Export file:

Format

  • RIS(for EndNote,Reference Manager,ProCite)
  • BibTex
  • Text

Content

  • Citation Only
  • Citation and Abstract

Development and application of DNA molecular probes

Department of Food Science, University of Udine, via Sondrio 2/A, 33100, Udine, Italy

Special Issues: Utilization of DNA in nanotechnology

The development of DNA probes started from 1950's for diagnostic purposes and it is still growing. DNA probes are applied in several fields such as food, medical, veterinary, environment and security, with the aim of prevention, diagnosis and treatment. The use of DNA probes permits microorganism identification, including pathogen detection, and their quantification when used in specific systems. Various techniques obtained success by the utilization of specific DNA probes, that allowed the obtainment of rapid and specific results. From PCR, qPCR and blotting techniques that were first used in well equipped laboratories to biosensors such as fiber optic, surface plasmon resonance (SPR), electrochemical, and quartz crystal microbalance (QCM) biosensors that use different transduction systems. This review describes i) the design and production of primers and probes, and their utilization from the traditional techniques to the new emerging techniques like biosensors used in current applications; ii) the possibility to use labelled-free probes and probes labelled with an enzyme/fluorophore, etc.; iii) the different sensitivity obtained by using specific systems; and iv) the advantage obtained by using biosensors.
  Figure/Table
  Supplementary
  Article Metrics

References

1. Li S, Qiu W, Zhang X, et al. (2016) A high-performance DNA biosensor based on the assembly of gold nanoparticles on the terminal of hairpin-structured probe DNA. Sens Actuat B Chem 223: 861-867.

2. Gudnason H, Dufva M, Duong BD, et al. (2008) An inexpensive and simple method for thermally stable immobilization of DNA on an unmodified glass surface: UV linking of poly(T)10-poly(C)10-tagged DNA probes. Biotechniques 45: 261-271.    

3. Sakata T, Kamahori M, and Miyahara Y. (2004) Immobilization of oligonucleotide probes on Si3N4 surface and its application to genetic field effect transistor. Mat Sci Eng C Bio S 24: 827-832.    

4. Kimura N (2006) One-step immobilization of poly(dT)-modified DNA onto non-modified plastic substrates by UV irradiation for microarrays. Biochem Biophys Res Commun 347: 477-484.    

5. Kimura N, Oda R, Inaki Y, et al. (2004) Attachment of oligonucleotide probes to poly carbodiimide-coated glass for microarray applications. Nucl Ac Res 32: e68.    

6. Zagorodko O, Spadavecchia J, Yanguas SA, et al. (2014) Highly sensitive detection of DNA hybridization on commercialized graphene-coated surface plasmon resonance interfaces. Anal Chem 86: 11211-11216.

7. Rodriguez LD, Gonzalez GP, Gattuso A, et al. (2014) Reducing time in the analysis of listeria monocytogenes in meat, dairy and vegetable products. Int J Food Microbiol 184: 98-105.    

8. Abdalhai MH, Fernandes AM, Bashari M, et al. (2014) Rapid and sensitive detection of foodborne pathogenic bacteria (staphylococcus aureus) using an electrochemical DNA genomic biosensor and its application in fresh beef. J Agric Food Chem 62: 12659-12667.    

9. Khemthongcharoen N, Wonglumsom W, Suppat A, et al. (2015) Piezoresistive microcantilever-based DNA sensor for sensitive detection of pathogenic vibrio cholerae O1 in food sample. Biosens Bioelectron 63: 347-353.    

10. Stuken A, Dittami SM, Eikrem W, et al. (2013) Novel hydrolysis-probe based qPCR assay to detect saxitoxin transcripts of dinoflagellates in environmental samples. Harmful Algae 28: 108-117.    

11. Ryu H, Henson M, Elk M, et al. (2013) Development of quantitative PCR assays targeting the 16S rRNA genes of enterococcus spp. and their application to the identification of enterococcus species in environmental samples. Appl Environ Microbiol 79: 196-204.

12. Khatera M, de Escosura MA, and Merkoçia A. (2016) Biosensors for plant pathogen detection. Biosens Bioelectron, In press.

13. Huang H, Bai W, Dong C, et al. (2015) An ultrasensitive electrochemical DNA biosensor based on graphene/Au nanorod/polythionine for human papillomavirus DNA detection. Biosens Bioelectron 68: 442-446.    

14. Znazen A, Sellam H, Elleuch E, et al. (2015) Comparison of two quantitative real time PCR assays for rickettsia detection in patients from tunisia. Plos Negl Trop Dis 9: e0003487.    

15. Essaidi LM, Lyon M, Mamin A, et al. (2016) A new real-time RT-qPCR assay for the detection, subtyping and quantification of human respiratory syncytial viruses positive- and negative-sense RNAs. J Virol Meth 235: 9-14.

16. Gokcea G, Erdem A, Ceylana C, et al. (2016) Voltammetric detection of sequence-selective DNA hybridization related to toxoplasma gondii in PCR amplicons. Talanta 149: 244-249.    

17. Knapp J, Millon L, Mouzo L, et al. (2014) Real time PCR to detect the environmental faecal contamination by echinococcus multilocularis from red fox stools. Vet Paras 201: 40-47.    

18. Chena Q, Zhang L, Jiang F, et al. (2017) MnO2 microsphere absorbing Cy5-labeled single strand DNA probe serving as powerful biosensor for effective detection of mycoplasma ovipneumoniae. Sens Actuat B Chem 244: 1138-1144.    

19. Zhu D, Yan Y, Lei P, et al. (2014) A novel electrochemical sensing strategy for rapid and ultrasensitive detection of salmonella by rolling circle amplification and DNA-AuNPs probe. Anal Chim Acta 846: 44-50.    

20. Blagden T, Schneider W, Melcher U, et al. (2016) Adaptation and validation of e-probe diagnostic nucleic acid analysis for detection of escherichia coli O157:H7 in metagenomic data from complex food matrices. J Food Prot 79: 574-581.    

21. Kashisha, Soni DK, Mishra SK, et al. (2015) Label-free impedimetric detection of listeria monocytogenes based on poly-5-carboxy indole modified ssDNA probe. J Biotechnol 200: 70-76.    

22. Vasavirama K (2013) Molecular probes and their application. Int J Lifesc Bt Pharm Res 2: 32-42.

23. Manzano M and Iacumin L. (2015) Molecular techniques in food microbiology, in current applications of biotechnology, EZ. Dundar M, Bruschi F, Deeni Y, et al., chapter 2, Erciyes, Turkey, 9-23.

24. Zhao X, Lin CW, Wang J, et al. (2014) Advances in rapid detection methods for foodborne pathogens. J Microbiol Biotechnol 24: 297-312.    

25. Manzano M, Cocolin L, Cantoni C, et al. (1997) Detection and identification of listeria monocytogenes from milk and cheese by a single step PCR. Mol Biotechnol 7: 85-88.    

26. Aznar R and Alarcòn B. (2003) PCR detection of listeria monocytogenes: a study of multiple factors affecting sensitivity. J Appl Microbiol 95: 958-966.    

27. Malorny B, Hoorfar J, Hugas M, et al. (2003) Interlaboratory diagnostic accuracy of a salmonella specific PCR-based method. Int J Food Microbiol 89: 241-249.    

28. Yamamoto Y (2002) PCR in diagnosis of infection: detection of bacteria in cerebrospinal fluids. Clin Diagn Lab Immunol 9: 508-514.

29. Al Dragy WA and Baqer AA. (2014) Detection of escherichia coli O157:H7 in human patients stool and food by using multiplex PCR assays targeting the rfbE and the eaea genes compared with detection by biochemical test and serological assay. JNUS 17: 124-131.

30. Juskowiak B (2011) Nucleic acid-based fluorescent probes and their analytical potential. Anal Bioanal Chem 399: 3157-3176.    

31. de Boer P, Rahaoui H, Leer RJ, et al. (2015) Real-time PCR detection of campylobacter spp.: a comparison to classic culturing and enrichment. Food Microbiol 51: 96-100.

32. Gianfranceschi MV, Rodriguez LD, Hernandez M, et al. (2014) European validation of a real-time PCR-based method for detection of listeria monocytogenes in soft cheese. Int J Food Microbiol 184: 128-133.    

33. Gattuso A, Gianfranceschi MV, Sonnessa M, et al. (2014) Optimization of a real time PCR based method for the detection of listeria monocytogenes in pork meat. Int J Food Microbiol 184: 106-108.    

34. Rodriguez LD, Pla M, Scortti M, et al. (2005) A novel real-time PCR for listeria monocytogenes that monitors analytical performance via an internal amplification control. Appl Environ Microbiol 71: 9008-9012.    

35. Brooks JP, McLaughlin MR, Adeli A, et al (2016) Cultivation and qPCR detection of pathogenic and adminntibiotic resistant bacterial establishment in naive broiler houses. J Environ Qual 45: 958-966.    

36. Vendrame M, Iacumin L, Manzano M, et al. (2013) Use of propidium monoazide for the enumeration of viable oenococcus oeni in must and wine by quantitative PCR. Food Microbiol 35: 49-57.    

37. Minguzzi S, Terlizzi F, Lanzoni C, et al. (2016) A rapid protocol of crude RNA/DNA extraction for RT-qPCR detection and quantification of 'candidatus phytoplasma prunorum'. Plos One 11: e0146515.    

38. Calgua B, Rodriguez MJ, Hundesa A, et al. (2013) New methods for the concentration of viruses from urban sewage using quantitative PCR. J Virol Meth 187: 215-221.    

39. Gimenez A, Clemente CP, Calgua B, et al. (2009) Comparison of methods for concentrating human adenoviruses, polyomavirus JC and noroviruses in source waters and drinking water using quantitative PCR. J Virol Meth 158: 104-109.    

40. de Keuckelaere A, Baert L, Duarte A, et al. (2013) Evaluation of viral concentration methods from irrigation and processing water. J Virol Meth 187: 294-303.    

41. Faye O, Diallo D, Diallo M, et al. (2013) Quantitative real-time PCR detection of zika virus and evaluation with field-caught mosquitoes. Virol J 10: 1-8.    

42. Keller G and Manak MM. (1989) DNA probes. Stokton, New York.

43. Komminoth P (1992) Digoxigenin as an alternative probe labeling for in situ hybridization. Diagn Mol Pathol 1: 142-150.    

44. Musiani M, Venturoli S, Gallinella G, et al. (2007) Qualitative PCR-ELISA protocol for the detection and typing of viral genomes. Nat Prot 2: 2502-2510.    

45. Sue MJ, Yeap SK, Omar AR, et al. (2014). Application of PCR-ELISA in molecular diagnosis. Biomed Res Int 653014: 1-6.

46. Laoboonchai A, Kawamoto F, Thanoosingha N, et al. (2001) PCR-based ELISA technique for malaria diagnosis of specimens from Thailand. Trop Med Int Health 6: 458-462.    

47. Kobets T, Badalov´a J, Grekov I, et al. (2010) Leishmania parasite detection and quantification using PCR-ELISA. Nat Prot 5: 1074-1080.    

48. Ziyaeyan M, Sabahi F, Alborzi A, et al. (2008) Quantification of human cytomegalovirus DNA by a new capture hybrid polymerase chain reaction enzyme-linked immunosorbent assay in plasma and peripheral bloodmononuclear cells of bonemarrow transplant recipients. Exp Clin Transplant 6: 294-300.

49. Peterson AW, Heaton RI, and Georgiadis RM. (2001) The effect of surface probe density on DNA hybridization. Nucl Acid Res 29: 5163-5168.    

50. Xing JM, Zhang S, Du Y, et al. (2009) Rapid detection of intestinal pathogens in fecal samples by an improved reverse dot blot method. World J Gastroenterol 15: 2537-2542.    

51. Cecchini F, Iacumin L, Fontanot M, et al. (2012) Identification of the unculturable bacteria candidatus arthromitus in the intestinal content of trouts using dot blot and southern blot techniques. Vet Microbiol 156: 384-394.

52. Chen GF, Zhang CY, Wang YY, et al. (2015) Application of reverse dot blot hybridization to simultaneous detection and identification of harmful algae. Environ Sci Pollut Res Int 22: 1-13.    

53. Nestorova GG, Adapa BS, Kopparthy VL, et al. (2016) Lab-on-a-chip thermoelectric DNA biosensor for label-free detection of nucleic acid sequences. Sens Actuat B Chem 225: 174-180.    

54. Wijesuriya D, Breslin K, Anderson G, et al. (1994). Regeneration of immobilized antibodies on fiber optic probes. Biosens Bioelectron 9: 585-592.    

55. Ferguson JA, Steemers FJ, and Walt DR. (2000). High-density fiber-optic DNA random microsphere array. Anal Chem 72: 5618-5624.    

56. Almadidy A, Watterson J, Piunno P, et al. (2003) A fibre-optic biosensor for detection of microbial contamination, Can J Chem 81: 339-349.

57. Cecchini F, Manzano M, Yohai MY, et al. (2012) Chemiluminescent DNA optical fibre sensor for brettanomyces bruxellensis detection. J Biotechnol 157: 25-30.    

58. Yin MJ, Wu C, Shao LY, et al. (2013) Label-free, disposable fiber-optic biosensors for DNA hybridization detection. Analyst 138: 1988-1994.    

59. Yoo SY, Kim DK, Park TJ, et al. (2010) Detection of the most common corneal dystrophies caused by BIGH3 gene point mutations using a multispot gold-capped nanoparticle array chip. Anal Chem 82: 1349-1357.    

60. Endo T, Kerman K, Nagatani N, et al. (2005) Label-free detection of peptide nucleic Admincid-DNA hybridization using localized surface plasmon resonance based optical biosensor. Anal Chem 77: 6976-6984.    

61. Cheng XR, Hau BY, Endo T, et al. (2014) Au nanoparticle-modified DNA sensor based on simultaneous electrochemical impedance spectroscopy and localized surface plasmon resonance. Biosens Bioelectron 53: 513-518.    

62. Qu J, Wu L, Liu H, et al. (2015) A novel electrochemical biosensor based on DNA for rapid and selective detection of cadmium. Int J Electrochem Sci 10: 4020-4028.

63. Patel MK, Solanki PR, Seth S, et al. (2009) CtrA gene based electrochemical DNA sensor for detection of meningitis. Electrochem Commun 11: 969-973.    

64. Li F, Chen W, and Zhang S. (2008) Development of DNA electrochemical biosensor based on covalent immobilization of probe DNA by direct coupling of sol-gel and self-assembly technologies. Biosens Bioelectron 24: 787-792.    

65. Li F, Chen W, Dong P, et al. (2009) A simple strategy of probe DNA immobilization by diazotization-coupling on self-assembled 4-aminothiophenol for DNA electrochemical biosensor. Biosens Bioelectron 24: 2160-2164.    

66. Chen KI, Li BR, and Chen YT. (2011) Silicon nanowire field-effect transistor-based biosensors for biomedical diagnosis and cellular recording investigation. Nano Today 6: 131-154.    

67. Lin CH, Hung CH, Hsiao CY, et al. (2009) Poly-silicon nanowire field-effect transistor for ultrasensitive and label-free detection of pathogenic DNA. Biosens Bioelectron 24: 3019-3024.    

68. Rahman SFA, Yusofa NA, Hashim U, et al. (2016) Enhanced sensing of dengue virus DNA detection using O2 plasma treated-silicon nanowire based electrical biosensor. Anal Chim Acta 942: 74-85.    

69. Gao AR, Lu N, Dai PF, et al. (2011) Silicon-nanowire-based CMOS-compatible field-effect transistor nanosensors for ultrasensitive electrical detection of nucleic acids. Nano Lett 11: 3974-3978.    

70. Zhang GJ and Ning Y. (2012) Silicon nanowire biosensor and its applications in disease diagnostics: a review. Anal Chim Acta 749:1-15.    

71. Dell'Atti D, Zavaglia M, Tombelli S, et al. (2007) Development of combined DNA-based piezoelectric biosensors for the simultaneous detection and genotyping of high risk human papilloma virus strains. Clin Chim Acta 383: 140-146.    

72. Hao RZ, Songc HB, Zuo GM, et al. (2011) DNA probe functionalized QCM biosensor based on gold nanoparticle amplification for bacillus anthracis detection. Biosens Bioelectron 26: 3398-3404.    

73. Moa XT, Zhoub YP, Leia H, et al. (2002) Microbalance-DNA probe method for the detection of specific bacteria in water. Enz Microb Technol 30: 583-589.    

74. Skládal P, Dos SRC, Yamanaka H, et al. (2004) Piezoelectric biosensors for real-time monitoring of hybridization and detection of hepatitis C virus. J Virol Meth 117: 145-151.    

75. Vizzini P (2013) QCM technique optimization for detection of brettanomyces bruxellensis. personal communication. University of Udine, Udine, Italy.

76. Yo Y, Moreira BG, Behlke MA, et al. (2006) Design of LNA probes that improve mismatch discrimination. Nucl Ac Res 34: e60.    

77. Johnson MP, Haupt LM, and Griffths LR. (2004) Locked nucleic acid (LNA) single nucleotide polymorphism (SNP) genotype analysis and validation using real-time PCR. Nucl Ac Res 32: e55.    

78. Yoon JH, Nam JS, Kim KJ, et al. (2013) Simple and rapid discrimination of embB codon 306 mutations in mycobacterium tuberculosis clinical isolates by a real-time PCR assay using an LNA-TaqMan probe. J Microbiol Meth 92: 301-306.    

79. Priya NG, Pandey N, and Rajagopal R. (2012) LNA probes substantially improve the detection of bacterial endosymbionts in whole mount of insects by fluorescent in-situ hybridization. BMC Microbiol 24: 12-18.

80. Wang Q, Wang X, Zhang J, et al. (2012) LNA real-time PCR probe quantification of hepatitis B virus DNA. Exper Therap Medic 3: 503-508.

81. Nitecki SS, Teape N, Carney BF, et al. (2015) A duplex qPCR for the simultaneous detection of escherichia coli O157:H7 and listeria monocytogenes using LNA probes. Lett Appl Microbiol 61: 20-27.    

82. Priya NG, Pandey N, and Rajagopal R. (2012) LNA probes substantially improve the detection of bacterial endosymbionts in whole mount of insects by fluorescent in-situ hybridization. BMC Microbiol 12: 1-9.    

83. Rohdea A, Hammerla JA, Appela B, et al. (2017) Differential detection of pathogenic yersinia spp. by fluorescence in situ hybridization. Food Microbiol 62: 39-45.

84. Rohdea A, Hammerl JA, and Dahouk SA. (2016) Detection of foodborne bacterial zoonoses by fluorescence in situ hybridization. Food Control 69: 297-305.    

85. Fontenete S, Guimarães N, Leite M, et al. (2013) Hybridization-based detection of helicobacter pylori at human body temperature using advanced locked nucleic acid (LNA) Probes. Plos One 8: e81230.    

86. Santos RS, Guimarães N, Madureira P, et al. (2014) Peptide nucleic acids with a structurally biased backbone: effects of conformational constraints and stereochemistry. J Biotechnol 187: 16-24.    

87. Stone NRH, Gorton RL, Barker K, et al. (2013) Evaluation of PNA-fish yeast traffic light for rapid identification of yeast directly from positive blood Cultures and adminssessment of clinical impact. J Clin Microbiol 51: 1301-1302.    

88. Ahn JJ, Lee SY, Hong JY, et al. (2015) Application of fluorescence melting curve analysis for dual DNA detection using single peptide nucleic acid probe. Biotechnol Prog 31: 730-735.    

89. Vilaivan T (2015) Pyrrolidinyl PNA with α/β-dipeptide backbone: from development to applications. Acc Chem Res 48: 1645-1656.    

90. Teengam P, Siangproh W, Tuantranont A, et al. (2017) Electrochemical paper-based peptide nucleic acid biosensor for detecting human papillomavirus. Anal Chim Acta 952: 32-40.    

Copyright Info: © 2017, Marisa Manzano, et al., licensee AIMS Press. This is an open access article distributed under the terms of the Creative Commons Attribution Licese (http://creativecommons.org/licenses/by/4.0)

Download full text in PDF

Export Citation

Article outline

Show full outline
Copyright © AIMS Press All Rights Reserved