Effects of Fluorescent Pair on the Kinetics of DNA Strand Displacement Reaction

Chengxu Li; Shiyan Xiao; Haojun Liang

doi:10.1063/1674-0068/cjcp2302015

Article Contents

Article Navigation > Chinese Journal of Chemical Physics > 2023 > Online First

Chengxu Li, Shiyan Xiao, Haojun Liang. Effects of Fluorescent Pair on the Kinetics of DNA Strand Displacement Reaction[J]. Chinese Journal of Chemical Physics . doi: 10.1063/1674-0068/cjcp2302015

Citation:

Chengxu Li, Shiyan Xiao, Haojun Liang. Effects of Fluorescent Pair on the Kinetics of DNA Strand Displacement Reaction[J]. Chinese Journal of Chemical Physics . doi: 10.1063/1674-0068/cjcp2302015

Chengxu Li, Shiyan Xiao, Haojun Liang. Effects of Fluorescent Pair on the Kinetics of DNA Strand Displacement Reaction[J]. Chinese Journal of Chemical Physics . doi: 10.1063/1674-0068/cjcp2302015

Citation:

Chengxu Li, Shiyan Xiao, Haojun Liang. Effects of Fluorescent Pair on the Kinetics of DNA Strand Displacement Reaction[J]. Chinese Journal of Chemical Physics . doi: 10.1063/1674-0068/cjcp2302015

PDF( 306 KB)

Effects of Fluorescent Pair on the Kinetics of DNA Strand Displacement Reaction

doi: 10.1063/1674-0068/cjcp2302015

Key Laboratory of Precision and Intelligent Chemistry, School of Chemistry and Materials Science, Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei 230026, China

More Information

Corresponding author: E-mail: xiaosy@ustc.edu.cn; hjliang@ustc.edu.cn
Received Date: 2023-02-15
Accepted Date: 2023-03-14

Available Online: 2023-03-16

Abstract

Abstract

Fluorescent labels are widely used in the characterizations of DNA-based reaction network operations. We systematically studied the effects of commonly used fluorescent pairs on thermal stabilities of signal-substrate duplex and the strand displacement kinetics. It is demonstrated that the modifications of duplex with fluorescent pairs stabilize DNA duplex by up to 3.5 °C, and the kinetics of DNA strand displacement circuit is also evidently slowed down. These results highlight the importance of fluorescent pairs towards the kinetic modulation in designing nucleic acid probes and complex DNA dynamic circuits.
- DNA strand displacement,
- Fluorescent label,
- Kinetics,
- Thermodynamic property

Prof. Liang passed away on February 11, 2022. This work is our tribute to our respectful supervisor.

FullText(HTML)

References(31)

References

[1]	Y. J. Chen, N. Dalchau, N. Srinivas, A. Phillips, L. Cardelli, D. Soloveichik, and G. Seelig, Nat. Nanotechnol. 8, 755 (2013). doi: 10.1038/nnano.2013.189
[2]	A. Phillips and L. Cardelli, J. R. Soc. Interface 6, S419 (2009). doi: 10.1098/rsif.2009.0072.focus
[3]	L. Qian, E. Winfree, and J. Bruck, Nature 475, 368 (2011). doi: 10.1038/nature10262
[4]	L. Qian and E. Winfree, Science 332, 1196 (2011). doi: 10.1126/science.1200520
[5]	A. J. Thubagere, W. Li, R. F. Johnson, Z. Chen, S. Doroudi, Y. L. Lee, G. Izatt, S. Wittman, N. Srinivas, D. Woods, E. Winfree, and L. Qian, Science 357, eaan6558 (2017). doi: 10.1126/science.aan6558
[6]	P. Wu, Y. Tu, Y. Qian, H. Zhang, and C. Cai, Chem. Commun. 50, 1012 (2014). doi: 10.1039/C3CC46773B
[7]	A. Ono, S. Cao, H. Togashi, M. Tashiro, T. Fujimoto, T. Machinami, S. Oda, Y. Miyake, I. Okamoto, and Y. Tanaka, Chem. Commun. 39, 4825 (2008). doi: 10.1039/b808686a
[8]	H. Yamaguchi, J. Šebera, J. Kondo, S. Oda, T. Komuro, T. Kawamura, T. Dairaku, Y. Kondo, I. Okamoto, A. Ono, J. V. Burda, C. Kojima, V. Sychrovský, and Y. Tanaka, Nucleic Acids Res. 42, 4094 (2014). doi: 10.1093/nar/gkt1344
[9]	L. Tang, Y. Liu, M. M. Ali, D. K. Kang, W. Zhao, and J. Li, Anal. Chem. 84, 4711 (2012). doi: 10.1021/ac203274k
[10]	D. Han, C. Wu, M. You, T. Zhang, S. Wan, T. Chen, L. Qiu, Z. Zheng, H. Liang, and W. Tan, Nat. Chem. 7, 835 (2015). doi: 10.1038/nchem.2325
[11]	P. Q. Ma, Q. Huang, H. D. Li, B. C. Yin, and B. C. Ye, J. Am. Chem. Soc. 142, 3851 (2020). doi: 10.1021/jacs.9b11545
[12]	B. Yurke, A. J. Turberfield, A. P. Mills, F. C. Simmel, and J. L. Neumann, Nature 406, 605 (2000). doi: 10.1038/35020524
[13]	D. Y. Zhang and E. Winfree, J. Am. Chem. Soc. 131, 17303 (2009). doi: 10.1021/ja906987s
[14]	D. Y. Zhang and G. Seelig, Nat. Chem. 3, 103 (2011). doi: 10.1038/nchem.957
[15]	D. Scalise and R. Schulman, Annu. Rev. Biomed. Eng. 21, 469 (2019). doi: 10.1146/annurev-bioeng-060418-052357
[16]	N. Srinivas, T. E. Ouldridge, P. Šulc, J. M. Schaeffer, B. Yurke, A. A. Louis, J. P. K. Doye, and E. Winfree, Nucleic Acids Res. 41, 10641 (2013). doi: 10.1093/nar/gkt801
[17]	R. R. F. Machinek, T. E. Ouldridge, N. E. C. Haley, J. Bath, and A. J. Turberfield, Nat. Commun. 5, 5324 (2014). doi: 10.1038/ncomms6324
[18]	P. Irmisch, T. E. Ouldridge, and R. Seidel, J. Am. Chem. Soc. 142, 11451 (2020). doi: 10.1021/jacs.0c03105
[19]	N. E. C. Haley, T. E. Ouldridge, I. Mullor Ruiz, A. Geraldini, A. A. Louis, J. Bath, and A. J. Turberfield, Nat. Commun. 11, 2562 (2020). doi: 10.1038/s41467-020-16353-y
[20]	A. J. Genot, D. Y. Zhang, J. Bath, and A. J. Turberfield, J. Am. Chem. Soc. 133, 2177 (2011). doi: 10.1021/ja1073239
[21]	Q. Li, G. Luan, Q. Guo, and J. Liang, Nucleic Acids Res. 30, e5 (2002). doi: 10.1093/nar/30.2.e5
[22]	S. Tyagi, D. P. Bratu, and F. R. Kramer, Nat. Biotechnol. 16, 49 (1998). doi: 10.1038/nbt0198-49
[23]	X. Sun, B. Wei, Y. Guo, S. Xiao, X. Li, D. Yao, X. Yin, S. Liu, and H. Liang, J. Am. Chem. Soc. 140, 9979 (2018). doi: 10.1021/jacs.8b05203
[24]	R. A. Cardullo, S. Agrawal, C. Flores, P. C. Zamecnik, and D. E. Wolf, Proc. Natl. Acad. Sci. USA 85, 8790 (1988). doi: 10.1073/pnas.85.23.8790
[25]	L. E. Morrison and L. M. Stols, Biochem. 32, 3095 (1993). doi: 10.1021/bi00063a022
[26]	B. G. Moreira, Y. You, M. A. Behlke, and R. Owczarzy, Biochem. Biophys. Res. Commun. 327, 473 (2005). doi: 10.1016/j.bbrc.2004.12.035
[27]	S. A. E. Marras, F. R. Kramer, and S. Tyagi, Nucleic Acids Res. 30, e122 (2002). doi: 10.1093/nar/gnf121
[28]	C. Li, Z. Li, W. Han, X. Yin, X. Liu, S. Xiao, and H. Liang, Chem. Commun. 58, 5849 (2022). doi: 10.1039/D2CC01072K
[29]	J. N. Zadeh, C. D. Steenberg, J. S. Bois, B. R. Wolfe, M. B. Pierce, A. R. Khan, R. M. Dirks, and N. A. Pierce, J. Comput. Chem. 32, 170 (2011). doi: 10.1002/jcc.21596
[30]	J. D. Puglisi and I. Tinoco Jr., Method Enzymol. 180, 304 (1989). doi: 10.1016/0076-6879(89)80108-9
[31]	L. A. Marky and K. J. Breslauer, Biopolymers 26, 1601 (1987). doi: 10.1002/bip.360260911