Electrically facilitated translocation of protein through solid nanopore

详细信息    查看全文

• 作者：Lingzhi Wu (1) (2)
  Hang Liu (1)
  Wenyuan Zhao (1)
  Lei Wang (1)
  Chuanrong Hou (1)
  Quanjun Liu (1)
  Zuhong Lu (1)
  
• 关键词：Protein translocation ; Solid state nanopore ; Current blockage ; Translocation time
• 刊名：Nanoscale Research Letters
• 出版年：2014
• 出版时间：December 2014
• 年：2014
• 卷：9
• 期：1
• 全文大小：722 KB
• 参考文献：1. Maitra RD, Kim J, Dunbar WB: lus-plus">Recent advances in nanopore sequencing. / Electrophoresis 2012, lus-plus">33:3418-428. CrossRef
  2. Miles BN, Ivanov AP, Wilson KA, Dogan F, Japrung D, Edel JB: lus-plus">Single molecule sensing with solid-state nanopores: novel materials, methods, and applications. / Chem Soc Rev 2013, lus-plus">42:15-8. CrossRef
  3. Cressiot B, Oukhaled A, Patriarche G, Pastoriza-Gallego M, Betton JM, Muthukumar M, Bacri L, Pelta J: lus-plus">Protein transport through a narrow solid-state nanopore at high voltage: experiments and theory. / ACS Nano 2012, lus-plus">6:6236-243. CrossRef
  4. Oukhaled A, Pastoriza-Gallego M, Bacri L, Mathe J, Auvray L, Pelta J: lus-plus">Protein unfolding through nanopores. / Protein Pept Lett 2014, lus-plus">21:266-74. CrossRef
  5. Kowalczyk SW, Kapinos L, Blosser TR, Magalhaes T, van Nies P, Lim RY, Dekker C: lus-plus">Single-molecule transport across an individual biomimetic nuclear pore complex. / Nat Nanotechnol 2011, lus-plus">6:433-38. CrossRef
  6. Oukhaled A, Bacri L, Pastoriza-Gallego M, Betton JM, Pelta J: lus-plus">Sensing proteins through nanopores: fundamental to applications. / ACS Chem Biol 2012, lus-plus">7:1935-949. CrossRef
  7. Kowalczyk SW, Blosser TR, Dekker C: lus-plus">Biomimetic nanopores: learning from and about nature. / Trends Biotechnol 2011, lus-plus">29:607-14. CrossRef
  8. Japrung D, Dogan J, Freedman KJ, Nadzeyka A, Bauerdick S, Albrecht T, Kim MJ, Jemth P, Edel JB: lus-plus">Single-molecule studies of intrinsically disordered proteins using solid-state nanopores. / Anal Chem 2013, lus-plus">85:2449-456. CrossRef
  9. Plesa C, Kowalczyk SW, Zinsmeester R, Grosberg AY, Rabin Y, Dekker C: lus-plus">Fast translocation of proteins through solid state nanopores. / Nano Lett 2013, lus-plus">13:658-63. CrossRef
  10. Freedman KJ, Haq SR, Edel JB, Jemth P, Kim MJ: lus-plus">Single molecule unfolding and stretching of protein domains inside a solid-state nanopore by electric field. / Sci Rep 2013, lus-plus">3:1638.
  11. Ding S, Gao C, Gu LQ: lus-plus">Capturing single molecules of immunoglobulin and ricin with an aptamer-encoded glass nanopore. / Anal Chem 2009, lus-plus">81:6649-655. CrossRef
  12. Li W, Bell NA, Hernandez-Ainsa S, Thacker VV, Thackray AM, Bujdoso R, Keyser UF: lus-plus">Single protein molecule detection by glass nanopores. / ACS Nano 2013, lus-plus">7:4129-134. CrossRef
  13. Merstorf C, Cressiot B, Pastoriza-Gallego M, Oukhaled A, Betton JM, Auvray L, Pelta J: lus-plus">Wild type, mutant protein unfolding and phase transition detected by single-nanopore recording. / ACS Chem Biol 2012, lus-plus">7:652-58. CrossRef
  14. Rotem D, Jayasinghe L, Salichou M, Bayley H: lus-plus">Protein detection by nanopores equipped with aptamers. / J Am Chem Soc 2012, lus-plus">134:2781-787. CrossRef
  15. Freedman KJ, Jurgens M, Prabhu A, Ahn CW, Jemth P, Edel JB, Kim MJ: lus-plus">Chemical, thermal, and electric field induced unfolding of single protein molecules studied using nanopores. / Anal Chem 2011, lus-plus">83:5137-144. CrossRef
  16. Oukhaled A, Cressiot B, Bacri L, Pastoriza-Gallego M, Betton JM, Bourhis E, Jede R, Gierak J, Auvray L, Pelta J: lus-plus">Dynamics of completely unfolded and native proteins through solid-state nanopores as a function of electric driving force. / ACS Nano 2011, lus-plus">5:3628-638. CrossRef
  17. Payet L, Martinho M, Pastoriza-Gallego M, Betton JM, Auvray L, Pelta J, Mathé J: lus-plus">Thermal unfolding of proteins probed at the single molecule level using nanopores. / Anal Chem 2012, lus-plus">84:4071-076. CrossRef
  18. Rodriguez-Larrea D, Bayley H: lus-plus">Multistep protein unfolding during nanopore translocation. / Nat Nanotechnol 2013, lus-plus">8:288-95. CrossRef
  19. Chu J, Gonzalez-Lopez M, Cockroft SL, Amorin M, Ghadiri MR: lus-plus">Real-time monitoring of DNA polymerase function and stepwise single-nucleotide DNA strand translocation through a protein nanopore. / Angew Chem Int Ed Engl 2010, lus-plus">49:10106-0109. CrossRef
  20. Freedman H, Huzil JT, Luchko T, Luduena RF, Tuszynski JA: lus-plus">Identification and characterization of an intermediate taxol binding site within microtubule nanopores and a mechanism for tubulin isotype binding selectivity. / J Chem Inf Model 2009, lus-plus">49:424-36. CrossRef
  21. Freedman KJ, Bastian AR, Chaiken I, Kim MJ: lus-plus">Solid-state nanopore detection of protein complexes: applications in healthcare and protein kinetics. / Small 2013, lus-plus">9:750-59. CrossRef
  22. Kowalczyk SW, Hall AR, Dekker C: lus-plus">Detection of local protein structures along DNA using solid-state nanopores. / Nano Lett 2010, lus-plus">10:324-28. CrossRef
  23. Nivala J, Marks DB, Akeson M: lus-plus">Unfoldase-mediated protein translocation through an alpha-hemolysin nanopore. / Nat Biotechnol 2013, lus-plus">31:247-50. CrossRef
  24. Oukhaled AG, Biance AL, Pelta J, Auvray L, Bacri L: lus-plus">Transport of long neutral polymers in the semidilute regime through a protein nanopore. / Phys Rev Lett 2012, lus-plus">108:088104. CrossRef
  25. Soskine M, Biesemans A, Moeyaert B, Cheley S, Bayley H, Maglia G: lus-plus">An engineered ClyA nanopore detects folded target proteins by selective external association and pore entry. / Nano Lett 2012, lus-plus">12:4895-900. CrossRef
  26. Zhao Q, de Zoysa RS, Wang D, Jayawardhana DA, Guan X: lus-plus">Real-time monitoring of peptide cleavage using a nanopore probe. / J Am Chem Soc 2009, lus-plus">131:6324-325. CrossRef
  27. Firnkes M, Pedone D, Knezevic J, Doblinger M, Rant U: lus-plus">Electrically facilitated translocations of proteins through silicon nitride nanopores: conjoint and competitive action of diffusion, electrophoresis, and electroosmosis. / Nano Lett 2010, lus-plus">10:2162-167. CrossRef
  28. Han A, Creus M, Schurmann G, Linder V, Ward TR, de Rooij NF, Staufer U: lus-plus">Label-free detection of single protein molecules and protein-protein interactions using synthetic nanopores. / Anal Chem 2008, lus-plus">80:4651-658. CrossRef
  29. Fologea D, Ledden B, McNabb DS, Li J: lus-plus">Electrical characterization of protein molecules by a solid-state nanopore. / Appl Phys Lett 2007, lus-plus">91:539011. CrossRef
  30. Hyun C, Kaur H, Rollings R, Xiao M, Li J: lus-plus">Threading immobilized DNA molecules through a solid-state nanopore at >100?μs per base rate. / ACS Nano 2013, lus-plus">7:5892-900. CrossRef
  31. Niedzwiecki DJ, Grazul J, Movileanu L: lus-plus">Single-molecule observation of protein adsorption onto an inorganic surface. / J Am Chem Soc 2010, lus-plus">132:10816-0822. CrossRef
  32. Sexton LT, Mukaibo H, Katira P, Hess H, Sherrill SA, Horne LP, Martin CR: lus-plus">An adsorption-based model for pulse duration in resistive-pulse protein sensing. / J Am Chem Soc 2010, lus-plus">132:6755-763. CrossRef
  33. Tsutsui M, He Y, Furuhashi M, Rahong S, Taniguchi M, Kawai T: lus-plus">Transverse electric field dragging of DNA in a nanochannel. / Sci Rep 2012, lus-plus">2:394.
  34. Yeh LH, Fang KY, Hsu JP, Tseng S: lus-plus">Influence of boundary on the effect of double-layer polarization and the electrophoretic behavior of soft biocolloids. / Colloids Surf B: Biointerfaces 2011, lus-plus">88:559-67. CrossRef
  35. Wanunu M, Morrison W, Rabin Y, Grosberg AY, Meller A: lus-plus">Electrostatic focusing of unlabelled DNA into nanoscale pores using a salt gradient. / Nat Nanotechnol 2010, lus-plus">5:160-65. CrossRef
  36. Jiang DE, Jin Z, Wu J: lus-plus">Oscillation of capacitance inside nanopores. / Nano Lett 2011, lus-plus">11:5373-377. CrossRef
  37. Luan B, Stolovitzky G: lus-plus">An electro-hydrodynamics-based model for the ionic conductivity of solid-state nanopores during DNA translocation. / Nanotechnology 2013, lus-plus">24:195702. CrossRef
  38. Kocer A, Tauk L, Dejardin P: lus-plus">Nanopore sensors: from hybrid to abiotic systems. / Biosens Bioelectron 2012, lus-plus">38:1-0. CrossRef
  39. Liu L, Zhu LZ, Ni ZH, Chen YF: lus-plus">Detecting a single molecule using a micropore-nanopore hybrid chip. / Nanoscale Res Lett 2013, lus-plus">8:498. CrossRef
  40. Liu Q, Wu H, Wu L, Xie X, Kong J, Ye X, Liu L: lus-plus">Voltage-driven translocation of DNA through a high throughput conical solid-state nanopore. / PLoS One 2012, lus-plus">7:e46014. CrossRef
  41. Hall AR, van Dorp S, Lemay SG, Dekker C: lus-plus">Electrophoretic force on a protein-coated DNA molecule in a solid-state nanopore. / Nano Lett 2009, lus-plus">9:4441-445. CrossRef
  42. Yusko EC, Johnson JM, Majd S, Prangkio P, Rollings RC, Li J, Yang J, Mayer M: lus-plus">Controlling protein translocation through nanopores with bio-inspired fluid walls. / Nat Nanotechnol 2011, lus-plus">6:253-60. CrossRef
  43. Yeh LH, Zhang M, Qian S: lus-plus">Ion transport in a pH-regulated nanopore. / Anal Chem 2013, lus-plus">85:7527-534. CrossRef
  44. Gershow M, Golovchenko JA: lus-plus">Recapturing and trapping single molecules with a solid-state nanopore. / Nat Nanotechnol 2007, lus-plus">2:775-79. CrossRef
  45. Smeets RMM, Keyser UF, Dekker NH, Dekker C: lus-plus">Noise in solid-state nanopores. / PNAS 2008, lus-plus">105:417-21. CrossRef
  46. Janssen XJ, Jonsson MP, Plesa C, Soni GV, Dekker C, Dekker NH: lus-plus">Rapid manufacturing of low-noise membranes for nanopore sensors by trans-chip illumination lithography. / Nanotechnology 2012, lus-plus">23:475302. CrossRef
  47. Li J, Talaga DS: lus-plus">The distribution of DNA translocation times in solid-state nanopores. / J Phys Condens Matter 2010, lus-plus">22:454129. CrossRef
  48. Talaga DS, Li J: lus-plus">Single-molecule protein unfolding in solid state nanopores. / J Am Chem Soc 2009, lus-plus">131:9287-297. CrossRef
  49. Dorp S, Keyser UF, Dekker NH, Dekker C, Lemay SG: lus-plus">Origin of the electrophoretic force on DNA in solid-state nanopores. / Nat Phys 2009, lus-plus">5:347-51. CrossRef
  50. Bujalowski PJ, Oberhauser AF: lus-plus">Tracking unfolding and refolding reactions of single proteins using atomic force microscopy methods. / Methods 2013, lus-plus">60:151-60. CrossRef
  51. Liu R, Garcia-Manyes S, Sarkar A, Badilla CL, Fernández JM: lus-plus">Mechanical characterization of protein L in the low-force regime by electromagnetic tweezers/evanescent nanometry. / Biophys J 2009, lus-plus">96:3810-821. CrossRef
  52. Sischka A, Spiering A, Khaksar M, Laxa M, K?nig J, Dietz KJ, Anselmetti D: lus-plus">Dynamic translocation of ligand-complexed DNA through solid-state nanopores with optical tweezers. / J Phys Condens Matter 2010, lus-plus">22:454121. CrossRef
  
• 作者单位：Lingzhi Wu (1) (2)
  Hang Liu (1)
  Wenyuan Zhao (1)
  Lei Wang (1)
  Chuanrong Hou (1)
  Quanjun Liu (1)
  Zuhong Lu (1)
  
  1. State Key Laboratory of Bioelectronics, Southeast University, Nanjing, 210096, China
  2. School of Geography and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing, 210046, China
  
• ISSN：1556-276X

文摘

Nanopores have been proven as versatile single-molecule sensors for individual unlabeled biopolymer detection and characterization. In the present work, a relative large nanopore with a diameter of about 60?nm has been used to detect protein translocation driven by a series of applied voltages. Compared with previous studied small nanopores, a distinct profile of protein translocation through a larger nanopore has been characterized. First, a higher threshold voltage is required to drive proteins into the large nanopore. With the increase of voltages, the capture frequency of protein into the nanopore has been markedly enhanced. And the distribution of current blockage events is characterized as a function of biased voltages. Due to the large dimension of the nanopore, the adsorption and desorption phenomenon of proteins observed with a prolonged dwell time has been weakened in our work. Nevertheless, the protein can still be stretched into an unfolded state by increased electric forces at high voltages. In consideration of the high throughput of the large nanopore, a couple of proteins passing through the nanopore simultaneously occur at high voltage. As a new feature, the feasibility and specificity of a nanopore with distinct geometry have been demonstrated for sensing protein translocation, which broadly expand the application of nanopore devices.