European Biophysics Journal

, 38:263 | Cite as

Probing DNA base pairing energy profiles using a nanopore

  • Virgile Viasnoff
  • Nicolas Chiaruttini
  • Ulrich Bockelmann
Biophysics Letter

Abstract

We experimentally show that the voltage driven unzipping of long DNA duplexes by an α-hemolysin pore is sensitive to the shape of the base pairing energy landscape. Two sequences of equal global stability were investigated. The sequence with an homogeneous base pairing profile translocates faster than the one with alternative weak and strong regions. We could qualitatively account for theses observations by theoretically describing the voltage driven translocation as a biased random walk of the unzipping fork in the sequence dependent energy landscape.

Keywords

Nanopore α-Hemolysin Unzipping DNA Sequence energy landscape 

Notes

Acknowledgments

The authors thank Laurent Lacroix (MNHN) for his precious help with the melting experiments. Financial support was provided by ANR PNANO grant ANR-06-NANO-015-01.

Supplementary material

249_2008_372_MOESM1_ESM.pdf (119 kb)
Supplementary Materials PDF (118 KB)

References

  1. Akeson M, Branton D, Kasianowicz JJ, Brandin E, Deamer DW (1999) Microsecond time-scale discrimination among polycytidylic acid, polyadenylic acid, and polyuridylic acid as homopolymers or as segments within single RNA molecules. Biophys J 77(6):3227–3233PubMedCrossRefGoogle Scholar
  2. Bockelmann U, Viasnoff V (2008) Theoretical study of sequence-dependent nanopore unzipping of DNA. Biophys J 94(7):2716–2724PubMedCrossRefGoogle Scholar
  3. Bockelmann U, Thomen P, Essevaz-Roulet B, Viasnoff V, Heslot F (2002) Unzipping DNAn with optical tweezers: high sequence sensitivity and force flips. Biophys J 82(3):1537–1553PubMedCrossRefGoogle Scholar
  4. Bundschuh R, Gerland U (2005) Coupled dynamics of RNA folding and nanopore translocation. Phys Rev Lett 95(20):208104PubMedCrossRefGoogle Scholar
  5. Collin D, Ritort F, Jarzynski C, Smith SB, Tinoco I, Bustamante C (2005) Verification of the crooks fluctuation theorem and recovery of RNA folding free energies. Nature 437(7056):231–234PubMedCrossRefGoogle Scholar
  6. deGennes PG (2001) Maximum pull out force on DNA hybrids. C R Acad Sci Paris IV:1505–1508Google Scholar
  7. Dudko OK, Mathe J, Szabo A, Meller A, Hummer G (2007) Extracting kinetics from single-molecule force spectroscopy: nanopore unzipping of DNA hairpins. Biophys J 92(12):4188–4195PubMedCrossRefGoogle Scholar
  8. Garcia-Manyes S, Brujic J, Badilla CL, Fernandez JM (2007) Force-clamp spectroscopy of single-protein monomers reveals the individual unfolding and folding pathways of i27 and ubiquitin. Biophys J 93(7):2436–2446PubMedCrossRefGoogle Scholar
  9. Gauthier MG, Slater GW (2008) A monte carlo algorithm to study polymer translocation through nanopores. i. theory and numerical approach. J Chem Phys 128(6):065–103CrossRefGoogle Scholar
  10. Greenleaf WJ, Woodside MT, Block SM (2007) High-resolution, single-molecule measurements of biomolecular motion. Annu Rev Biophys Biomol Struct 36:171–190PubMedCrossRefGoogle Scholar
  11. Greenleaf WJ, Frieda KL, Foster DA, Woodside MT, Block SM (2008) Direct observation of hierarchical folding in single riboswitch aptamers. Science 319(5863):630–633PubMedCrossRefGoogle Scholar
  12. Harlepp S, Marchal T, Robert J, Leger JF, Xayaphoumine A, Isambert H, Chatenay D (2003) Probing complex RNA structures by mechanical force. Eur Phys J E 12(4):605–615PubMedCrossRefGoogle Scholar
  13. Kasianowicz JJ, Brandin E, Branton D, Deamer DW (1996) Characterization of individual polynucleotide molecules using a membrane channel. Proc Natl Acad Sci USA 93(24):13770–13773PubMedCrossRefGoogle Scholar
  14. Lakatos G, Chou T, Bergersen B, Patey GN (2005) First passage times of driven DNA hairpin unzipping. Phys Biol 2(3):166–174PubMedCrossRefGoogle Scholar
  15. Larson MH, Greenleaf WJ, Landick R, Block SM (2008) Applied force reveals mechanistic and energetic details of transcription termination. Cell 132(6):971–982PubMedCrossRefGoogle Scholar
  16. Li PTX, Bustamante C, Tinoco I (2007) Real-time control of the energy landscape by force directs the folding of RNA molecules. Proc Natl Acad Sci USA 104(17):7039–7044PubMedCrossRefGoogle Scholar
  17. Luo KF, Ala-Nissila T, Ying SC, Bhattacharya A (2007) Heteropolymer translocation through nanopores. J Chem Phys 126(14):145101PubMedCrossRefGoogle Scholar
  18. Mathe J, Visram H, Viasnoff V, Rabin Y, Meller A (2004) Nanopore unzipping of individual DNA hairpin molecules. Biophys J 87(5):3205–3212PubMedCrossRefGoogle Scholar
  19. Meller A, Branton D (2002) Single molecule measurements of DNA transport through a nanopore. Electrophoresis 23(16):2583–2591PubMedCrossRefGoogle Scholar
  20. Meller A, Nivon L, Brandin E, Golovchenko J, Branton D (2000) Rapid nanopore discrimination between single polynucleotide molecules. Proc Natl Acad Sci USA 97(3):1079–1084PubMedCrossRefGoogle Scholar
  21. Meller A, Nivon L, Branton D (2001) Voltage-driven DNA translocations through a nanopore. Phys Rev Lett 86(15):3435–3438PubMedCrossRefGoogle Scholar
  22. Mergny JL, Lacroix L (2003) Analysis of thermal melting curves. Oligonucleotides 13(6):515–537PubMedCrossRefGoogle Scholar
  23. SantaLucia J (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci USA 95(4):1460–1465PubMedCrossRefGoogle Scholar
  24. Sauer-Budge AF, Nyamwanda JA, Lubensky DK, Branton D (2003) Unzipping kinetics of double-stranded DNA in a nanopore. Phys Rev Lett 90(23):238101PubMedCrossRefGoogle Scholar
  25. Tropini C, Marziali A (2007) Multi-nanopore force spectroscopy for DNA analysis. Biophys J 92(5):1632–1637PubMedCrossRefGoogle Scholar
  26. Vercoutere W, Winters-Hilt S, Olsen H, Deamer D, Haussler D, Akeson M (2001) Rapid discrimination among individual DNA hairpin molecules at single-nucleotide resolution using an ion channel. Nat Biotechnol 19(3):248–252PubMedCrossRefGoogle Scholar
  27. Vercoutere WA, Winters-Hilt S, DeGuzman VS, Deamer D, Ridino SE, Rodgers JT, Olsen HE, Marziali A, Akeson M (2003) Discrimination among individual watson–crick base pairs at the termini of single DNA hairpin molecules. Nucleic Acids Res 31(4):1311–1318PubMedCrossRefGoogle Scholar
  28. Zhao Q, Comer J, Dimitrov V, Yemenicioglu S, Aksimentiev A, Timp G (2008) Stretching and unzipping nucleic acid hairpins using a synthetic nanopore. Nucleic Acids Res 36(5):1532–1541PubMedCrossRefGoogle Scholar
  29. Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31(13):3406–3415PubMedCrossRefGoogle Scholar

Copyright information

© European Biophysical Societies' Association 2008

Authors and Affiliations

  • Virgile Viasnoff
    • 1
  • Nicolas Chiaruttini
    • 1
  • Ulrich Bockelmann
    • 1
  1. 1.Laboratoire de NanobiophysiqueCNRS, ESPCI ParisTechParisFrance

Personalised recommendations