Measuring the Reaction Rates of High Affinity Reactions by Single-molecule Magnetic Tweezers†

doi:10.7503/cjcu20180083

Abstract

Abstract:

A method based on single molecule experiment was adopted. Single-molecule magnetic tweezers was used to study the different binding process of SSB(E. coli single-stranded DNA binding protein) and ssDNA(single-stranded DNA) in different conditions, and get the reaction rate and reaction detailed information. This method can be used in similar reactions.

Key words: Reaction rate, Reaction dynamics, Single-molecule magnetic tweezers, Single-stranded DNA binding protein

CLC Number:

O643.11

TrendMD:

LU Yue, MA Jianbing, HUANG Xingyuan, XIAO Xue, LI Ming, LU Ying, XU Chunhua. Measuring the Reaction Rates of High Affinity Reactions by Single-molecule Magnetic Tweezers^†[J]. Chem. J. Chinese Universities, 2018, 39(6): 1228.

Figures/Tables 8

Fig.1 Free energy landscape and the corresponding chemical reaction rates

Fig.2 Single-molecule measurement of binding/unbinding

Fig.3 “Double-state” interaction of SSB/ssDNA(A) Time traces of the length of ssDNA under different SSB concentrations; a. no SSB, b. 10 nmol/L SSB, c. 20 nmol/L SSB; (B) statistical distribution of the change in ssDNA length.

Fig.4 Dwell time distributions of extended(A) and wrapped(B) state under different SSB concentrations

Fig.5 Diagram of the interaction between SSB and ssDNA

Fig.6 “Three-state” interaction of SSB/ssDNA(A) Time traces of the ssDNA under different SSB concentrations; a. no SSB, b. 10 nmol/L SSB, c. 20 nmol/L SSB; (B) statistical distribution of the change in ssDNA length.

Fig.7 Dwell time distributions of extended(A), wrapped(B) and the further wrapped(C) state under different SSB concentrations

Fig.8 Diagram of the interaction between SSB and ssDNA

References 29

[1]	Woodside M. T., Block S. M., Annu. Rev. Biophys., 2014, 43, 19—39
[2]	Kramers H.A., Physica, 1940, 7, 284—304
[3]	Dudko O. K., Hummer G., Szabo A., Phys. Rev. Lett., 2006, 96, 108101
[4]	Dudko O. K., Hummer G., Szabo A., Proc. Natl. Acad. Sci. USA, 2008, 105, 15755—15760
[5]	Bevilacqua P. C., Kierzek R., Johnson K. A., Turner D. H., Science, 1992, 258, 1355—1358
[6]	Lambeir A., Engelborghs Y., J. Biol. Chem., 1981, 256, 3279—3282
[7]	Kozlov A. G., Lohman T. M., Biochemistry, 2002, 41, 6032—6044
[8]	Otto M.R., Lillo M. P., Beechem J. M., Biophys. J., 1994, 67, 2511—2521
[9]	Van L.A., Loontiens F. G., Clegg R. M., Jovin T. M., Febs. J., 1980, 103, 313—321
[10]	Bell G.I., Science, 1978, 200, 618—627
[11]	Taniguchi Y., Nishiyama M., Ishii Y., Yanagida T., Nat. Chem. Biol., 2005, 1, 342—347
[12]	Rice S., Cui Y., Sindelar C., Naber N., Matuska M., Vale R., Cooke R., Biophys. J., 2003, 84, 1844—1854
[13]	Wang M. D., Schnitzer M. J., Yin H., Landick R., Gelles J., Block S. M., Science, 1998, 282, 902—907
[14]	Mazumdar M., Cross R. A., J. Biol. Chem., 1998, 273, 29352—29359
[15]	Eyring H., J. Chem. Phys., 1935, 3, 107—115
[16]	Yang W. Y., Gruebele M., Nature, 2003, 423, 193—197
[17]	Chase J. W., Williams K. R., Annu. Rev. Biochem., 1986, 55, 103—136
[18]	Meyer R. R., Laine P. S., Microbiol. Rev., 1990, 54, 342—380
[19]	Yuzhakov A., Kelman Z., O’Donnell M., Cell, 1999, 96, 153—163
[20]	Sun W., Godson G. N., J. Mol. Biol., 1998, 276, 689—703
[21]	Lohman T. M., Ferrari M. E., Annu. Rev. Biochem., 1994, 63, 527—570
[22]	Bujalowski W., Lohman T.M., Biochemistry, 1986, 25, 7799—7802
[23]	Lohman T. M., Bujalowski W., Overman L. B., Trends. Biochem. Sci., 1988, 13, 250—255
[24]	Roy R., Kozlov A. G., Lohman T. M., Ha T., J. Mol. Biol., 2007, 369, 1244—1257
[25]	Lohman T. M., Overman L. B., J. Biol. Chem., 1984, 260, 3594—3603
[26]	Zhou R. B., Kozlov A. G., Roy R., Zhang J. C., Korolev S., Lohman T. M., Ha T., Cell, 2011, 146, 222—232
[27]	Li J. H., Lin W. X., Zhang B., Nong D. G., Ju H. P., Ma J. B., Xu C. H., Ye F. F., Xi X. G., Li M., Lu Y., Dou S. X., Nucleic. Acids. Res., 2016, 44, 4330—4339
[28]	Lu H. P., Xun L., Xie X. S., Science, 1998, 282, 1877—1882
[29]	Evans E., Ritchie K., Biophys. J., 1997, 72, 1541—1555