Erratum: Quantifying Short-Lived Events in Multistate Ionic Channel Measurements (ACS Nano (2014) 8 (1547-1553) DOI: 10.1021/nn405761y);Quantifying short-lived events in multistate ionic current measurements

ACS Nano

Volumn 8, Issue 2, 2014, Pages 1547-1553

  Balijepalli, Arvind ^a   Ettedgui, Jessica ^a   Cornio, Andrew T ^a   Robertson, Joseph W F ^a   Cheung, Kin P ^a   Kasianowicz, John J ^a   Vaz, Canute ^a  

^a NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY   (United States)

Author keywords

DNA sequencing; electrical circuit models; nanopores; single molecule measurements

Indexed keywords

DNA; DNA SEQUENCES; ELECTRIC CURRENT MEASUREMENT; ELECTRIC NETWORK PARAMETERS; GENE ENCODING; NANOPORES; POLYMERS;

DNA SEQUENCING; ELECTRICAL CIRCUIT MODELS; EQUIVALENT ELECTRICAL CIRCUITS; EXPONENTIAL DISTRIBUTIONS; ION-CHANNEL RECORDING; PHYSICAL INTERACTIONS; SINGLE MOLECULE MEASUREMENTS; SINGLE-MOLECULE CHARACTERIZATION;

RESIDENCE TIME DISTRIBUTION;

ION; MACROGOL DERIVATIVE; POLYMER;

ARTICLE; CHEMISTRY; NANOPORE;

IONS; NANOPORES; POLYETHYLENE GLYCOLS; POLYMERS;

EID: 84894610757     PISSN: 19360851     EISSN: 1936086X     Source Type: Journal    
DOI: 10.1021/acsnano.5b06216     Document Type: Erratum

References (49)

1. Katz, B. Nerve, Muscle, and Synapse; McGraw-Hill: New York, 1966.
2. Kandel, E.; Schwartz, J.; Jessell, T. Principles of Neural Science, 5 ed.; McGraw-Hill Medical: New York, 2000.
3. Hille, B. Ionic Channels of Excitable Membranes, 3 rd ed.; Sinauer Associates, Incorporated: Sunderland, MA, 2001.
4. Nonner, W.; Eisenberg, B. Electrodiffusion in Ionic Channels of Biological Membranes J. Mol. Liq. 2000, 87, 149-162
5. Bezanilla, F. The Voltage Sensor in Voltage-Dependent Ion Channels Physiol. Rev. 2000, 80, 555-592
6. Rabiner, L.; Juang, B. H. An Introduction to Hidden Markov Models IEEE ASSP Mag. 1986, 3, 4-16
7. Qin, F.; Auerbach, A.; Sachs, F. A Direct Optimization Approach to Hidden Markov Modeling for Single Channel Kinetics Biophys. J. 2000, 79, 1915-1927
8. Qin, F.; Auerbach, A.; Sachs, F. Hidden Markov Modeling for Single Channel Kinetics with Filtering and Correlated Noise Biophys. J. 2000, 79, 1928-1944
9. Rosales, R.; Stark, J. A.; Fitzgerald, W. J.; Hladky, S. B. Bayesian Restoration of Ion Channel Records Using Hidden Markov Models Biophys. J. 2001, 80, 1088-1103
10. Milescu, L. S.; Yildiz, A.; Selvin, P. R.; Sachs, F. Maximum Likelihood Estimation of Molecular Motor Kinetics From Staircase Dwell-Time Sequences Biophys. J. 2006, 91, 1156-1168
11. Shelley, C.; Magleby, K. L. Linking Exponential Components to Kinetic States in Markov Models for Single-Channel Gating J. Gen. Physiol. 2008, 132, 295-312
12. Blatz, A. L.; Magleby, K. L. Correcting Single Channel Data for Missed Events Biophys. J. 1986, 49, 967-980
13. Qin, F.; Auerbach, A.; Sachs, F. Estimating Single-Channel Kinetic Parameters From Idealized Patch-Clamp Data Containing Missed Events Biophys. J. 1996, 70, 264-280
14. Colquhoun, D.; Hawkes, A. G. On the Stochastic Properties of Bursts of Single Ion Channel Openings and of Clusters of Bursts Philos. Trans. R. Soc. London, Ser. B 1982, 300, 1-59
15. Magleby, K. L.; Weiss, D. S. Estimating Kinetic Parameters for Single Channels with Simulation. A General Method That Resolves the Missed Event Problem and Accounts for Noise Biophys. J. 1990, 58, 1411-1426
16. Colquhoun, D.; Hatton, C. J.; Hawkes, A. G. The Quality of Maximum Likelihood Estimates of Ion Channel Rate Constants J. Physiol. 2003, 547, 699-728
17. Colquhoun, D.; Sigworth, F. J. Fitting and Statistical Analysis of Single-Channel Records. In Single-Channel Recording; Sakmann, B.; Neher, E., Eds.; Springer: New York, 1995; pp 483-587.
18. Kasianowicz, J. J.; Robertson, J. W. F.; Chan, E. R.; Reiner, J. E.; Stanford, V. M. Nanoscopic Porous Sensors Ann. Rev. Anal. Chem. 2008, 1, 737-766
19. Reiner, J. E.; Balijepalli, A.; Robertson, J. W. F.; Campbell, J.; Suehle, J.; Kasianowicz, J. J. Disease Detection and Management via Single Nanopore-Based Sensors Chem. Rev. 2012, 112, 6432-6451
20. Robertson, J. W. F.; Kasianowicz, J. J.; Banerjee, S. Analytical Approaches for Studying Transporters, Channels and Porins Chem. Rev. 2012, 112, 6227-6249
21. Kasianowicz, J.; Brandin, E.; Branton, D.; Deamer, D. Characterization of Individual Polynucleotide Molecules Using a Membrane Channel Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 13770-13773
22. Manrao, E. A.; Derrington, I. M.; Laszlo, A. H.; Langford, K. W.; Hopper, M. K.; Gillgren, N.; Pavlenok, M.; Niederweis, M.; Gundlach, J. H. Reading DNA at Single-Nucleotide Resolution with a Mutant MspA Nanopore and Phi29 DNA Polymerase Nat. Biotechnol. 2012, 30, 349-353
23. Kumar, S.; Tao, C.; Chien, M.; Hellner, B.; Balijepalli, A.; Robertson, J. W. F.; Li, Z.; Russo, J. J.; Reiner, J. E.; Kasianowicz, J. J. et al. PEG-Labeled Nucleotides and Nanopore Detection for Single Molecule DNA Sequencing by Synthesis Sci. Rep. 2012, 2, 684
24. Suzuki, Y.; Dudko, O. K. Biomolecules Under Mechanical Stress: A Simple Mechanism of Complex Behavior J. Chem. Phys. 2011, 134, 065102
25. Robertson, J. W. F.; Rodrigues, C. G.; Stanford, V. M.; Rubinson, K. A.; Krasilnikov, O. V.; Kasianowicz, J. J. Single-Molecule Mass Spectrometry in Solution Using a Solitary Nanopore Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 8207-8211
26. Reiner, J. E.; Kasianowicz, J. J.; Nablo, B. J.; Robertson, J. W. F. Theory for Polymer Analysis Using Nanopore-Based Single-Molecule Mass Spectrometry Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 12080-12085
27. Merzlyak, P. G.; Yuldasheva, L. N.; Rodrigues, C. G.; Carneiro, C. M. M.; Krasilnikov, O. V.; Bezrukov, S. M. Polymeric Nonelectrolytes to Probe Pore Geometry: Application to the Alpha-Toxin Transmembrane Channel Biophys. J. 1999, 77, 3023-3033
28. Robertson, J. W. F.; Kasianowicz, J. J.; Reiner, J. E. Changes in Ion Channel Geometry Resolved to Sub-Ångström Precision via Single Molecule Mass Spectrometry J. Phys.: Condens. Matter 2010, 22, 454108
29. Pedone, D.; Firnkes, M.; Rant, U. Data Analysis of Translocation Events in Nanopore Experiments Anal. Chem. 2009, 81, 9689-9694
30. Dimitrov, V.; Mirsaidov, U.; Wang, D.; Sorsch, T.; Mansfield, W.; Miner, J.; Klemens, F.; Cirelli, R.; Yemenicioglu, S.; Timp, G. Nanopores in Solid-State Membranes Engineered for Single Molecule Detection Nanotechnology 2010, 21, 065502
31. Krems, M.; Pershin, Y. V.; Di Ventra, M. Ionic Memcapacitive Effects in Nanopores Nano Lett. 2010, 10, 2674-2678
32. Albrecht, T. How to Understand and Interpret Current Flow in Nanopore/Electrode Devices ACS Nano 2011, 5, 6714-6725
33. Timp, W.; Comer, J.; Aksimentiev, A. DNA Base-Calling From a Nanopore Using a Viterbi Algorithm Biophys. J. 2012, 102, L37-L39
34. Hall, J. E. Access Resistance of a Small Circular Pore J. Gen. Physiol. 1975, 66, 531-532
35. Bezrukov, S. M.; Vodyanoy, I. Probing Alamethicin Channels with Water-Soluble Polymers. Effect on Conductance of Channel States Biophys. J. 1993, 64, 16-25
36. Bezrukov, S.; Vodyanoy, I.; Brutyan, R.; Kasianowicz, J. Dynamics and Free Energy of Polymers Partitioning Into a Nanoscale Pore Macromolecules 1996, 29, 8517-8522
37. White, R. J.; Ervin, E. N.; Yang, T.; Chen, X.; Daniel, S.; Cremer, P. S.; White, H. S. Single Ion-Channel Recordings Using Glass Nanopore Membranes J. Am. Chem. Soc. 2007, 129, 11766-11775
38. Balijepalli, A.; Robertson, J. W. F.; Reiner, J. E.; Kasianowicz, J. J.; Pastor, R. W. Theory of Polymer-Nanopore Interactions Refined Using Molecular Dynamics Simulations J. Am. Chem. Soc. 2013, 135, 7064-7072
39. Clarke, J.; Wu, H.-C.; Jayasinghe, L.; Patel, A.; Reid, S.; Bayley, H. Continuous Base Identification for Single-Molecule Nanopore DNA Sequencing Nat. Nanotechnol. 2009, 4, 265-270
40. Eisenberg, R. S.; Gage, P. W. Ionic Conductances of the Surface and Transverse Tubular Membranes of Frog Sartorius Fibers J. Gen. Physiol. 1969, 53, 279-297
41. Sigworth, F. J. Electronic Design of the Patch Clamp. In Single-Channel Recording; Sakmann, B.; Neher, E., Eds.; Springer: New York, 1995; pp 95-127.
42. Lathrop, D. K.; Ervin, E. N.; Barrall, G. A.; Keehan, M. G.; Kawano, R.; Krupka, M. A.; White, H. S.; Hibbs, A. H. Monitoring the Escape of DNA From a Nanopore Using an Alternating Current Signal J. Am. Chem. Soc. 2010, 132, 1878-1885
43. Rosenstein, J. K.; Wanunu, M.; Merchant, C. A.; Drndić, M.; Shepard, K. L. Integrated Nanopore Sensing Platform with Sub-Microsecond Temporal Resolution Nat. Methods 2012, 9, 487-492
44. Zwolak, M.; Di Ventra, M. Electronic Signature of DNA Nucleotides via Transverse Transport Nano Lett. 2005, 5, 421-424
45. Carminati, M.; Ferrari, G.; Ivanov, A. P.; Albrecht, T. Design and Characterization of a Current Sensing Platform for Silicon-Based Nanopores with Integrated Tunneling Nanoelectrodes Analog Integr. Circ. Sig. Process. 2013, 77, 333-343
46. Xie, P.; Xiong, Q.; Fang, Y.; Qing, Q.; Lieber, C. M. Local Electrical Potential Detection of DNA by Nanowire-Nanopore Sensors Nat. Nanotechnol. 2011, 7, 119-125
47. Montal, M.; Mueller, P. Formation of Bimolecular Membranes From Lipid Monolayers and a Study of Their Electrical Properties Proc. Natl. Acad. Sci. U.S.A. 1972, 69, 3561-3566
48. Menestrina, G. Ionic Channels Formed by Staphylococcus Aureus Alpha-Toxin: Voltage-Dependent Inhibition by Divalent and Trivalent Cations J. Membr. Biol. 1986, 90, 177-190
49. Kasianowicz, J. J.; Bezrukov, S. M. Protonation Dynamics of the Alpha-Toxin Ion Channel From Spectral Analysis of pH-Dependent Current Fluctuations Biophys. J. 1995, 69, 94-105