microscopy images and other hierarchical datasets.

Caldas VE, Punter CM, Ghodke H, Robinson A, van Oijen AM.

Mol Biosyst. 2015 Oct;11(10):2699-708. doi: 10.1039/c5mb00321k.

PMID:
26198886
48.

External control of reactions in microdroplets.

Mashaghi S, van Oijen AM.

Sci Rep. 2015 Jul 2;5:11837. doi: 10.1038/srep11837.

49.

Single-molecule observation of prokaryotic DNA replication.

Geertsema HJ, Duderstadt KE, van Oijen AM.

Methods Mol Biol. 2015;1300:219-38. doi: 10.1007/978-1-4939-2596-4_14.

PMID:
25916715
50.

Chikungunya virus fusion properties elucidated by single-particle and bulk approaches.

van Duijl-Richter MKS, Blijleven JS, van Oijen AM, Smit JM.

J Gen Virol. 2015 Aug;96(8):2122-2132. doi: 10.1099/vir.0.000144. Epub 2015 Apr 13.

PMID:
25872739

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