Creating a Single Sensing Zone Within an Alpha-Hemolysin Pore via Site-Directed Mutagenesis

Springer Science and Business Media LLC - Tập 4 Số 1 - Trang 78-84 - 2014
Eric N. Ervin1, Geoffrey A. Barrall1, Prithwish Pal1, Megan K. Bean1, Anna E. P. Schibel1, Andrew D. Hibbs1
1Electronic BioSciences, Inc, San Diego, USA

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Tài liệu tham khảo

Kasianowicz, J. J., Brandin, E., Branton, D., Deamer, D. W. (1996). Characterization of individual polynucleotide molecules using a membrane channel. Proceedings of the National Academy of Sciences of the United States of America, 93, 13770–13773.

Branton, D., Deamer, D. W., Marziali, A., Bayley, H., Benner, S. A., Butler, T., et al. (2008). The potential and challenges of nanopore sequencing. Nature Biotechnology, 26, 1146–1153.

Deamer, D. W., & Akeson, M. (2000). Nanopores and nucleic acids: prospects for ultrarapid sequencing. Trends in Biotechnology, 18, 147–151.

Venta, K., Shemer, G., Puster, M., Rodriguez-Manzo, J. A., Balan, A., Rosenstein, J. K., et al. (2013). Differentiation of short single-stranded DNA homopolymers in solid-state nanopores. ACS Nano, 7, 4629–4636.

Timp, W., Comer, J., Aksimentiev, A. (2012). DNA base-calling from a nanoproe using a viterbi algorithm. Biophysical Journal, 102, L37–L39.

Manrao, E. A., Derrington, I. M., Laszlo, A. H., Langford, K. W., Hopper, M. K., Gillgren, N., et al. (2012). Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase. Nature Biotechnology, 30, 349–353.

Manrao, E. A., Derrington, I. M., Pavlenok, M., Niederweis, M., Gundlach, J. H. (2011). Nucleotide discrimination with DNA immobilized in the MspA nanopore. PLoS One, 6, e25723.

Meller, A., Nivon, L., Brandin, E., Golovchenko, J., Branton, D. (2000). Rapid nanopore discrimination between single polynucleotide molecules. Proceedings of the National Academy of Sciences of the United States of America, 97, 1079–1084.

Meller, A. (2003). “Dynamics of polynucleotide transport through nanometre-scale pores”. Journal of Physics: Condensed Matter, 15, R581.

Meller, A., Nivon, L., Branton, D. (2001). Voltage-driven DNA translocations through a nanopore. Biophysical Reviews and Letters, 86, 3435–3438.

Deamer, D. W., & Branton, D. (2002). Characterization of nucleic acids by nanopore analysis. Accounts of Chemical Research, 35, 817–825.

Cherf, G. M., Lieberman, K. R., Rashid, H., Lam, C. E., Karplus, K., Akeson, M. (2012). Automated forward and reverse ratcheting of DNA in a nanopore at 5-A precision. Nature Biotechnology, 30, 344–348.

Lieberman, K. R., Cherf, G. M., Doody, M. J., Olasagasti, F., Kolodji, Y., Akeson, M. (2010). Processive replication of single DNA molecules in a nanopore catalyzed by phi29 DNA polymerase. Journal of the American Chemical Society, 132, 17961–17972.

Stoddart, D., Heron, A. J., Mikhailova, E., Maglia, G., Bayley, H. (2009). Single-nucleotide discrimination in immobilized DNA oligonucleotides with a biological nanopore. Proceedings of the National Academy of Sciences of the United States of America, 106, 7702–7707.

Stoddart, D., Heron, A. J., Klingelhoefer, J., Mikhailova, E., Maglia, G., Bayley, H. (2010). Nucleobase recognition in ssDNA at the central constriction of the α-hemolysin pore. Nano Letters, 10(9), 3633–3637.

Purnell, R. F., Mehta, K. K., Schmidt, J. J. (2008). Nucleotide identification and orientation discrimination of DNA homopolymers immobilized in a protein nanopore. Nano Letters, 8, 3029–3034.

Henrickson, S. E., Misakian, M., Robertson, B., Kasianowicz, J. J. (2000). Driven DNA transport into an asymmetric nanometer-scale pore. Physical Review Letters, 85, 3057–3060.

Song, L., Hobaugh, M. R., Shustak, C., Cheley, S., Bayley, H., Gouaux, J. E. (1996). Structure of staphylococcal α-hemolysin, a heptameric transmembrane pore. Science, 274, 1859–1865.

Ashkenasy, N., Sanchez-Quesada, J., Bayley, H., Ghadiri, M. R. (2005). “Recognizing a single base in an individual DNA strand: a step toward DNA sequencing in nanopores”. Angewandte Chemie International Edition, 117, 1425–1428.

Gyarfas, B., Olasagasti, F., Benner, S., Garalde, D., Lieberman, K. R., Akeson, M. (2009). Mapping the position of DNA polymerase-bound DNA templates in a nanopore at 5 Å resolution. ACS Nano, 3, 1457–1466.

Zhang, B., Galusha, J., Shiozawa, P. G., Wang, G., Bergren, A. J., Jones, R. M., et al. (2007). Bench-top method for fabricating glass-sealed nanodisk electrodes, glass nanopore electrodes, and glass nanopore membranes of controlled size. Analytical Chemistry, 79, 4778–4787.

White, R. J., Zhang, B., Daniel, S., Tang, J. M., Ervin, E. N., Cremer, P. S., et al. (2006). Ionic conductivity of the aqueous layer separating a lipid bilayer membrane and a glass support. Langmuir, 22, 10777–10783.

White, R. J., Ervin, E. N., Yang, T., Chen, X., Daniel, S., Cremer, P. S., et al. (2007). Single ion-channel recordings using glass nanopore membranes. Journal of the American Chemical Society, 129, 11766–11775.

Ervin, E. N., Kawano, R., White, R. J., White, H. S. (2008). Simultaneous alternating and direct current readout of protein ion channel blocking events using glass nanopore membranes. Analytical Chemistry, 80, 2069–2076.

Lathrop, D. K., Ervin, E. N., Barrall, G. A., Keehan, M. G., Kawano, R., Krupka, M. A., et al. (2009). Monitoring the escape of DNA from a nanopore using an alternating current signal. Journal of the American Chemical Society, 132, 1878–1885.

Schibel, A. E. P., An, N., Jin, Q., Fleming, A. M., Burrows, C. J., White, H. S. (2010). Nanopore detection of 8-Oxo-7, 8-dihydro-2-deoxyguanosine in immobilized single-stranded DNA via adduct formation to the DNA damage site. Journal of the American Chemical Society, 132, 17992–17995.

Butler, T. Z., Gundlach, J. H., Troll, M. (2007). Ionic current blockades from DNA and RNA molecules in the α-hemolysin nanopore. Biophysical Journal, 93, 3229–3240.

Wanunu, M., Chakrabarti, B., Mathe, J., Nelson, D. R., Meller, A. (2008). Orientation-dependent interactions of DNA with an α-hemolysin channel. Physical Review E, 77, 031904.

Mathe, J., Aksimentiev, A., Nelson, D. R., Schulten, K., Meller, A. (2005). Orientation discrimination of single-stranded DNA inside the α-hemolysin membrane channel. Proceedings of the National Academy of Sciences of the United States of America, 102, 12377–12382.

Movileanu, L., Cheley, S., Howorka, S., Braha, O., Bayley, H. (2001). Location of a constriction in the lumen of a transmembrane pore by targeted covalent attachment of polymer molecules. Journal of General Physiology, 117, 239–251.

Nakane, J., Wiggin, M., Marziali, A. (2004). “A nanosensor for transmembrane capture and identification of single nucleic acid molecules”. Biophysical Journal, 87, 615–621. July 1, 2004.

DeGuzman, V. S., Lee, C. C., Deamer, D. W., Vercoutere, W. A. (2006). “Sequence-dependent gating of an ion channel by DNA hairpin molecules”. Nuclear Acids Research, 34, 6425–6437. December 2, 2006.