Citation: Jia-Bao Long, Ying-Xin Liu, Qing-Feng Cao, Qiu-Ping Guo, Shu-Ya Yan, Xiang-Xian Meng. Sensitive and enzyme-free detection for single nucleotide polymorphism using microbead-assisted toehold-mediated strand displacement reaction[J]. Chinese Chemical Letters, ;2015, 26(8): 1031-1035. doi: 10.1016/j.cclet.2015.05.036 shu

Sensitive and enzyme-free detection for single nucleotide polymorphism using microbead-assisted toehold-mediated strand displacement reaction

1.
a College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China;
2.
b Department of Bioengineering and Environment Science, Changsha University, Changsha 410003, China

Corresponding author: Xiang-Xian Meng,
Received Date: 3 December 2014
Available Online: 7 April 2015
Fund Project: This work is supported by National Natural Science Foundation of China (No. 21275043) (No. 21275043)National Basic Research Program of China under Grants (No. 2009CB421601). (No. 2009CB421601)

This report described a free-enzyme, convenient and inexpensive genotyping biosensor capable of detecting single nucleotide polymorphism at normal temperature based on the combination of toeholdmediated strand displacement reaction (toehold-SDR) and microbead-capture technique. The biosensor consists of a pre-hybridized strand formed by a reporter probe and a capture probe. In the presence of a mutant sequence, there is no toehold-mediated strand displacement and the reporter probe cannot be released from the pre-hybridized strand. Microbeads capture the fluorescent pre-hybridized strand through biotin-streptavidin interaction, so microbeads give out significant fluorescence signal, while there is no fluorescence in the solution. However, in the presence of a matched target, the strand displacement is effectively initiated and the reporter probe is released from pre-hybridized strand. After addingmicrobeads, the solution produces bright fluorescence, while microbeads have no obvious signal. Genotypes are identified conveniently according to the fluorescence intensity of the solution. The method provides a simple and inexpensive strategy to detect point mutation. Moreover, this biosensor shows the linear relationship in the range of 1-40 nmol/L and reaches a detection limit of 0.3 nmol/L.
- Enzyme-free,
- Microbead-assisted,
- Toehold-mediated strand displacement,
- Point mutation
1. [1]
  [1] L. Kruglyak, D.A. Nickerson, Variation is the spice of life, Nat. Genet. 27 (2001) 234-236.
2. [2]
  [2] D.J. Eastburn, A. Sciambi, A.R. Abate, Picoinjection enables digital detection of RNA with droplet RT-PCR, PLoS One 8 (2013) e62961.
3. [3]
  [3] A. Klindworth, E. Pruesse, T. Schweer, et al., Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies, Nucleic Acids Res. 41 (2013) e1.
4. [4]
  [4] H.L. Cheng, S.S. Chiou, Y.M. Liao, Y.L. Chen, S.M. Wu, Genotyping of single nucleotide polymorphism in γ-glutamyl hydrolase gene by capillary electrophoresis, Electrophoresis 32 (2011) 2021-2027.
5. [5]
  [5] T. Murakami, J. Sumaoka, M. Komiyama, Sensitive isothermal detection of nucleicacid sequence by primer generation-rolling circle amplification, Nucleic Acids Res. 37 (2009) e19.
6. [6]
  [6] Y.T. Zhou, Q. Huang, J.M. Gao, et al., A dumbbell probe-mediated rolling circle amplification strategy for highly sensitive microRNA detection, Nucleic Acids Res. 38 (2010) e156.
7. [7]
  [7] F. Xuan, X.T. Luo, I.M. Hsing, Sensitive immobilization-free electrochemical DNA sensor based on isothermal circular strand displacement polymerization reaction, Biosens. Bioelectron. 35 (2012) 230-234.
8. [8]
  [8] H.Y. Su, X.C. Meng, Q.P. Guo, et al., Label-free DNA sensor with PCR-like sensitivity based on background reduction and target-triggered polymerization amplification, Biosens. Bioelectron. 52 (2014) 417-421.
9. [9]
  [9] L.I. Ward, S.J. Harper, Loop-mediated isothermal amplification for the detection of plant pathogens, Methods Mol. Biol. 862 (2012) 161-170.
10. [10]
  [10] A. Valoczi, C. Hornyik, N. Varga, et al., Sensitive and specific detection of micro-RNAs by northern blot analysis using LNA-modified oligonucleotide probes, Nucleic Acids Res. 32 (2004) e175.
11. [11]
  [11] D.J. Caruana, A. Heller, Enzyme-amplified amperometric detection of hybridization and of a single base pair mutation in an 18-base oligonucleotide on a 7-mmdiameter microelectrode, J. Am. Chem. Soc. 121 (1999) 769-774.
12. [12]
  [12] K. Knez, D. Spasic, K.P.F. Janssen, J. Lammertyn, Emerging technologies for hybridization based single nucleotide polymorphism detection, Analyst 139 (2014) 353-370.
13. [13]
  [13] Y. Xiao, B.D. Piorek, K.W. Plaxco, A.J. Heeger, A reagentless signal-on architecture for electronic, aptamer-based sensors via target-induced strand displacement, J. Am. Chem. Soc. 127 (2005) 17990-17991.
14. [14]
  [14] A.J. Genot, D.Y. Zhang, J. Bath, A.J. Turberfield, Remote toehold: amechanism for flexible control of DNA hybridization kinetics, J. Am. Chem. Soc. 133 (2011) 2177-2182.
15. [15]
  [15] B. Yurke, A.P. Mills Jr., Using DNA to power nanostructures, Genet. Program Evolv. Mach. 4 (2003) 111-122.
16. [16]
  [16] Z. Zhang, D.D. Zeng, H.W. Ma, et al., A DNA-origami chip platform for label-free SNP genotyping using toehold-mediated strand displacement, Small 6 (2010) 1854-1858.
17. [17]
  [17] X.Y. Wang, M.J. Zou, H.D. Huang, et al., Gold nanoparticle enhanced fluorescence anisotropy for the assay of single nucleotide polymorphisms (SNPs) based on toehold-mediated strand-displacement reaction, Biosens. Bioelectron. 41 (2013) 569-575.
18. [18]
  [18] D.Z. Wang, W. Tang, X.J. Wu, et al., Highly selective detection of singlenucleotide polymorphisms using a quartz crystal microbalance biosensor based on the toehold-mediated strand displacement reaction, Anal. Chem. 84 (2012) 7008-7014.
19. [19]
  [19] X.X. Meng, X.H. Yang, K.M. Wang, et al., Direct fluorescence detection of point mutations in human genomic DNA using microbead-based ligase chain reaction, Talanta 80 (2010) 1725-1729.
20. [20]
  [20] L.J. Zhou, K.M. Wang, W.H. Tan, et al., Quantitative intracellular molecular profiling using a one-dimensional flow system, Anal. Chem. 78 (2006) 6246-6251.
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沈阳化工大学材料科学与工程学院沈阳 110142