Skip to main content
SpringerLink
Log in

Detection of mismatched caspase-3 DNA oligonucleotides with an SPR biosensor following amplification by Taq polymerase

  • Original Paper
  • Published:
Microchimica Acta Aims and scope Submit manuscript

Abstract

We demonstrate that base mismatches of caspase-3 DNA sequences can be detected by surface plasmon resonance (SPR) following signal amplification by polymerase from Thermus aquaticus (Taq). The concentration of magnesium ions and the respective dNTPs for polymerase binding to the oligonucleotides on the sensing surface were optimized. Taq polymerase binds to double-stranded DNA that is self-assembled on the gold surface of the biosensor to induce an SPR signal. Experiments are presented on the effect of Mg(II) and dNTP concentrations on the activity of the polymerase on the sensing surface. The detection limits are 50 pM, 0.1 nM, 0.7 nM, 7 nM, and 20 nM for correctly matched, single-base mismatched, two-base mismatched, three-base mismatched and four-base mismatched DNA of caspase-3, respectively. This is attributed to the optimized experimental conditions, with samples containing 2 μM of Mg(II) and 0.3 mM of dNTP.

The process of detecting mismatched caspase-3 DNA oligonucleotides with SPR biosensor

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7

Similar content being viewed by others

References

  1. Kothakota S, Azuma T (1997) Caspase-3–generated fragment of gelsolin: effector of morphological change in apoptosis. Science 278:294–298

    Article  CAS  Google Scholar 

  2. Cragg GM, Grothaus PG, Newman DJ (2009) Impact of natural products on developing new anti-cancer agents. Chem Rev 109:3012–3043

    Article  CAS  Google Scholar 

  3. Zhou FF, Da X, Wu SN et al (2010) Intravital imaging of tumor apoptosis with FRET probes during tumor therapy. Mol Imaging Biol 12:63–70

    Article  Google Scholar 

  4. Benyahia S, Benayache S, Benayache F et al (2004) Isolation from eucalyptus occidentalis and identification of a new kaempferol derivative that induces apoptosis in human myeloid leukemia cells. J Nat Prod 67:527–531

    Article  CAS  Google Scholar 

  5. Liu WK, Cheung FW, Che CT (2008) Stellettin A induces oxidative stress and apoptosis in HL-60 human leukemia and LNCaP prostate cancer cell lines. J Nat Prod 69:934–937

    Article  Google Scholar 

  6. Chen CY, Chen CH, Lo YC et al (2008) Anticancer activity of isoobtusilactone A from Cinnamomum kotoense: involvement of apoptosis, cell-cycle dysregulation, mitochondria regulation, and reactive oxygen species. J Nat Prod 71:933–940

    Article  CAS  Google Scholar 

  7. Lakhani SA, Kuid AM, Porter GA et al (2006) Caspases 3 and 7: key mediators of mitochondrial events of apoptosis. Science 311:847–851

    Article  CAS  Google Scholar 

  8. Yakovlev AG, Ota K, Wang GP et al (2001) Differential expression of apoptotic protease-activating factor-1 and caspase-3 genes and susceptibility to apoptosis during brain development and after traumatic brain injury. J Neurosci 21:7439–7446

    CAS  Google Scholar 

  9. Talanian RV, Brady KD, Cryns VL (2000) Caspases as targets for anti-inflammatory and anti-apoptotic drug discovery. J Med Chem 43:3351–3371

    Article  CAS  Google Scholar 

  10. Kim K, Lee M, Park H et al (2006) Cell-permeable and biocompatible polymeric nanoparticles for apoptosis imaging. J Am Chem Soc 128:3490–3491

    Article  CAS  Google Scholar 

  11. Lecaruyer P, Mannelli I, Courtois V et al (2006) Surface plasmon resonance imaging as a multidimensional surface characterization instrument –Application to biochip genotyping. Anal Chim Acta 573(574):333–340

    Article  Google Scholar 

  12. Tsoi PY, Yang MS (2004) Surface plasmon resonance study of the molecular recognition between polymerase and DNA containing various mismatches and conformational changes of DNA-protein complexes. Biosens Bioelectron 19:1209–1218

    Article  CAS  Google Scholar 

  13. Sakao Y, Nakamura F, Ueno N et al (2005) Hybridization of oligonucleotide by using DNA self-assembled monolayer. Colloid Surface B 40:149–152

    Article  CAS  Google Scholar 

  14. Homola J, Wolfbeis OS (2006) Surface plasmon resonance based sensors. In: Homola J, Piliarik M (eds) Surface plasmon resonance sensors. Springer, Berlin Heidelberg, pp 45–68

    Chapter  Google Scholar 

  15. Hasenbank MS, Fu E, Yager P (2006) Lateral spread of an amplification signal using an enzymatic system on a conductive surface. Langmuir 22:7451–7453

    Article  CAS  Google Scholar 

  16. Lee HJ, Wark AW, Goodrich TT et al (2005) Surface enzyme kinetics for biopolymer microarrays: a combination of langmuir and michaelis-menten concepts. Langmuir 21:4050–4057

    Article  CAS  Google Scholar 

  17. Gorodkiewicz E, Ostrowska H, Sankiewicz A (2011) SPR imaging biosensor for the 20S proteasome: sensor development and application to measurement of proteasomes in human blood plasma. Microchim Acta 175:177–184

    Article  CAS  Google Scholar 

  18. Fujii E, Koike T, Nakamura K et al (2002) Application of an absorption-based surface plasmon resonance principle to the development of SPR ammonium ion and enzyme sensors. Anal Chem 74:6106–6110

    Article  CAS  Google Scholar 

  19. He YH, Nie F (2011) Chemiluminescence assay for angiogenin using a signal amplification technology based on the cleavage of nicking endonucleases. Microchim Acta 174:375–382

    Article  CAS  Google Scholar 

  20. Nakatani K, Sando S, Saito I (2001) Scanning of guanine–guanine mismatches in DNA by synthetic ligands using surface plasmon resonance. Nat Biotech 19:51–55

    Article  CAS  Google Scholar 

  21. Hagihara S, Kumasawa H, Goto Y et al (2004) Detection of guanine- adenine mismatches by surface plasmon resonance sensor carrying naphthyridine- azaquinolone hybrid on the surface. Nucleic Acids Res 32:278–286

    Article  CAS  Google Scholar 

  22. Huang MM, Arnheim N, Goodman MF (1992) Extension of base mispairs by taq DNA polymerase: implications for single nucleotide discrimination in PCR. Nucl Acids Res 20:4567–4573

    Article  CAS  Google Scholar 

  23. Lee W, Lee DB, Oh BK et al (2004) Nanoscale fabrication of protein A on self-assembled monolayer and its application to surface plasmon resonance immunosensor. Enzyme Microb Tech 35:678–682

    Article  CAS  Google Scholar 

  24. Singh A, Snyder S, Lee L et al (2010) Effect of oligonucleotide length on the assembly of DNA materials: molecular dynamics simulations of layer-by-layer DNA films. Langmuir 26:17339–17347

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This work was supported by National Natural Science Foundation of China (31070772), Doctoral Program of Higher Education(200901011110136), Science and Technology Programs of Zhejiang Province (2011 C37029) and Science and Technology Programs of Suzhou (ZXG0920).

Author information

Authors and Affiliations

  1. Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310058, China

    Ying Zhang, Ying Mu, Chao Zhou, Qi Song, Wei Jin & Qinhan Jin

Authors
  1. Ying Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ying Mu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Chao Zhou
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Qi Song
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Wei Jin
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Qinhan Jin
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Ying Mu or Wei Jin.

Electronic supplementary material

Below is the link to the electronic supplementary material.

ESM 1

(DOC 1475 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Zhang, Y., Mu, Y., Zhou, C. et al. Detection of mismatched caspase-3 DNA oligonucleotides with an SPR biosensor following amplification by Taq polymerase. Microchim Acta 177, 435–441 (2012). https://doi.org/10.1007/s00604-012-0799-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00604-012-0799-0

Keywords

Search

Navigation