Advertisement

Analytical and Bioanalytical Chemistry

, Volume 410, Issue 23, pp 5817–5823 | Cite as

A many probes-one spot hybridization oligonucleotide microarray

  • Elena V. Kostina
  • Alexander N. Sinyakov
  • Vladimir A. RyabininEmail author
Research Paper

Abstract

A variant of the hybridization oligonucleotide microarray, utilizing the principle of many probes-one spot (MPOS-microarrays), is proposed. A case study based on Orthopoxviruses (Variola, Monkeypox, and Ectromelia viruses) demonstrates a considerable increase in the fluorescence signal (up to 100-fold) when several oligonucleotide probes are printed to one spot. Moreover, the specificity of detection also increases (almost 1000-fold), allowing the use of probes that individually lack such high specificity. The optimal probes have a Tm of 32–37 °C and length of 13–15 bases. We suggest that the high specificity and sensitivity of the MPOS-microarray is a result of cooperativity of DNA binding with all probes immobilized in the spot. This variant of DNA detection can be useful for designing biosensors, tools for point-of-care (POC) diagnostics, microbial ecology, analysis of clustered regularly interspaced short palindromic repeats (CRISPR), and others.

Graphical abstract

Keywords

MPOS-microarray Orthopoxviruses Diagnostics Hybridization 

Notes

Funding information

The work was supported by Russian State-funded budget project (VI.62.1.4, 0309-2016-0004).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

216_2018_1190_MOESM1_ESM.pdf (178 kb)
ESM 1 (PDF 178 kb)
216_2018_1190_MOESM2_ESM.avi (1.3 mb)
ESM 2 (AVI 1379 kb)

References

  1. 1.
    Rogers JV, editor. Microarrays: principles, applications and technologies. New York: Nova Science Publishers, Inc; 2014.Google Scholar
  2. 2.
    Miller MB, Tang YW. Basic concepts of microarrays and potential applications in clinical microbiology. Clin Microbiol Rev. 2009;22:611–33.CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    Hoheisel JD. Microarray technology: beyond transcript profiling and genotype analysis. Nat Rev Genet. 2006;7:200–10.CrossRefPubMedGoogle Scholar
  4. 4.
    Zhang Y, Liu Q, Wang D, Chen S, Wang S. Simultaneous detection of oseltamivir- and amantadine-resistant influenza by oligonucleotide microarray visualization. PLoS One. 2013.  https://doi.org/10.1371/journal.pone.0057154.
  5. 5.
    Li MH, Fu SB, Xiao HS. Genome-wide analysis of microRNA and mRNA expression signatures in cancer. Acta Pharmacol Sin. 2015;36:1200–11.CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Kirschner M, Pujol G, Radu A. Oligonucleotide microarray data mining: search for age-dependent gene expression. Biochem Biophys Res Commun. 2002;298:772–8.CrossRefPubMedGoogle Scholar
  7. 7.
    Golden TR, Hubbard A, Melov S. Microarray analysis of variation in individual aging C. elegans: approaches and challenges. Exp Gerontol. 2006;41:1040–5.CrossRefPubMedGoogle Scholar
  8. 8.
    Yoo SM, Choi JH, Lee SY, Yoo NC. Applications of DNA microarray in disease diagnostics. J Microbiol Biotechnol. 2009;19:635–46.PubMedGoogle Scholar
  9. 9.
    Marzancola M, Sedighi A, Li PC. DNA microarray-based diagnostics. Methods Mol Biol. 2016;1368:161–78.CrossRefPubMedGoogle Scholar
  10. 10.
    Ryabinin VA, Kostina EV, Maksakova GA, Neverov AA, Chumakov KM, Sinyakov AN. Universal oligonucleotide microarray for sub-typing of influenza a virus. PLoS One. 2011.  https://doi.org/10.1371/journal.pone.0017529.
  11. 11.
    Zimenkov DV, Kulagina EV, Antonova OV, Krasnova MA, Chernyaeva EN, Zhuravlev VY, et al. Evaluation of a low-density hydrogel microarray technique for mycobacterial species identification. J Clin Microbiol. 2015.  https://doi.org/10.1128/JCM.02579-14.
  12. 12.
    Sakai T, Kohzaki K, Watanabe A, Tsuneoka H, Shimadzu M. Use of DNA microarray analysis in diagnosis of bacterial and fungal endophthalmitis. Clin Ophthalmol. 2012.  https://doi.org/10.2147/OPTH.S29230.
  13. 13.
    Mathur M, Singh E, Poduval TB, Rao AV. Indian J Med Res. 2015;141:175–86.CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Feyzkhanova GU, Filippova MA, Talibov VO, Dementieva EI, Maslennikov VV, Reznikov YP, et al. Development of hydrogel biochip for in vitro allergy diagnostics. Immunol Methods. 2014.  https://doi.org/10.1016/j.jim.2014.03.003.
  15. 15.
    Zimenkov DV, Antonova OV, Kuz'min AV, Isaeva YD, Krylova LY, Popov SA, et al. Detection of second-line drug resistance in Mycobacterium tuberculosis using oligonucleotide microarrays. BMC Infect Dis. 2013.  https://doi.org/10.1186/1471-2334-13-240.
  16. 16.
    Lezar S, Barros E. Oligonucleotide microarray for the identification of potential mycotoxigenic fungi. BMC Microbiol. 2010.  https://doi.org/10.1186/1471-2180-10-87.
  17. 17.
    Chung IH, Kang S, Kim YR, Kim JH, Jung JW, Lee S, et al. Development of a low-density DNA microarray for diagnosis of target-site mutations of pyrethroid and organophosphate resistance mutations in thewhitefly Bemisia tabaci. Pest Manag Sci. 2011;67:1541–8.CrossRefPubMedGoogle Scholar
  18. 18.
    Kostina EV, Ryabinin VA, Maksakova GA, Sinyakov AN. A second generation universal microarray for subtyping influenza A virus. Russ J Bioorg Chem. 2012;38:599–604.CrossRefGoogle Scholar
  19. 19.
    Ryabinin VA, Kostina EV, Sinyakov AN. A compact microarray for subtyping of influenza A virus. Russ J Bioorg Chem. 2013;39:378–80.CrossRefGoogle Scholar
  20. 20.
    Nilsson M, Malmgren H, Samiotaki M, Kwiatkowski M, Chowdhary BP, Landegren U. Padlock probes: circularizing oligonucleotides for localized DNA detection. Science. 1994;265(5181):2085–8.CrossRefPubMedGoogle Scholar
  21. 21.
    Ke R, Zorzet A, Göransson J, Lindegren G, Sharifi-Mood B, Chinikar S, et al. Colorimetric nucleic acid testing assay for RNA virus detection based on circle-to-circle amplification of padlock probes. J Clin Microbiol. 2011;49:4279–85.CrossRefPubMedPubMedCentralGoogle Scholar
  22. 22.
    Bates SR, Baldwin DA, Channing A, Gifford LK, Hsu A, Lu P. Cooperativity of paired oligonucleotide probes for microarray hybridization assays. Anal Biochem. 2005;342:59–68.CrossRefPubMedGoogle Scholar
  23. 23.
    Gentalen E, Chee M. Quantitative detection of microbial genes by using DNA microarrays. Nucleic Acids Res. 1999;27:1485–91.CrossRefPubMedPubMedCentralGoogle Scholar
  24. 24.
    Laassri M, Chizhikov V, Mikheev M, Shchelkunov S, Chumakov K. Detection and discrimination of orthopoxviruses using microarrays of immobilized oligonucleotides. J Virol Methods. 2003;112:67–78.CrossRefPubMedGoogle Scholar
  25. 25.
    Ryabinin VA, Shundrin LA, Kostina EV, Laassri M, Chizhikov V, Shchelkunov SN, et al. Microarray assay for detection and discrimination of Orthopoxvirus species. J Med Virol. 2006;78:1325–40.CrossRefPubMedGoogle Scholar
  26. 26.
    Ryabinin VA, Shundrin LA, Kostina EV, Laassri M, Chizhikov VE, Maksakova GA, et al. An oligonucleotide microarray for detection and discrimination of orthopoxviruses based on oligonucleotide sequences of two viral genes. Mol Gen Mikrobiol Virusol. 2006;4:23–30.Google Scholar
  27. 27.
    Letowski J, Brousseau R, Masson L. Designing better probes: effect of probe size, mismatch position and number on hybridization in DNA oligonucleotide microarrays. J Microbiol Methods. 2004;57:269–78.CrossRefPubMedGoogle Scholar
  28. 28.
    Rennie C, Noyes HA, Kemp SJ, Hulme H, Brass A, Hoyle DC. Strong position-dependent effects of sequence mismatches on signal ratios measured using long oligonucleotide microarrays. BMC Genomics. 2008.  https://doi.org/10.1186/1471-2164-9-317.
  29. 29.
    Williamson JR. Cooperativity in macromolecular assembly. Nat Chem Biol. 2008;4:458–65.CrossRefPubMedGoogle Scholar
  30. 30.
    Mahadevi AS, Sastry GN. Cooperativity in noncovalent interactions. Chem Rev. 2016;116:2775–825.CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Elena V. Kostina
    • 1
  • Alexander N. Sinyakov
    • 1
  • Vladimir A. Ryabinin
    • 1
    Email author
  1. 1.Institute of Chemical Biology and Fundamental Medicine, Siberian BranchRussian Academy of SciencesNovosibirskRussia

Personalised recommendations