Chapter 11
Single-molecule FRET Studies of Helicases and Holliday Junctions
Taekjip Ha,
Taekjip Ha
University of Illinoism Urbana-Champaign, Urbana, Il 61801, USA and Howard Hughes Medical Institute, Department of Physics, Urbana, Il 61801, USA
Search for more papers by this authorTaekjip Ha,
Taekjip Ha
University of Illinoism Urbana-Champaign, Urbana, Il 61801, USA and Howard Hughes Medical Institute, Department of Physics, Urbana, Il 61801, USA
Search for more papers by this authorBook Editor(s):Prof. Dr. Toshio Yanagida,
Dr. Yoshiharu Ishii,
Prof. Dr. Toshio Yanagida
Osaka University, Graduate School of Frontier Bioscience and Graduate School of Medicine, 1-3 Yamada-oka, Suita, Osaka 562-0871, Japan
Search for more papers by this authorDr. Yoshiharu Ishii
CREST, Soft nano-machine Project JST, 1-3 Yamada-oka, Suita, Osaka 562-0871, Japan
Search for more papers by this authorFirst published: 15 October 2008
Summary
This chapter contains sections titled:
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Introduction
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Single-molecule FRET
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smFRET Studies of Rep Helicase
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SmFRET Studies of Holliday Junction
-
Outlook
-
References
References
- Weiss, S. (1999) Science, 283, 1676–1683.
- Weiss, S. (2000) Nat. Struct. Biol., 7, 724–729.
- Forster, T. (ed.) (1965) Modern Quantum Chemistry (Ed. O. Sinanoglu), Academic, New York.
- Stryer, L. and Haugland, R.P. (1967) Proc. Natl. Acad. Sci. USA, 58, 719–726.
- Selvin, P.R. (2000) Nat. Struct. Biol., 7, 730–734.
- Deniz, A.A., Laurence, T.A., Dahan, M., Chemla, D.S., Schultz, P.G. and Weiss, S. (2001) Annu. Rev. Phys. Chem., 52, 233–253.
- Ha, T. (2001) Methods, 25, 78.
- Ha, T. (2001) Curr. Opin. Struct. Biol., 11, 287–292.
- Ha, T. (2004) Biochemistry, 43, 4055–4063.
- Ha, T., Enderle, T., Ogletree, D.F., Chemla, D.S., Selvin, P.R. and Weiss, S. (1996) Proc. Natl Acad. Sci. USA, 93, 6264–6268.
- Deniz, A.A., Dahan, M., Grunwell, J.R., Ha, T.J., Faulhaber, A.E., Chemla, D.S., Weiss, S. and Schultz, P.G. (1999) Proc. Natl Acad. Sci. USA, 96, 3670–3675.
- Lee, J.Y., Okumus, B., Kim, D.S. and Ha, T. (2005) Proc. Natl Acad. Sci. USA, 102, 18938–18943.
- Murphy, M.C., Rasnik, I., Cheng, W., Lohman, T.M. and Ha, T. (2004) Biophys. J., 86, 2530–2537.
- McKinney, S.A., Declais, A.C., Lilley, D.M.J. and Ha, T. (2003) Nat. Struct. Biol., 10, 93–97.
- McKinney, S.A., Freeman, A.D., Lilley, D.M. and Ha, T. (2005) Proc. Natl Acad. Sci. USA, 102, 5715–5720.
- Buranachai, C., McKinney, S.A. and Ha, T. (2006) Nano Lett., 6, 496–500.
- Clamme, J.P. and Deniz, A.A. (2005) Chemphyschem, 6, 74–77.
- Laurence, T.A., Kong, X., Jager, M. and Weiss, S. (2005) Proc. Natl Acad. Sci. USA, 102, 17348–17353.
- Ha, T., Zhuang, X.W., Kim, H.D., Orr, J.W., Williamson, J.R. and Chu, S. (1999) Proc. Natl Acad. Sci. USA, 96, 9077–9082.
- Zhuang, X.W., Bartley, L.E., Babcock, H.P., Russell, R., Ha, T.J., Herschlag, D. and Chu, S. (2000) Science, 288, 2048–2051.
- Zhuang, X.W., Kim, H., Pereira, M.J.B., Babcock, H.P., Walter, N.G. and Chu, S. (2002) Science, 296, 1473–1476.
- Bokinsky, G., Rueda, D., Misra, V.K., Rhodes, M.M., Gordus, A., Babcock, H.P., Walter, N.G. and Zhuang, X. (2003) Proc. Natl Acad. Sci. USA, 100, 9302–9307.
- Rueda, D., Bokinsky, G., Rhodes, M.M., Rust, M.J., Zhuang, X. and Walter, N.G. (2004) Proc. Natl Acad. Sci. USA, 101, 10066–10071.
- Xie, Z., Srividya, N., Sosnick, T.R., Pan, T. and Scherer, N.F. (2004) Proc. Natl Acad. Sci. USA, 101, 534–539.
- Tan, E., Wilson, T.J., Nahas, M.K., Clegg, R.M., Lilley, D.M.J. and Ha, T. (2003) Proc. Natl Acad. Sci. USA, 100, 9308.
- Nahas, M.K., Wilson, T.J., Hohng, S., Lilley, D.M.J. and Ha, T. (2004) Nat. Struct. Mol. Biol., 11, 1107–1113.
- Hohng, S., Wilson, T.J., Tan, E., Clegg, R.M., Lilley, D.M. and Ha, T. (2004) J. Mol. Biol., 336, 69–79.
- Hodak, J.H., Fiore, J.L., Nesbitt, D.J., Downey, C.D. and Pardi, A. (2005) Proc. Natl Acad. Sci. USA, 102, 10505–10510.
- Brasselet, S., Peterman, E.J.G., Miyawaki, A. and Moerner, W.E. (2000) J. Phys. Chem. B, 104, 3676–3682.
- Pljevaljcic, G., Millar, D.P. and Deniz, A.A. (2004) Biophys. J., 87, 457–467.
- Kim, H.D., Nienhaus, G.U., Ha, T., Orr, J.W., Williamson, J.R. and Chu, S. (2002) Proc. Natl Acad. Sci. USA, 99, 4284–4289.
- Deniz, A.A., Laurence, T.A., Beligere, G.S., Dahan, M., Martin, A.B., Chemla, D.S., Dawson, P.E., Schultz, P.G. and Weiss, S. (2000) Proc. Natl Acad. Sci. USA, 97, 5179–5184.
- Lipman, E.A., Schuler, B., Bakajin, O. and Eaton, W.A. (2003) Science, 301, 1233–1235.
- Schuler, B., Lipman, E.A. and Eaton, W.A. (2002) Nature, 419, 743–747.
- Diez, M., Zimmermann, B., Borsch, M., Konig, M., Schweinberger, E., Steigmiller, S., Reuter, R., Felekyan, S., Kudryavtsev, V., Seidel, C.A. and Graber, P. (2004) Nat. Struct. Mol. Biol., 11, 135–141.
- Zimmermann, B., Diez, M., Zarrabi, N., Graber, P. and Borsch, M. (2005) EMBO J., 24, 2053–2063.
- Rasnik, I., Myong, S., Cheng, W., Lohman, T.M. and Ha, T. (2004) J. Mol. Biol., 336, 395–498.
- Myong, S., Rasnik, I., Joo, C., Lohman, T.M. and Ha, T. (2005) Nature, 437, 1321–1325.
- Joo, C., McKinney, S.A., Nakamura, M., Rasnik, I., Myong, S. and Ha, T. (2006) Cell, 126, 515–527.
- Kapanidis, A.N., Margeat, E., Laurence, T.A., Doose, S., Ho, S.O., Mukhopadhyay, J., Kortkhonjia, E., Mekler, V., Ebright, R.H. and Weiss, S. (2005) Mol. Cell, 20, 347–356.
- Blanchard, S.C., Gonzalez, R.L., Kim, H.D., Chu, S. and Puglisi, J.D. (2004) Nat. Struct. Mol. Biol., 11, 1008–1014.
- Blanchard, S.C., Kim, H.D., Gonzalez, R.L., Jr., Puglisi, J.D. and Chu, S. (2004) Proc. Natl Acad. Sci. USA, 101, 12893–12898.
- Ha, T.J., Ting, A.Y., Liang, J., Caldwell, W.B., Deniz, A.A., Chemla, D.S., Schultz, P.G. and Weiss, S. (1999) Proc. Natl Acad. Sci. USA, 96, 893–898.
- Cognet, L., Harms, G.S., Blab, G.A., Lommerse, P.H.M. and Schmidt, T. (2000) Appl. Phys. Lett., 77, 4052–4054.
- Rasnik, I., McKinney, S.A. and Ha, T. (2005) Acc. Chem. Res., 38, 542–548.
- Sofia, S.J., Premnath, V. and Merrill, E.W. (1998) Macromolecules, 31, 5059.
- Prime, K.L. and Whitesides, G.M. (1991) Science, 252, 1164.
- Ha, T., Rasnik, I., Cheng, W., Babcock, H.P., Gauss, G., Lohman, T.M. and Chu, S. (2002) Nature, 419, 638–641.
- Kuzmenkina, E.V., Heyes, C.D. and Nienhaus, G.U. (2005) Proc. Natl Acad. Sci. USA, 102, 15471–15476.
- Kuzmenkina, E.V., Heyes, C.D. and Nienhaus, G.U. (2006) J. Mol. Biol., 357, 313–324.
- Margeat, E., Kapanidis, A.N., Tinnefeld, P., Wang, Y., Mukhopadhyay, J., Ebright, R.H. and Weiss, S. (2006) Biophys. J., 90, 1419–1431.
- Blainey, P.C., van Oijen, A.M., Banerjee, A., Verdine, G.L. and Xie, X.S. (2006) Proc. Natl Acad. Sci. USA, 103, 5752–5757.
- van Oijen, A.M., Blainey, P.C., Crampton, D.J., Richardson, C.C., Ellenberger, T. and Xie, X.S. (2003) Science, 301, 1235–1238.
- Lee, J.B., Hite, R.K., Hamdan, S.M., Xie, X.S., Richardson, C.C. and van Oijen, A.M. (2006) Nature, 439, 621–624.
- Cosa, G., Zeng, Y., Liu, H.W., Landes, C.F., Makarov, D.E., Musier-Forsyth, K. and Barbara, P.F. (2006) J. Phys. Chem. B Condens. Matter Mater. Surf. Interfaces, Biophys., 110, 2419–2426.
- Liu, H.W., Cosa, G., Landes, C.F., Zeng, Y., Kovaleski, B.J., Mullen, D.G., Barany, G., Musier-Forsyth, K. and Barbara, P.F. (2005) Biophys. J., 89, 3470–3479.
- Roy, R., Kozlov, A.G., Lohman, T.M. and Ha, T.(in preparation).
- Okumus, B., Wilson, T.J., Lilley, D.M.J. and Ha, T. (2004) Biophys. J., 87, 2798–2806.
- Dohoney, K.M. and Gelles, J. (2001) Nature, 409, 370–374.
- Bianco, P.R., Brewer, L.R., Corzett, M., Balhhorn, R., Yeh, Y., Kowalczykowski, S.C. and Baskin, R.J. (2001) Nature, 409, 374–378.
- Abdel-Monem, M., Durwald, H. and Hoffmann-Berling, H. (1976) Eur. J. Biochem., 65, 441–449.
- Abdel-Monem, M. and Hoffmann-Berling, H. (1976) Eur. J. Biochem., 65, 431–440.
- Lohman, T.M. and Bjornson, K.P. (1996) Annu. Rev. Biochem., 65, 169–214.
- Hall, M.C. and Matson, S.W. (1999) Mol. Microbiol., 34, 867–877.
- Patel, S.S. and Picha, K.M. (2000) Annu. Rev. Biochem., 69, 651–697.
- von Hippel, P.H. and Delagouette, E. (2001) Cell, 104, 177–190.
- Eoff, R.L. and Raney, K.D. (2005) Biochem. Soc. Trans., 33, 1474–1478.
- Cordin, O., Banroques, J., Tanner, N.K. and Linder, P. (2006) Gene, 367, 17–37.
- Sung, P., Bailly, V., Weber, C., Thompson, L.H., Prakash, L. and Prakash, S. (1993) Nature, 365, 852–855.
- Ellis, N.A., Groden, J., Ye, T.Z., Straughen, J., Lennon, D.J., Ciocci, S., Proytcheva, M. and German, J. (1995) Cell, 83, 655–666.
- Gray, M.D., Shen, J.C., Kamath-Loeb, A.S., Blank, A., Sopher, B.L., Martin, G.M., Oshima, J. and Loeb, L.A. (1997) Nat. Genet., 17, 100–103.
- Kitao, S., Shimamoto, A., Goto, M., Miller, R.W., Smithson, W.A., Lindor, N.M. and Furuichi, Y. (1999) Nat. Genet., 22, 82–84.
- Hickson, I.D. (2003) Nat. Rev. Cancer, 3, 169–178.
- von Hippel, P.H. (2004) Nat. Struct. Mol. Biol., 11, 494–496.
- Korolev, S., Hsieh, J., Gauss, G.H., Lohman, T.M. and Waksman, G. (1997) Cell, 90, 635–647.
- Velankar, S.S., Soultanas, P., Dillingham, M.S., Subramanya, H.S. and Wigley, D.B. (1999) Cell, 97, 75–84.
- Cheng, W., Hsieh, J., Brendza, K.M. and Lohman, T.M. (2001) J. Mol. Biol., 310, 327–350.
- Cheng, W., Brendza, K.M., Gauss, G.H., Korolev, S., Waksman, G. and Lohman, T.M. (2002) Proc. Natl Acad. Sci. USA, 99, 16006–16011.
- Brendza, K.M., Cheng, W., Fischer, C.J., Chesnik, M.A., Niedziela-Majka, A. and Lohman, T.M. (2005) Proc. Natl Acad. Sci. USA, 102, 10076–10081.
- Kim, J.L., Morgenstern, K.A., Griffith, J.P., Dwyer, M.D., Thomson, J.A., Murcko, M.A., Lin, C. and Caron, P.R. (1998) Structure, 6, 89–100.
- Bernstein, D.A., Zittel, M.C. and Keck, J.L. (2003) EMBO J., 22, 4910–4921.
- Singleton, M.R., Dillingham, M.S., Gaudier, M., Kowalczykowski, S.C. and Wigley, D.B. (2004) Nature, 432, 187–193.
- Singleton, M.R., Sawaya, M.R., Ellenberger, T. and Wigley, D.B. (2000) Cell, 101, 589–600.
- Li, D., Zhao, R., Lilyestrom, W., Gai, D., Zhang, R., DeCaprio, J.A., Fanning, E., Jochimiak, A., Szakonyi, G. and Chen, X.S. (2003) Nature, 423, 512–518.
- Rasnik, I., Myong, S. and Ha, T. (2006) Nucleic Acids Res.
- Perkins, T.T., Li, H.W., Dalal, R.V., Gelles, J. and Block, S.M. (2004) Biophys. J., 86, 1640–1648.
- Dumont, S., Cheng, W., Serebrov, V., Beran, R.K., Tinoco, I., Jr., Pyle, A.M. and Bustamante, C. (2006) Nature, 439, 105–108.
- Dessinges, M.N., Lionnet, T., Xi, X.G., Bensimon, D. and Croquette, V. (2004) Proc. Natl Acad. Sci. USA, 101, 6439–6444.
- Dennis, C., Fedorov, A., Kas, E., Salome, L. and Grigoriev, M. (2004) EMBO J., 23, 2413–2422.
- Dawid, A., Croquette, V., Grigoriev, M. and Heslot, F. (2004) Proc. Natl Acad. Sci. USA, 101, 11611–11616.
- Amit, R., Gileadi, O. and Stavans, J. (2004) Proc. Natl Acad. Sci. USA, 101, 11605–11610.
- Bustamante, C., Chemla, Y.R., Forde, N.R. and Izhaky, D. (2004) Annu. Rev. Biochem., 73, 705–748.
- Scott, J.F., Eisenberg, S., Bertsch, L.L. and Kornberg, A. (1977) Proc. Natl Acad. Sci. USA, 74, 193–197.
- Sandler, S.J. (2000) Genetics, 155, 487–497.
- Marians, K.J. (2004) Phil. Trans. R. Soc. Lond. B Biol. Sci., 359, 71–77.
- Holliday, R. (1964) Genet. Res., 5, 282–304.
- Kowalczykowski, S.C. (2000) Trends Biochem. Sci., 25, 156–165.
- Lilley, D.M.J. (2000) Quart. Rev. Biophys., 33, 109–159.
- Lilley, D.M.J. and White, M.F. (2001) Nat. Rev. Mol. Cell Biol., 2, 433–443.
- Murchie, A.I., Clegg, R.M., von Kitzing, E., Duckett, D.R., Diekmann, S. and Lilley, D.M. (1989) Nature, 341, 763–766.
- Clegg, R.M., Murchie, A.I.H. and Lilley, D.M.J. (1994) Biophys. J., 66, 99–109.
- Clegg, R.M., Murchie, A.I., Zechel, A., Carlberg, C., Diekmann, S. and Lilley, D.M. (1992) Biochemistry, 31, 4846–4856.
- Cooper, J.P. and Hagerman, P.J. (1989) Proc. Natl Acad. Sci. USA, 86, 7336–7340.
- Churchill, M.E., Tullius, T.D., Kallenbach, N.R. and Seeman, N.C. (1988) Proc. Natl Acad. Sci. USA, 85, 4653–4656.
- Duckett, D.R., Murchie, A.I., Diekmann, S., von Kitzing, E., Kemper, B. and Lilley, D.M. (1988) Cell, 55, 79–89.
- Chen, J.H., Churchill, M.E., Tullius, T.D., Kallenbach, N.R. and Seeman, N.C. (1988) Biochemistry, 27, 6032–6038.
- Nowakowski, J., Shim, P.J., Stout, C.D. and Joyce, G.F. (2000) J. Mol. Biol., 300, 93–102.
- Nowakowski, J., Shim, P.J., Prasad, G.S., Stout, C.D. and Joyce, G.F. (1999) Nat. Struct. Biol., 6, 151–156.
- Eichman, B.F., Vargason, J.M., Mooers, B.H.M. and Ho, P.S. (2000) Proc. Natl Acad. Sci. USA, 97, 3971–3976.
- Ortiz-Lombardia, M., Gonzalez, A., Eritja, R., Aymami, J., Azorin, F. and Coll, M. (1999) Nat. Struct. Biol., 6, 913–917.
- Eichman, B.F., Mooers, B.H.M., Alberti, M., Hearst, J.E. and Ho, P.S. (2001) J. Mol. Biol., 308, 15–26.
- Shlyakhtenko, L.S., Potaman, V.N., Sinden, R.R. and Lyubchenko, Y.L. (1998) J. Mol. Biol., 280, 61–72.
- Lushnikov, A.Y., Bogdanov, A. and Lyubchenko, Y.L. (2003) J. Biol. Chem., 278, 43130–43134.
- Sha, R.J., Liu, F.R. and Seeman, N.C. (2002) Biochemistry, 41, 5950–5955.
- Nollmann, M., Stark, W.M. and Byron, O. (2004) Biophys. J., 86, 3060–3069.
- Pikkemaat, J.A., Overmars, F.J.J., Dreeftromp, C.M., Vandenelst, H., Vanboom, J.H. and Altona, C. (1996) J. Mol. Biol., 262, 349–357.
- Overmars, F.J.J. and Altona, C. (1997) J. Mol. Biol., 273, 519–524.
- Overmars, F.J.J., Lanzotti, V., Galeone, A., Pepe, A., Mayol, L., Pikkemaat, J.A. and Altona, C. (1997) Eur. J. Biochem., 249, 576–583.
- Carlstrom, G. and Chazin, W.J. (1996) Biochemistry, 35, 3534–3544.
- Chen, S.M. and Chazin, W.J. (1994) Biochemistry, 33, 11453–11459.
- Miick, S.M., Fee, R.S., Millar, D.P. and Chazin, W.J. (1997) Proc. Natl Acad. Sci. USA, 94, 9080–9084.
- Seeman, N.C. (1982) J. Theor. Biol., 99, 237–247.
- Kallenbach, N.R., Ma, R.I. and Seeman, N.C. (1983) Nature, 305, 829–831.
- Hsu, P.L. and Landy, A. (1984) Nature, 311.
- von Kitzing, E., Lilley, D.M.J. and Diekmann, S. (1990) Nucleic Acids Res., 18, 2671–2683.
- Torbet, J. (1992) Methods Enzymol., 211, 518–532.
- Mao, C.D., Sun, W.Q. and Seeman, N.C. (1999) J. Am. Chem. Soc., 121, 5437–5443.
- Murchie, A.I., Portugal, J. and Lilley, D.M. (1991) EMBO J., 10, 731–738.
- Li, X.J., Wang, H. and Seeman, N.C. (1997) Biochemistry, 36, 4240–4247.
- Grainger, R.J., Murchie, A.I.H. and Lilley, D.M.J. (1998) Biochemistry, 37, 23–32.
- Joo, C., McKinney, S.A., Lilley, D.M.J. and Ha, T. (2004) J. Mol. Biol., 341, 739–751.
- Hohng, S., Joo, C. and Ha, T. (2004) Biophys. J., 87, 1328–1337.