Skip to main content
SpringerLink
Log in

Colored noise in the fluctuations of an extended DNA molecule detected by optical trapping

  • Original Paper
  • Published:
European Biophysics Journal Aims and scope Submit manuscript

Abstract

We studied fluctuations of an optically trapped bead connected to a single DNA molecule anchored between the bead and a cover glass or between two optically trapped beads. Power spectral densities of the bead position for different extensions of the molecule were compared with the power spectral density of the position fluctuations of the same bead without the molecule attached. Experiments showed that the fluctuations of the DNA molecule extended up to 80% by a force of 3 pN include the colored noise contribution with spectral dependence 1/f α with α ∼ 0.75.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8

Similar content being viewed by others

References

  • Abbondanzieri EA, Greenleaf WJ, Shaevitz JW, Landick R, Block SM (2005) Direct observation of base-pair stepping by RNA polymerase. Nature 438:460–465

    Article  PubMed  CAS  Google Scholar 

  • Bag BC, Hubc CK, Li MS (2010) Colored noise, folding rates and departure from Kramers behavior. Phys Chem Chem Phys 12:11753–11762

    Google Scholar 

  • Bustamante C, Bryant Z, Smith SB (2003) Ten years of tension: single-molecule DNA mechanics. Nature 421:423–427

    Article  PubMed  Google Scholar 

  • Bustamante C, Chemla YR, Forde NR, Izhaky D (2004) Mechanical processes in biochemistry. Annu Rev Biochem 73:705–748

    Article  PubMed  CAS  Google Scholar 

  • Carter AR, King GM, Perkins TT (2007) Back-scattering detection provides atomic-scale localization precision, stability, and registration in 3D. Opt Exp 15:13434–13445

    Article  PubMed  Google Scholar 

  • Carter AR, Seol Y, Perkins TT (2009) Precision surface-coupled optical-trapping assay with one-basepair resolution. Biophys J 96:2926–2934

    Article  PubMed  CAS  Google Scholar 

  • Cluzel P, Lebrun A, Heller C, Lavery R, Viovy JL, Chatenay D, Caron F (1996) DNA: an extensible molecule. Science 271:792–794

    Article  PubMed  CAS  Google Scholar 

  • Dutra RS, Viana NB, MaiaNeto PA, Nussenzveig HM (2007) Polarization effects in optical tweezers. J Opt A: Pure Appl Opt 9:S221–S227

    Article  Google Scholar 

  • Gallet F, Arcizet D, Bohec P, Richert A (2009) Power spectrum of out-of-equilibrium forces in living cells: amplitude and frequency dependence. Soft Matter 5:2947–2953

    Article  CAS  Google Scholar 

  • Gennes PGD (1974) Coil-stretch transition of dilute flexible polymers under ultrahigh velocity gradients. J Chys Chem 60:5030–5042

    Google Scholar 

  • Greenleaf WJ, Woodside MT, Block SM (2007) High-resolution, single-molecule measurements of biomolecular motion. Annu Rev Biophys Biomol Struc 36:171–190

    Article  CAS  Google Scholar 

  • Gueroui Z, Freyssingeas E, Place C, Berge B (2003) Transverse fluctuation analysis of single extended DNA molecules. Eur Phys J E 11:105–108

    Article  PubMed  CAS  Google Scholar 

  • Hanggi P (1994) Escape over fluctuating barriers driven by colored noise. Chem Phys 180:157–166

    Article  Google Scholar 

  • Hanggi P, Jung P (1990) Colored noise in dynamical systems. Adv Chem Phys 89:239–326

    Article  Google Scholar 

  • Hanggi P, Talkner P, Borcovec M (1990) Reaction-rate theory: fifty years after Kramers. Rev Mod Phys 62:251–341

    Article  Google Scholar 

  • Hooge FN (2002) 1/f noise. Phys B+C 83:14–23

    Article  Google Scholar 

  • Keshner MS (1982) 1/f noise. IEEE Proc 79:212–218

    Article  Google Scholar 

  • Lang MJ, Asbury CL, Shaevitz JW, Block SV (2002) An automated two-dimensional optical force clamp for single molecule studies. Biophys J 83:491–501

    Article  PubMed  CAS  Google Scholar 

  • Leibler S (1994) Moving forward noisily. Nature 370:412–414

    Article  PubMed  CAS  Google Scholar 

  • Li W, Holste D (2005) Universal 1/f noise, crossovers of scaling exponents, and chromosome-specific patterns of guanine–cytosine content in DNA sequences of the human genome. Phys Rev E 71:041910-1–041910-9

    Google Scholar 

  • Lien CH, Wei MT, Tseng TY, Lee CD, Wang C, Wang TF, Ou-Yang HD, Chiou A (2009) Probing of dynamic differential stiffness of dsDNA interacting with RecA in the enthalpic regime. Opt Exp 17:20376–20385

    Article  PubMed  CAS  Google Scholar 

  • Marko JF, Siggia ED (1995) Stretching DNA. Macromolecules 28:8759–8770

    Article  CAS  Google Scholar 

  • Meiners JC, Quake SR (2000) Femtonewton force spectroscopy of single extended DNA molecules. Phys Rev Lett 84:5014–5017

    Article  PubMed  CAS  Google Scholar 

  • Merchant CA, Healy K, Wanunu M, Ray V, Peterman N, Bartel J, Fischbein MD, Venta K, Luo Z, Johnson ATC, Drndić M (2010) DNA Translocation through graphene nanopores. Nano Lett 10(8):2915–2921

    Article  PubMed  CAS  Google Scholar 

  • Moffitt JR, Chemla YR, Izhaky D, Bustamante C (2006) Differential detection of dual traps improves the spatial resolution of optical tweezers. PNAS 103:9006–9011

    Article  PubMed  CAS  Google Scholar 

  • Moffitt JR, Chemla YR, Smith SB, Bustamante C (2008) Recent advances in optical tweezers. Annu Rev Biochem 77:205–228

    Article  PubMed  CAS  Google Scholar 

  • Nagapriya KS, Raychaudhuri AK, Chatterji D (2006) Direct observation of large temperature fluctuations during DNA thermal denaturation. Phys Rev Lett 96:038102-1–038102-4

    Article  Google Scholar 

  • Perkins TT (2009) Optical traps for single molecule biophysics: a primer. Laser Photon Rev 3:203–220

    Article  CAS  Google Scholar 

  • Pincus P (1976) Excluded volume effects and stretched polymer chains. Macromolecules 9:386–388

    Article  CAS  Google Scholar 

  • Planxco KW, Baker D (1998) Limited internal friction in the rate-limiting step of a two-state protein folding reaction. PNAS 95:13591–13596

    Article  Google Scholar 

  • Quake SR, Babcock H, Chu S (1997) The dynamics of partially extended single molecules of DNA. Nature 388:151–154

    Article  PubMed  CAS  Google Scholar 

  • Rao S, Raj S, Balint S, Fons CB, Campoy S, Llagostera M, Petrov D (2010) Single DNA molecule detection in an optical trap using surface-enhanced Raman scattering. Appl Phys Lett 96:213701-1–213701-3

    Google Scholar 

  • Ritort F (2006) Single-molecule experiments in biological physics: methods and applications. J Phys: Condens Matter 18:R531–R583

    Article  CAS  Google Scholar 

  • Shaevitz JW, Abbondanzieri EA, Landick R, Block SM (2003) Backtracking by single RNA polymerase molecules observed at near-base-pair resolution. Nature 426:684–687

    Article  PubMed  CAS  Google Scholar 

  • Smith SB, Finzi L, Bustamante C (1992) Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads. Science 258:1122–1126

    Article  PubMed  CAS  Google Scholar 

  • Smith SB, Cui Y, Bustamante C (1996) Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules. Science 271:795–799

    Article  PubMed  CAS  Google Scholar 

  • Tolić-Norrelykke SF, Schäffer E, Howard J, Pavone FS, Jülicher F, Flyvbjerg H (2006) Calibration of optical tweezers with positional detection in the back focal plane. Rev Sc Instrum 77(10):103101-1–103101-11

    Google Scholar 

  • Voss RF (1992) Evolution of long-range fractal correlations and 1/f noise in DNA base sequences. Phys Rev Lett 68:3805–3808

    Article  PubMed  CAS  Google Scholar 

  • Wang MD, Yin H, Landick R, Gelles J, Block SM (1997) Stretching DNA with optical tweezers. Biophys J 72:1335–1346

    Article  CAS  Google Scholar 

  • Yoon YZ, Kotar J, Brown AT, Cicuta P (2011) Red blood cell dynamics: from spontaneous fluctuations to non-linear response. Soft Matter 7:2042–2051

    Article  CAS  Google Scholar 

Download references

Acknowledgments

We acknowledge support from MIIN FIS2008-00114 (Spain), Fundació privada Cellex Barcelona and discussions with S. Rao, F. Beunis, S. Campoy, J.M.R. Parrondo and M. Rubi.

Author information

Authors and Affiliations

  1. ICFO—The Institute of Photonic Sciences, Av. Carl Friedrich Gauss, 3, 08860, Castelldefels, Barcelona, Spain

    Ignacio A. Martínez, Saurabh Raj & Dmitri Petrov

  2. ICREA—Institucio Catalana de Recerca i Estudis Avancats, 08010, Barcelona, Spain

    Dmitri Petrov

Authors
  1. Ignacio A. Martínez
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Saurabh Raj
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Dmitri Petrov
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Dmitri Petrov.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Martínez, I.A., Raj, S. & Petrov, D. Colored noise in the fluctuations of an extended DNA molecule detected by optical trapping. Eur Biophys J 41, 99–106 (2012). https://doi.org/10.1007/s00249-011-0763-7

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00249-011-0763-7

Keywords

Search

Navigation