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Items: 1 to 50 of 93

1.

Single-Crystal Rutile TiO2 Nanocylinders are Highly Effective Transducers of Optical Force and Torque.

Ha S, Tang Y, van Oene MM, Janissen R, Dries RM, Solano B, Adam AJL, Dekker NH.

ACS Photonics. 2019 May 15;6(5):1255-1265. doi: 10.1021/acsphotonics.9b00220. Epub 2019 Apr 22.

2.

Predicting Intraserotypic Recombination in Enterovirus 71.

Woodman A, Lee KM, Janissen R, Gong YN, Dekker NH, Shih SR, Cameron CE.

J Virol. 2019 Feb 5;93(4). pii: e02057-18. doi: 10.1128/JVI.02057-18. Print 2019 Feb 15.

3.

Global DNA Compaction in Stationary-Phase Bacteria Does Not Affect Transcription.

Janissen R, Arens MMA, Vtyurina NN, Rivai Z, Sunday ND, Eslami-Mossallam B, Gritsenko AA, Laan L, de Ridder D, Artsimovitch I, Dekker NH, Abbondanzieri EA, Meyer AS.

Cell. 2018 Aug 23;174(5):1188-1199.e14. doi: 10.1016/j.cell.2018.06.049. Epub 2018 Jul 26.

4.

Publisher's Note: Biological Magnetometry: Torque on Superparamagnetic Beads in Magnetic Fields [Phys. Rev. Lett. 114, 218301 (2015)].

van Oene MM, Dickinson LE, Pedaci F, Köber M, Dulin D, Lipfert J, Dekker NH.

Phys Rev Lett. 2018 Jun 22;120(25):259901. doi: 10.1103/PhysRevLett.120.259901.

PMID:
29979053
5.

Probing Chromatin Structure with Magnetic Tweezers.

Kaczmarczyk A, Brouwer TB, Pham C, Dekker NH, van Noort J.

Methods Mol Biol. 2018;1814:297-323. doi: 10.1007/978-1-4939-8591-3_18.

PMID:
29956240
6.

Discovery of Enterovirus A71-like nonstructural genomes in recent circulating viruses of the Enterovirus A species.

Lee KM, Gong YN, Hsieh TH, Woodman A, Dekker NH, Cameron CE, Shih SR.

Emerg Microbes Infect. 2018 Jun 21;7(1):111. doi: 10.1038/s41426-018-0107-0.

7.

Corrigendum: Applying torque to the Escherichia coli flagellar motor using magnetic tweezers.

van Oene MM, Dickinson LE, Cross B, Pedaci F, Lipfert J, Dekker NH.

Sci Rep. 2018 May 18;8:46980. doi: 10.1038/srep46980.

8.

Quantifying the Precision of Single-Molecule Torque and Twist Measurements Using Allan Variance.

van Oene MM, Ha S, Jager T, Lee M, Pedaci F, Lipfert J, Dekker NH.

Biophys J. 2018 Apr 24;114(8):1970-1979. doi: 10.1016/j.bpj.2018.02.039.

9.

Modification of the histone tetramer at the H3-H3 interface impacts tetrasome conformations and dynamics.

Ordu O, Kremser L, Lusser A, Dekker NH.

J Chem Phys. 2018 Mar 28;148(12):123323. doi: 10.1063/1.5009100.

PMID:
29604863
10.

What is all this fuss about Tus? Comparison of recent findings from biophysical and biochemical experiments.

Berghuis BA, Raducanu VS, Elshenawy MM, Jergic S, Depken M, Dixon NE, Hamdan SM, Dekker NH.

Crit Rev Biochem Mol Biol. 2018 Feb;53(1):49-63. doi: 10.1080/10409238.2017.1394264. Epub 2017 Nov 6. Review.

PMID:
29108427
11.

Signatures of Nucleotide Analog Incorporation by an RNA-Dependent RNA Polymerase Revealed Using High-Throughput Magnetic Tweezers.

Dulin D, Arnold JJ, van Laar T, Oh HS, Lee C, Perkins AL, Harki DA, Depken M, Cameron CE, Dekker NH.

Cell Rep. 2017 Oct 24;21(4):1063-1076. doi: 10.1016/j.celrep.2017.10.005.

12.

Single-molecule force spectroscopy on histone H4 tail-cross-linked chromatin reveals fiber folding.

Kaczmarczyk A, Allahverdi A, Brouwer TB, Nordenskiöld L, Dekker NH, van Noort J.

J Biol Chem. 2017 Oct 20;292(42):17506-17513. doi: 10.1074/jbc.M117.791830. Epub 2017 Aug 30.

13.

Measuring In Vivo Protein Dynamics Throughout the Cell Cycle Using Microfluidics.

de Leeuw R, Brazda P, Charl Moolman M, Kerssemakers JWJ, Solano B, Dekker NH.

Methods Mol Biol. 2017;1624:237-252. doi: 10.1007/978-1-4939-7098-8_18.

PMID:
28842888
14.

Probing the salt dependence of the torsional stiffness of DNA by multiplexed magnetic torque tweezers.

Kriegel F, Ermann N, Forbes R, Dulin D, Dekker NH, Lipfert J.

Nucleic Acids Res. 2017 Jun 2;45(10):5920-5929. doi: 10.1093/nar/gkx280.

15.

Applying torque to the Escherichia coli flagellar motor using magnetic tweezers.

van Oene MM, Dickinson LE, Cross B, Pedaci F, Lipfert J, Dekker NH.

Sci Rep. 2017 Mar 7;7:43285. doi: 10.1038/srep43285. Erratum in: Sci Rep. 2018 May 18;8:46980.

16.

Recent insights from in vitro single-molecule studies into nucleosome structure and dynamics.

Ordu O, Lusser A, Dekker NH.

Biophys Rev. 2016;8(Suppl 1):33-49. doi: 10.1007/s12551-016-0212-z. Epub 2016 Oct 18. Review.

17.

The progression of replication forks at natural replication barriers in live bacteria.

Moolman MC, Tiruvadi Krishnan S, Kerssemakers JW, de Leeuw R, Lorent V, Sherratt DJ, Dekker NH.

Nucleic Acids Res. 2016 Jul 27;44(13):6262-73. doi: 10.1093/nar/gkw397. Epub 2016 May 10.

18.

Tunable top-down fabrication and functional surface coating of single-crystal titanium dioxide nanostructures and nanoparticles.

Ha S, Janissen R, Ussembayev YY, van Oene MM, Solano B, Dekker NH.

Nanoscale. 2016 May 19;8(20):10739-48. doi: 10.1039/c6nr00898d.

PMID:
27160731
19.

Hysteresis in DNA compaction by Dps is described by an Ising model.

Vtyurina NN, Dulin D, Docter MW, Meyer AS, Dekker NH, Abbondanzieri EA.

Proc Natl Acad Sci U S A. 2016 May 3;113(18):4982-7. doi: 10.1073/pnas.1521241113. Epub 2016 Apr 18.

20.

High-throughput, high-force probing of DNA-protein interactions with magnetic tweezers.

Berghuis BA, Köber M, van Laar T, Dekker NH.

Methods. 2016 Aug 1;105:90-8. doi: 10.1016/j.ymeth.2016.03.025. Epub 2016 Mar 30.

21.

High Spatiotemporal-Resolution Magnetic Tweezers: Calibration and Applications for DNA Dynamics.

Dulin D, Cui TJ, Cnossen J, Docter MW, Lipfert J, Dekker NH.

Biophys J. 2015 Nov 17;109(10):2113-25. doi: 10.1016/j.bpj.2015.10.018.

22.

Comparing the Assembly and Handedness Dynamics of (H3.3-H4)2 Tetrasomes to Canonical Tetrasomes.

Vlijm R, Lee M, Ordu O, Boltengagen A, Lusser A, Dekker NH, Dekker C.

PLoS One. 2015 Oct 27;10(10):e0141267. doi: 10.1371/journal.pone.0141267. eCollection 2015.

23.

Backtracking behavior in viral RNA-dependent RNA polymerase provides the basis for a second initiation site.

Dulin D, Vilfan ID, Berghuis BA, Poranen MM, Depken M, Dekker NH.

Nucleic Acids Res. 2015 Dec 2;43(21):10421-9. doi: 10.1093/nar/gkv1098. Epub 2015 Oct 22.

24.

Untangling reaction pathways through modern approaches to high-throughput single-molecule force-spectroscopy experiments.

Dulin D, Berghuis BA, Depken M, Dekker NH.

Curr Opin Struct Biol. 2015 Oct;34:116-22. doi: 10.1016/j.sbi.2015.08.007. Epub 2015 Oct 1. Review.

PMID:
26434413
25.

Quantitative Analysis of Intracellular Fluorescent Foci in Live Bacteria.

Moolman MC, Kerssemakers JW, Dekker NH.

Biophys J. 2015 Sep 1;109(5):883-91. doi: 10.1016/j.bpj.2015.07.013.

26.

Strand separation establishes a sustained lock at the Tus-Ter replication fork barrier.

Berghuis BA, Dulin D, Xu ZQ, van Laar T, Cross B, Janissen R, Jergic S, Dixon NE, Depken M, Dekker NH.

Nat Chem Biol. 2015 Aug;11(8):579-85. doi: 10.1038/nchembio.1857. Epub 2015 Jul 6.

PMID:
26147356
27.

Essential validation methods for E. coli strains created by chromosome engineering.

Tiruvadi Krishnan S, Moolman MC, van Laar T, Meyer AS, Dekker NH.

J Biol Eng. 2015 Jul 1;9:11. doi: 10.1186/s13036-015-0008-x. eCollection 2015.

28.

Biological magnetometry: torque on superparamagnetic beads in magnetic fields.

van Oene MM, Dickinson LE, Pedaci F, Köber M, Dulin D, Lipfert J, Dekker NH.

Phys Rev Lett. 2015 May 29;114(21):218301. Epub 2015 May 27. Erratum in: Phys Rev Lett. 2018 Jun 22;120(25):259901.

PMID:
26066460
29.

Corrigendum: Freely orbiting magnetic tweezers to directly monitor changes in the twist of nucleic acids.

Lipfert J, Wiggin M, Kerssemakers JW, Pedaci F, Dekker NH.

Nat Commun. 2015 May 27;6:7192. doi: 10.1038/ncomms8192. No abstract available.

30.

Elongation-Competent Pauses Govern the Fidelity of a Viral RNA-Dependent RNA Polymerase.

Dulin D, Vilfan ID, Berghuis BA, Hage S, Bamford DH, Poranen MM, Depken M, Dekker NH.

Cell Rep. 2015 Feb 17;10(6):983-992. doi: 10.1016/j.celrep.2015.01.031. Epub 2015 Feb 12.

31.

Nucleosome assembly dynamics involve spontaneous fluctuations in the handedness of tetrasomes.

Vlijm R, Lee M, Lipfert J, Lusser A, Dekker C, Dekker NH.

Cell Rep. 2015 Jan 13;10(2):216-25. doi: 10.1016/j.celrep.2014.12.022. Epub 2015 Jan 8.

32.

A force calibration standard for magnetic tweezers.

Yu Z, Dulin D, Cnossen J, Köber M, van Oene MM, Ordu O, Berghuis BA, Hensgens T, Lipfert J, Dekker NH.

Rev Sci Instrum. 2014 Dec;85(12):123114. doi: 10.1063/1.4904148.

PMID:
25554279
33.

Torque spectroscopy for the study of rotary motion in biological systems.

Lipfert J, van Oene MM, Lee M, Pedaci F, Dekker NH.

Chem Rev. 2015 Feb 11;115(3):1449-74. doi: 10.1021/cr500119k. Epub 2014 Dec 26. Review. No abstract available.

PMID:
25541648
34.

Slow unloading leads to DNA-bound β2-sliding clamp accumulation in live Escherichia coli cells.

Moolman MC, Krishnan ST, Kerssemakers JW, van den Berg A, Tulinski P, Depken M, Reyes-Lamothe R, Sherratt DJ, Dekker NH.

Nat Commun. 2014 Dec 18;5:5820. doi: 10.1038/ncomms6820.

35.

An optimized software framework for real-time, high-throughput tracking of spherical beads.

Cnossen JP, Dulin D, Dekker NH.

Rev Sci Instrum. 2014 Oct;85(10):103712. doi: 10.1063/1.4898178.

PMID:
25362408
36.

Double-stranded RNA under force and torque: similarities to and striking differences from double-stranded DNA.

Lipfert J, Skinner GM, Keegstra JM, Hensgens T, Jager T, Dulin D, Köber M, Yu Z, Donkers SP, Chou FC, Das R, Dekker NH.

Proc Natl Acad Sci U S A. 2014 Oct 28;111(43):15408-13. doi: 10.1073/pnas.1407197111. Epub 2014 Oct 13.

37.

Invincible DNA tethers: covalent DNA anchoring for enhanced temporal and force stability in magnetic tweezers experiments.

Janissen R, Berghuis BA, Dulin D, Wink M, van Laar T, Dekker NH.

Nucleic Acids Res. 2014 Oct;42(18):e137. doi: 10.1093/nar/gku677. Epub 2014 Aug 19.

38.

Magnetic tweezers for the measurement of twist and torque.

Lipfert J, Lee M, Ordu O, Kerssemakers JW, Dekker NH.

J Vis Exp. 2014 May 19;(87). doi: 10.3791/51503.

39.

Structural and torsional properties of the RAD51-dsDNA nucleoprotein filament.

Lee M, Lipfert J, Sanchez H, Wyman C, Dekker NH.

Nucleic Acids Res. 2013 Aug;41(14):7023-30. doi: 10.1093/nar/gkt425. Epub 2013 May 22.

40.

Electron beam fabrication of a microfluidic device for studying submicron-scale bacteria.

Moolman MC, Huang Z, Krishnan ST, Kerssemakers JW, Dekker NH.

J Nanobiotechnology. 2013 Apr 10;11:12. doi: 10.1186/1477-3155-11-12.

41.

Studying genomic processes at the single-molecule level: introducing the tools and applications.

Dulin D, Lipfert J, Moolman MC, Dekker NH.

Nat Rev Genet. 2013 Jan;14(1):9-22. doi: 10.1038/nrg3316. Epub 2012 Oct 30. Review.

PMID:
23150038
42.

Rapid manufacturing of low-noise membranes for nanopore sensors by trans-chip illumination lithography.

Janssen XJ, Jonsson MP, Plesa C, Soni GV, Dekker C, Dekker NH.

Nanotechnology. 2012 Nov 30;23(47):475302. doi: 10.1088/0957-4484/23/47/475302. Epub 2012 Oct 26.

PMID:
23103750
43.

Electromagnetic torque tweezers: a versatile approach for measurement of single-molecule twist and torque.

Janssen XJ, Lipfert J, Jager T, Daudey R, Beekman J, Dekker NH.

Nano Lett. 2012 Jul 11;12(7):3634-9. doi: 10.1021/nl301330h. Epub 2012 Jun 8.

PMID:
22642488
44.

Calibration of the optical torque wrench.

Pedaci F, Huang Z, van Oene M, Dekker NH.

Opt Express. 2012 Feb 13;20(4):3787-802. doi: 10.1364/OE.20.003787.

PMID:
22418136
45.

A method to track rotational motion for use in single-molecule biophysics.

Lipfert J, Kerssemakers JJ, Rojer M, Dekker NH.

Rev Sci Instrum. 2011 Oct;82(10):103707. doi: 10.1063/1.3650461.

PMID:
22047303
46.

Freely orbiting magnetic tweezers to directly monitor changes in the twist of nucleic acids.

Lipfert J, Wiggin M, Kerssemakers JW, Pedaci F, Dekker NH.

Nat Commun. 2011 Aug 23;2:439. doi: 10.1038/ncomms1450. Erratum in: Nat Commun. 2015;6:7192.

47.

Single-molecule investigations of the stringent response machinery in living bacterial cells.

English BP, Hauryliuk V, Sanamrad A, Tankov S, Dekker NH, Elf J.

Proc Natl Acad Sci U S A. 2011 Aug 2;108(31):E365-73. doi: 10.1073/pnas.1102255108. Epub 2011 Jul 5.

48.

The passage of homopolymeric RNA through small solid-state nanopores.

van den Hout M, Skinner GM, Klijnhout S, Krudde V, Dekker NH.

Small. 2011 Aug 8;7(15):2217-24. doi: 10.1002/smll.201100265. Epub 2011 Jun 3.

PMID:
21638785
49.

Electron beam fabrication of birefringent microcylinders.

Huang Z, Pedaci F, van Oene M, Wiggin MJ, Dekker NH.

ACS Nano. 2011 Feb 22;5(2):1418-27. doi: 10.1021/nn1034108. Epub 2011 Jan 31.

PMID:
21280614
50.

Distinguishable populations report on the interactions of single DNA molecules with solid-state nanopores.

van den Hout M, Krudde V, Janssen XJ, Dekker NH.

Biophys J. 2010 Dec 1;99(11):3840-8. doi: 10.1016/j.bpj.2010.10.012.

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