Magnetic Tweezers Measurement of Single Molecule Torque

Overview

Journal Nano Lett

Publisher American Chemical Society

Specialty Biotechnology

Date 2009 Mar 24

PMID 19301859

Citations 46

Authors

Alfredo Celedon

Ilana M Nodelman

Bridget Wildt

Rohit Dewan

Peter Searson

Denis Wirtz

Gregory D Bowman

Sean X Sun

Affiliations

Soon will be listed here.

Abstract

Torsional stress in linear biopolymers such as DNA and chromatin has important consequences for nanoscale biological processes. We have developed a new method to directly measure torque on single molecules. Using a cylindrical magnet, we manipulate a novel probe consisting of a nanorod with a 0.1 microm ferromagnetic segment coupled to a magnetic bead. We achieve controlled introduction of turns into the molecule and precise measurement of torque and molecule extension as a function of the number of turns at low pulling force. We show torque measurement of single DNA molecules and demonstrate for the first time measurements of single chromatin fibers.

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References

Charvin G, Strick T, Bensimon D, Croquette V . Tracking topoisomerase activity at the single-molecule level. Annu Rev Biophys Biomol Struct. 2005; 34:201-19. DOI: 10.1146/annurev.biophys.34.040204.144433. View

Lia G, Semsey S, Lewis D, Adhya S, Bensimon D, Dunlap D . The antiparallel loops in gal DNA. Nucleic Acids Res. 2008; 36(12):4204-10. PMC: 2475638. DOI: 10.1093/nar/gkn389. View

Whitney T, Searson P, Jiang J, Chien C . Fabrication and magnetic properties of arrays of metallic nanowires. Science. 1993; 261(5126):1316-9. DOI: 10.1126/science.261.5126.1316. View

Strick T, Allemand J, Bensimon D, Bensimon A, Croquette V . The elasticity of a single supercoiled DNA molecule. Science. 1996; 271(5257):1835-7. DOI: 10.1126/science.271.5257.1835. View

Revyakin A, Ebright R, Strick T . Promoter unwinding and promoter clearance by RNA polymerase: detection by single-molecule DNA nanomanipulation. Proc Natl Acad Sci U S A. 2004; 101(14):4776-80. PMC: 387324. DOI: 10.1073/pnas.0307241101. View

Gosse C, Croquette V . Magnetic tweezers: micromanipulation and force measurement at the molecular level. Biophys J. 2002; 82(6):3314-29. PMC: 1302119. DOI: 10.1016/S0006-3495(02)75672-5. View

Bryant Z, Stone M, Gore J, Smith S, Cozzarelli N, Bustamante C . Structural transitions and elasticity from torque measurements on DNA. Nature. 2003; 424(6946):338-41. DOI: 10.1038/nature01810. View

Peter B, Arsuaga J, Breier A, Khodursky A, Brown P, Cozzarelli N . Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli. Genome Biol. 2004; 5(11):R87. PMC: 545778. DOI: 10.1186/gb-2004-5-11-r87. View

Leuba S, Karymov M, Tomschik M, Ramjit R, Smith P, Zlatanova J . Assembly of single chromatin fibers depends on the tension in the DNA molecule: magnetic tweezers study. Proc Natl Acad Sci U S A. 2003; 100(2):495-500. PMC: 141023. DOI: 10.1073/pnas.0136890100. View

10.

Bancaud A, Conde E Silva N, Barbi M, Wagner G, Allemand J, Mozziconacci J . Structural plasticity of single chromatin fibers revealed by torsional manipulation. Nat Struct Mol Biol. 2006; 13(5):444-50. DOI: 10.1038/nsmb1087. View

11.

Bancaud A, Wagner G, Conde E Silva N, Lavelle C, Wong H, Mozziconacci J . Nucleosome chiral transition under positive torsional stress in single chromatin fibers. Mol Cell. 2007; 27(1):135-47. DOI: 10.1016/j.molcel.2007.05.037. View

12.

Oroszi L, Galajda P, Kirei H, Bottka S, Ormos P . Direct measurement of torque in an optical trap and its application to double-strand DNA. Phys Rev Lett. 2006; 97(5):058301. DOI: 10.1103/PhysRevLett.97.058301. View

13.

Koster D, Croquette V, Dekker C, Shuman S, Dekker N . Friction and torque govern the relaxation of DNA supercoils by eukaryotic topoisomerase IB. Nature. 2005; 434(7033):671-4. DOI: 10.1038/nature03395. View

14.

Kouzine F, Sanford S, Elisha-Feil Z, Levens D . The functional response of upstream DNA to dynamic supercoiling in vivo. Nat Struct Mol Biol. 2008; 15(2):146-54. DOI: 10.1038/nsmb.1372. View

15.

Pomerantz R, Ramjit R, Gueroui Z, Place C, Anikin M, Leuba S . A tightly regulated molecular motor based upon T7 RNA polymerase. Nano Lett. 2005; 5(9):1698-703. DOI: 10.1021/nl0509125. View

16.

Deufel C, Forth S, Simmons C, Dejgosha S, Wang M . Nanofabricated quartz cylinders for angular trapping: DNA supercoiling torque detection. Nat Methods. 2007; 4(3):223-5. DOI: 10.1038/nmeth1013. View

17.

Gore J, Bryant Z, Stone M, Nollmann M, Cozzarelli N, Bustamante C . Mechanochemical analysis of DNA gyrase using rotor bead tracking. Nature. 2006; 439(7072):100-104. PMC: 1440892. DOI: 10.1038/nature04319. View

18.

Yan J, Maresca T, Skoko D, Adams C, Xiao B, Christensen M . Micromanipulation studies of chromatin fibers in Xenopus egg extracts reveal ATP-dependent chromatin assembly dynamics. Mol Biol Cell. 2006; 18(2):464-74. PMC: 1783770. DOI: 10.1091/mbc.e06-09-0800. View

19.

Koster D, Palle K, Bot E, Bjornsti M, Dekker N . Antitumour drugs impede DNA uncoiling by topoisomerase I. Nature. 2007; 448(7150):213-7. DOI: 10.1038/nature05938. View

20.

Revyakin A, Liu C, Ebright R, Strick T . Abortive initiation and productive initiation by RNA polymerase involve DNA scrunching. Science. 2006; 314(5802):1139-43. PMC: 2754787. DOI: 10.1126/science.1131398. View