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Items: 1 to 50 of 56

1.

Extreme mechanical diversity of human telomeric DNA revealed by fluorescence-force spectroscopy.

Mitra J, Makurath MA, Ngo TTM, Troitskaia A, Chemla YR, Ha T.

Proc Natl Acad Sci U S A. 2019 Apr 23;116(17):8350-8359. doi: 10.1073/pnas.1815162116. Epub 2019 Apr 3.

PMID:
30944218
2.

Blue Light Is a Universal Signal for Escherichia coli Chemoreceptors.

Perlova T, Gruebele M, Chemla YR.

J Bacteriol. 2019 May 8;201(11). pii: e00762-18. doi: 10.1128/JB.00762-18. Print 2019 Jun 1.

PMID:
30858302
3.

Regulation of Rep helicase unwinding by an auto-inhibitory subdomain.

Makurath MA, Whitley KD, Nguyen B, Lohman TM, Chemla YR.

Nucleic Acids Res. 2019 Mar 18;47(5):2523-2532. doi: 10.1093/nar/gkz023.

4.

Optical Control of Metal Ion Probes in Cells and Zebrafish Using Highly Selective DNAzymes Conjugated to Upconversion Nanoparticles.

Yang Z, Loh KY, Chu YT, Feng R, Satyavolu NSR, Xiong M, Nakamata Huynh SM, Hwang K, Li L, Xing H, Zhang X, Chemla YR, Gruebele M, Lu Y.

J Am Chem Soc. 2018 Dec 19;140(50):17656-17665. doi: 10.1021/jacs.8b09867. Epub 2018 Dec 4.

PMID:
30427666
5.

Free-energy simulations reveal molecular mechanism for functional switch of a DNA helicase.

Ma W, Whitley KD, Chemla YR, Luthey-Schulten Z, Schulten K.

Elife. 2018 Apr 17;7. pii: e34186. doi: 10.7554/eLife.34186.

6.

Ultrashort Nucleic Acid Duplexes Exhibit Long Wormlike Chain Behavior with Force-Dependent Edge Effects.

Whitley KD, Comstock MJ, Chemla YR.

Phys Rev Lett. 2018 Feb 9;120(6):068102. doi: 10.1103/PhysRevLett.120.068102.

PMID:
29481284
7.

Altering the speed of a DNA packaging motor from bacteriophage T4.

Lin S, Alam TI, Kottadiel VI, VanGessel CJ, Tang WC, Chemla YR, Rao VB.

Nucleic Acids Res. 2017 Nov 2;45(19):11437-11448. doi: 10.1093/nar/gkx809.

8.

Mapping cell surface adhesion by rotation tracking and adhesion footprinting.

Li IT, Ha T, Chemla YR.

Sci Rep. 2017 Mar 14;7:44502. doi: 10.1038/srep44502.

9.

Preface.

Spies M, Chemla YR.

Methods Enzymol. 2017;582:xv-xvi. doi: 10.1016/S0076-6879(16)30443-8. No abstract available.

PMID:
28062047
10.

High-Resolution Optical Tweezers Combined With Single-Molecule Confocal Microscopy.

Whitley KD, Comstock MJ, Chemla YR.

Methods Enzymol. 2017;582:137-169. doi: 10.1016/bs.mie.2016.10.036. Epub 2016 Dec 14.

11.

Elasticity of the transition state for oligonucleotide hybridization.

Whitley KD, Comstock MJ, Chemla YR.

Nucleic Acids Res. 2017 Jan 25;45(2):547-555. doi: 10.1093/nar/gkw1173. Epub 2016 Nov 29.

12.

High-Resolution "Fleezers": Dual-Trap Optical Tweezers Combined with Single-Molecule Fluorescence Detection.

Whitley KD, Comstock MJ, Chemla YR.

Methods Mol Biol. 2017;1486:183-256. doi: 10.1007/978-1-4939-6421-5_8.

13.

Preface.

Spies M, Chemla YR.

Methods Enzymol. 2016;581:xvii-xviii. doi: 10.1016/S0076-6879(16)30407-4. No abstract available.

PMID:
27793295
14.

High-resolution, hybrid optical trapping methods, and their application to nucleic acid processing proteins.

Chemla YR.

Biopolymers. 2016 Oct;105(10):704-14. doi: 10.1002/bip.22880. Review.

PMID:
27225537
15.

Defining Single Molecular Forces Required for Notch Activation Using Nano Yoyo.

Chowdhury F, Li IT, Ngo TT, Leslie BJ, Kim BC, Sokoloski JE, Weiland E, Wang X, Chemla YR, Lohman TM, Ha T.

Nano Lett. 2016 Jun 8;16(6):3892-7. doi: 10.1021/acs.nanolett.6b01403. Epub 2016 May 12.

16.

Constructing modular and universal single molecule tension sensor using protein G to study mechano-sensitive receptors.

Wang X, Rahil Z, Li IT, Chowdhury F, Leckband DE, Chemla YR, Ha T.

Sci Rep. 2016 Feb 15;6:21584. doi: 10.1038/srep21584.

17.

Structural dynamics of E. coli single-stranded DNA binding protein reveal DNA wrapping and unwrapping pathways.

Suksombat S, Khafizov R, Kozlov AG, Lohman TM, Chemla YR.

Elife. 2015 Aug 25;4. doi: 10.7554/eLife.08193.

18.

The Behavioral Space of Zebrafish Locomotion and Its Neural Network Analog.

Girdhar K, Gruebele M, Chemla YR.

PLoS One. 2015 Jul 1;10(7):e0128668. doi: 10.1371/journal.pone.0128668. eCollection 2015.

19.

Protein structure. Direct observation of structure-function relationship in a nucleic acid-processing enzyme.

Comstock MJ, Whitley KD, Jia H, Sokoloski J, Lohman TM, Ha T, Chemla YR.

Science. 2015 Apr 17;348(6232):352-4. doi: 10.1126/science.aaa0130. Epub 2015 Apr 16.

20.

Protein structure. Engineering of a superhelicase through conformational control.

Arslan S, Khafizov R, Thomas CD, Chemla YR, Ha T.

Science. 2015 Apr 17;348(6232):344-7. doi: 10.1126/science.aaa0445.

21.

A nutrient-tunable bistable switch controls motility in Salmonella enterica serovar Typhimurium.

Koirala S, Mears P, Sim M, Golding I, Chemla YR, Aldridge PD, Rao CV.

MBio. 2014 Aug 26;5(5):e01611-14. doi: 10.1128/mBio.01611-14.

22.

Biophysics. Ultraslow relaxation of confined DNA.

Chemla YR, Ha T.

Science. 2014 Jul 25;345(6195):380-1. doi: 10.1126/science.1256359. No abstract available.

PMID:
25061189
23.

Escherichia coli swimming is robust against variations in flagellar number.

Mears PJ, Koirala S, Rao CV, Golding I, Chemla YR.

Elife. 2014 Feb 11;3:e01916. doi: 10.7554/eLife.01916.

24.

Sequence-dependent base pair stepping dynamics in XPD helicase unwinding.

Qi Z, Pugh RA, Spies M, Chemla YR.

Elife. 2013 May 28;2:e00334. doi: 10.7554/eLife.00334.

25.

In vivo optical trapping indicates kinesin's stall force is reduced by dynein during intracellular transport.

Blehm BH, Schroer TA, Trybus KM, Chemla YR, Selvin PR.

Proc Natl Acad Sci U S A. 2013 Feb 26;110(9):3381-6. doi: 10.1073/pnas.1219961110. Epub 2013 Feb 12. Erratum in: Proc Natl Acad Sci U S A. 2013 Jun 4;110(23):9613.

26.

DNA target sequence identification mechanism for dimer-active protein complexes.

Landry MP, Zou X, Wang L, Huang WM, Schulten K, Chemla YR.

Nucleic Acids Res. 2013 Feb 1;41(4):2416-27. doi: 10.1093/nar/gks1345. Epub 2012 Dec 28.

27.

The dynamic pause-unpackaging state, an off-translocation recovery state of a DNA packaging motor from bacteriophage T4.

Kottadiel VI, Rao VB, Chemla YR.

Proc Natl Acad Sci U S A. 2012 Dec 4;109(49):20000-5. doi: 10.1073/pnas.1209214109. Epub 2012 Nov 19.

28.

Chemotactic adaptation kinetics of individual Escherichia coli cells.

Min TL, Mears PJ, Golding I, Chemla YR.

Proc Natl Acad Sci U S A. 2012 Jun 19;109(25):9869-74. doi: 10.1073/pnas.1120218109. Epub 2012 Jun 7.

29.

Single-molecule studies of viral DNA packaging.

Chemla YR, Smith DE.

Adv Exp Med Biol. 2012;726:549-84. doi: 10.1007/978-1-4614-0980-9_24. Review.

30.

Better biomolecule thermodynamics from kinetics.

Girdhar K, Scott G, Chemla YR, Gruebele M.

J Chem Phys. 2011 Jul 7;135(1):015102. doi: 10.1063/1.3607605.

PMID:
21744920
31.

A promiscuous DNA packaging machine from bacteriophage T4.

Zhang Z, Kottadiel VI, Vafabakhsh R, Dai L, Chemla YR, Ha T, Rao VB.

PLoS Biol. 2011 Feb 15;9(2):e1000592. doi: 10.1371/journal.pbio.1000592.

32.

Ultrahigh-resolution optical trap with single-fluorophore sensitivity.

Comstock MJ, Ha T, Chemla YR.

Nat Methods. 2011 Apr;8(4):335-40. doi: 10.1038/nmeth.1574. Epub 2011 Feb 20.

33.

FliZ induces a kinetic switch in flagellar gene expression.

Saini S, Koirala S, Floess E, Mears PJ, Chemla YR, Golding I, Aldridge C, Aldridge PD, Rao CV.

J Bacteriol. 2010 Dec;192(24):6477-81. doi: 10.1128/JB.00751-10. Epub 2010 Oct 8.

34.

Mechanistic constraints from the substrate concentration dependence of enzymatic fluctuations.

Moffitt JR, Chemla YR, Bustamante C.

Proc Natl Acad Sci U S A. 2010 Sep 7;107(36):15739-44. doi: 10.1073/pnas.1006997107. Epub 2010 Aug 20.

35.

Methods in statistical kinetics.

Moffitt JR, Chemla YR, Bustamante C.

Methods Enzymol. 2010;475:221-57. doi: 10.1016/S0076-6879(10)75010-2.

PMID:
20627160
36.

A comparative study of multivariate and univariate hidden Markov modelings in time-binned single-molecule FRET data analysis.

Liu Y, Park J, Dahmen KA, Chemla YR, Ha T.

J Phys Chem B. 2010 Apr 29;114(16):5386-403. doi: 10.1021/jp9057669.

PMID:
20361785
37.

Revealing the base pair stepping dynamics of nucleic acid motor proteins with optical traps.

Chemla YR.

Phys Chem Chem Phys. 2010 Apr 7;12(13):3080-95. doi: 10.1039/b920234j. Epub 2010 Feb 19.

PMID:
20237694
38.

High-resolution dual-trap optical tweezers with differential detection: an introduction.

Bustamante C, Chemla YR, Moffitt JR.

Cold Spring Harb Protoc. 2009 Oct;2009(10):pdb.top60. doi: 10.1101/pdb.top60.

PMID:
20147062
39.

High-resolution dual-trap optical tweezers with differential detection: alignment of instrument components.

Bustamante C, Chemla YR, Moffitt JR.

Cold Spring Harb Protoc. 2009 Oct;2009(10):pdb.ip76. doi: 10.1101/pdb.ip76.

PMID:
20147041
40.

High-resolution dual-trap optical tweezers with differential detection: minimizing the influence of measurement noise.

Bustamante C, Chemla YR, Moffitt JR.

Cold Spring Harb Protoc. 2009 Oct;2009(10):pdb.ip75. doi: 10.1101/pdb.ip75.

PMID:
20147040
41.

High-resolution dual-trap optical tweezers with differential detection: data collection and instrument calibration.

Bustamante C, Chemla YR, Moffitt JR.

Cold Spring Harb Protoc. 2009 Oct;2009(10):pdb.ip74. doi: 10.1101/pdb.ip74.

PMID:
20147039
42.

High-resolution dual-trap optical tweezers with differential detection: instrument design.

Bustamante C, Chemla YR, Moffitt JR.

Cold Spring Harb Protoc. 2009 Oct;2009(10):pdb.ip73. doi: 10.1101/pdb.ip73.

PMID:
20147038
43.

High-resolution dual-trap optical tweezers with differential detection: managing environmental noise.

Bustamante C, Chemla YR, Moffitt JR.

Cold Spring Harb Protoc. 2009 Oct;2009(10):pdb.ip72. doi: 10.1101/pdb.ip72.

PMID:
20147037
44.

Characterization of photoactivated singlet oxygen damage in single-molecule optical trap experiments.

Landry MP, McCall PM, Qi Z, Chemla YR.

Biophys J. 2009 Oct 21;97(8):2128-36. doi: 10.1016/j.bpj.2009.07.048.

45.

High-resolution, long-term characterization of bacterial motility using optical tweezers.

Min TL, Mears PJ, Chubiz LM, Rao CV, Golding I, Chemla YR.

Nat Methods. 2009 Nov;6(11):831-5. doi: 10.1038/nmeth.1380. Epub 2009 Oct 4.

46.

Substrate interactions and promiscuity in a viral DNA packaging motor.

Aathavan K, Politzer AT, Kaplan A, Moffitt JR, Chemla YR, Grimes S, Jardine PJ, Anderson DL, Bustamante C.

Nature. 2009 Oct 1;461(7264):669-73. doi: 10.1038/nature08443.

47.

Proofreading dynamics of a processive DNA polymerase.

Ibarra B, Chemla YR, Plyasunov S, Smith SB, Lázaro JM, Salas M, Bustamante C.

EMBO J. 2009 Sep 16;28(18):2794-802. doi: 10.1038/emboj.2009.219. Epub 2009 Aug 6.

48.

Intersubunit coordination in a homomeric ring ATPase.

Moffitt JR, Chemla YR, Aathavan K, Grimes S, Jardine PJ, Anderson DL, Bustamante C.

Nature. 2009 Jan 22;457(7228):446-50. doi: 10.1038/nature07637. Epub 2009 Jan 7.

49.

Exact solutions for kinetic models of macromolecular dynamics.

Chemla YR, Moffitt JR, Bustamante C.

J Phys Chem B. 2008 May 15;112(19):6025-44. doi: 10.1021/jp076153r. Epub 2008 Mar 29.

PMID:
18373360
50.

Recent advances in optical tweezers.

Moffitt JR, Chemla YR, Smith SB, Bustamante C.

Annu Rev Biochem. 2008;77:205-28. doi: 10.1146/annurev.biochem.77.043007.090225. Review.

PMID:
18307407

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