Display options
Cite
Alvarez JR, Skachkov D, Massey SE, et al. DNA/RNA transverse current sequencing: intrinsic structural noise from neighboring bases. Front Genet. 2015;6:213doi: 10.3389/fgene.2015.00213.
Alvarez, J. R., Skachkov, D., Massey, S. E., Kalitsov, A., & Velev, J. P. (2015). DNA/RNA transverse current sequencing: intrinsic structural noise from neighboring bases. Frontiers in genetics, 6213. https://doi.org/10.3389/fgene.2015.00213
Alvarez, Jose R, et al. "DNA/RNA transverse current sequencing: intrinsic structural noise from neighboring bases." Frontiers in genetics vol. 6 (2015): 213. doi: https://doi.org/10.3389/fgene.2015.00213
Alvarez JR, Skachkov D, Massey SE, Kalitsov A, Velev JP. DNA/RNA transverse current sequencing: intrinsic structural noise from neighboring bases. Front Genet. 2015 Jun 19;6:213. doi: 10.3389/fgene.2015.00213. eCollection 2015. PMID: 26150827; PMCID: PMC4473640.
Copy Download .nbib Format: NLM
Share it on

Front Genet. 2015 Jun 19;6:213. doi: 10.3389/fgene.2015.00213. eCollection 2015.

DNA/RNA transverse current sequencing: intrinsic structural noise from neighboring bases.

Frontiers in genetics

Jose R Alvarez, Dmitry Skachkov, Steven E Massey, Alan Kalitsov, Julian P Velev

Affiliations

  1. Department of Physics, University of Puerto Rico San Juan, PR, USA.
  2. Department of Biology, University of Puerto Rico San Juan, PR, USA.
  3. Department of Physics, University of Puerto Rico San Juan, PR, USA ; Department of Physics, University of Nebraska Lincoln, NE, USA ; Université Grenoble Alpes/CNRS/CEA, INAC-SPINTEC Grenoble, France.

PMID: 26150827 PMCID: PMC4473640 DOI: 10.3389/fgene.2015.00213

Abstract

Nanopore DNA sequencing via transverse current has emerged as a promising candidate for third-generation sequencing technology. It produces long read lengths which could alleviate problems with assembly errors inherent in current technologies. However, the high error rates of nanopore sequencing have to be addressed. A very important source of the error is the intrinsic noise in the current arising from carrier dispersion along the chain of the molecule, i.e., from the influence of neighboring bases. In this work we perform calculations of the transverse current within an effective multi-orbital tight-binding model derived from first-principles calculations of the DNA/RNA molecules, to study the effect of this structural noise on the error rates in DNA/RNA sequencing via transverse current in nanopores. We demonstrate that a statistical technique, utilizing not only the currents through the nucleotides but also the correlations in the currents, can in principle reduce the error rate below any desired precision.

Keywords: DNA; RNA; nanopore sequencing; third-generation sequencing; transverse current

References

  1. Phys Rev Lett. 2003 Sep 5;91(10):108101 - PubMed
  2. Nature. 2001 Jul 12;412(6843):166-9 - PubMed
  3. Sci Rep. 2012;2:501 - PubMed
  4. Nano Lett. 2005 Oct;5(10):1905-9 - PubMed
  5. Curr Opin Struct Biol. 2012 Jun;22(3):251-61 - PubMed
  6. Nat Biotechnol. 2008 Oct;26(10):1146-53 - PubMed
  7. Nanotechnology. 2013 Aug 30;24(34):342501 - PubMed
  8. Proc Natl Acad Sci U S A. 1996 Nov 26;93(24):13770-3 - PubMed
  9. Nat Nanotechnol. 2009 Apr;4(4):265-70 - PubMed
  10. Nat Nanotechnol. 2007 Dec;2(12):775-9 - PubMed
  11. Biochem J. 1951 Sep;49(4):463-81 - PubMed
  12. J Chem Phys. 2004 Apr 22;120(16):7811-9 - PubMed
  13. Nat Nanotechnol. 2010 Apr;5(4):286-90 - PubMed
  14. Curr Opin Chem Biol. 2006 Dec;10(6):628-37 - PubMed
  15. Nat Nanotechnol. 2007 Apr;2(4):209-15 - PubMed
  16. Biophys J. 2009 Oct 7;97(7):1990-6 - PubMed
  17. Nat Rev Genet. 2010 Jan;11(1):31-46 - PubMed
  18. Nanotechnology. 2009 Mar 11;20(10):105302 - PubMed
  19. Phys Rev Lett. 2002 Jun 24;88(25 Pt 1):256803 - PubMed
  20. Phys Rev Lett. 2008 Jan 11;100(1):018105 - PubMed
  21. J Chem Phys. 2006 Aug 28;125(8):084302 - PubMed
  22. Nano Lett. 2011 Jan 12;11(1):279-85 - PubMed
  23. Front Genet. 2015 Jan 07;5:449 - PubMed
  24. Nano Lett. 2009 Oct;9(10):3498-502 - PubMed
  25. Eur Phys J E Soft Matter. 2010 Jul;32(3):291-305 - PubMed
  26. Nano Lett. 2005 Mar;5(3):421-4 - PubMed
  27. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463-7 - PubMed
  28. Chem Phys Lett. 2009 Jun 4;474(4):362-365 - PubMed
  29. Biophys J. 2007 Oct 1;93(7):2384-90 - PubMed
  30. Sci Rep. 2011;1:46 - PubMed
  31. Nano Lett. 2006 Apr;6(4):779-82 - PubMed
  32. Nano Lett. 2008 Aug;8(8):2530-4 - PubMed
  33. J Chem Phys. 2008 Sep 7;129(9):095104 - PubMed
  34. Methods Mol Biol. 2012;870:149-63 - PubMed
  35. Nano Lett. 2008 Sep;8(9):3029-34 - PubMed
  36. Nano Lett. 2005 Jul;5(7):1193-7 - PubMed
  37. Biophys J. 1999 Dec;77(6):3227-33 - PubMed
  38. Proc Natl Acad Sci U S A. 2009 May 12;106(19):7702-7 - PubMed
  39. Nano Lett. 2013;13(12):6144-50 - PubMed
  40. Nat Biotechnol. 2008 Oct;26(10):1135-45 - PubMed
  41. Nano Lett. 2010 Mar 10;10(3):1070-5 - PubMed
  42. Biophys J. 2012 May 16;102(10):L37-9 - PubMed
  43. Nano Lett. 2013 Jun 12;13(6):2500-5 - PubMed
  44. Nano Lett. 2010 Feb 10;10(2):738-42 - PubMed
  45. Hum Mol Genet. 2010 Oct 15;19(R2):R227-40 - PubMed
  46. Genome Res. 1996 Nov;6(11):1029-49 - PubMed
  47. Nat Mater. 2008 Jan;7(1):68-74 - PubMed
  48. Nano Lett. 2012 Nov 14;12(11):5637-43 - PubMed
  49. Phys Rev Lett. 1992 Apr 20;68(16):2512-2515 - PubMed

Publication Types