Probe Amplification Technologies

  • Fei Ye
  • Miao Cui
  • Tao Feng
  • Ivy Lee
  • Josephine Wu
  • Bingjiao Yin
  • David Zhang
Chapter

Abstract

Oligonucleotide probes provide a useful tool for the detection of target nucleic acids by the formation of a double-helical structure between complementary sequences. The stringent requirements of Watson–Crick base pairing make hybridization extremely specific. However, the detection of target sequence by hybridization is often insensitive due to the limited number of signal molecules that can be labeled on the probe. In general, the analytical sensitivity of probe hybridization is in the order of 106 molecules. Therefore, it cannot meet the needs of most clinical diagnostic applications. Many technologies have been developed to improve the detection sensitivity by amplifying the probe sequence bound to the target. All probe amplification technologies are developed based on the recent advancement in molecular biology and the understanding of in vivo nucleic acid synthesis, i.e., ligation, polymerization, transcription, digestion/cleavage, etc.

Keywords

Hepatitis Dust Tuberculosis Electrophoresis Polyacrylamide 

References

  1. 1.
    Nilsson M, Malmgren H, Samiotaki M, Kwiatkowski M, Chowdhary BP, Landegren U (1994) Padlock probes: circularizing oligonucleotides for localized DNA detection. Science 265:2085–2088PubMedCrossRefGoogle Scholar
  2. 2.
    Zhang DY, Brandwein M, Hsuih TC, Li H (1998) Amplification of target-specific, ligation-dependent circular probe. Gene 211:277–285PubMedCrossRefGoogle Scholar
  3. 3.
    Baner J, Nilsson M, Mendel-Hartvig M, Landegren U (1998) Signal amplification of padlock probes by rolling circle replication. Nucleic Acids Res 26:5073–5078PubMedCrossRefGoogle Scholar
  4. 4.
    Fire A, Xu SQ (1995) Rolling replication of short DNA circles. Proc Natl Acad Sci U S A 92:4641–4645PubMedCrossRefGoogle Scholar
  5. 5.
    Zhang DY, Zhang W, Li X, Konomi Y (2001) Detection of rare DNA targets by isothermal ramification amplification. Gene 274:209–216PubMedCrossRefGoogle Scholar
  6. 6.
    Murakami T, Sumaoka J, Komiyama M (2009) Sensitive isothermal detection of nucleic-acid sequence by primer generation-rolling circle amplification. Nucleic Acids Res 37:e19PubMedCrossRefGoogle Scholar
  7. 7.
    Nallur G, Luo C, Fang L et al (2001) Signal amplification by rolling circle amplification on DNA microarrays. Nucleic Acids Res 29:E118PubMedCrossRefGoogle Scholar
  8. 8.
    Mayer-Enthart E, Sialelli J, Rurack K, Resch-Genger U, Koster D, Seitz H (2008) Toward improved biochips based on rolling circle amplification – influences of the microenvironment on the fluorescence properties of labeled DNA oligonucleotides. Ann N Y Acad Sci 1130:287–292PubMedCrossRefGoogle Scholar
  9. 9.
    Schweitzer B, Wiltshire S, Lambert J et al (2000) Immunoassays with rolling circle DNA amplification: a versatile platform for ultrasensitive antigen detection. Proc Natl Acad Sci U S A 97:10113–10119PubMedCrossRefGoogle Scholar
  10. 10.
    Schweitzer B, Roberts S, Grimwade B et al (2002) Multiplexed protein profiling on microarrays by rolling-circle amplification. Nat Biotechnol 20:359–365PubMedCrossRefGoogle Scholar
  11. 11.
    Terletskaia-Ladwig E, Leinmuller M, Schneider F, Meier S, Enders M (2007) Laboratory approaches to the diagnosis of adenovirus infection depending on clinical manifestations. Infection 35:438–443PubMedCrossRefGoogle Scholar
  12. 12.
    Kobori T, Matsumoto A, Takahashi H, Sugiyama S (2009) Rolling circle amplification for signal enhancement in ovalbumin detection. Anal Sci 25:1381–1383PubMedCrossRefGoogle Scholar
  13. 13.
    Kim TE, Park SW, Cho NY et al (2002) Quantitative measurement of serum allergen-specific IgE on protein chip. Exp Mol Med 34:152–158PubMedGoogle Scholar
  14. 14.
    Wiltshire S, O’Malley S, Lambert J et al (2000) Detection of multiple allergen-specific IgEs on microarrays by immunoassay with rolling circle amplification. Clin Chem 46:1990–1993PubMedGoogle Scholar
  15. 15.
    Zhang DY, Brandwein M, Hsuih T, Li HB (2001) Ramification amplification: a novel isothermal DNA amplification method. Mol Diagn 6:141–150PubMedCrossRefGoogle Scholar
  16. 16.
    Lizardi PM, Huang X, Zhu Z, Bray-Ward P, Thomas DC, Ward DC (1998) Mutation detection and single-molecule counting using isothermal rolling-circle amplification. Nat Genet 19:225–232PubMedCrossRefGoogle Scholar
  17. 17.
    Thomas DC, Nardone GA, Randall SK (1999) Amplification of padlock probes for DNA diagnostics by cascade rolling circle amplification or the polymerase chain reaction. Arch Pathol Lab Med 123:1170–1176PubMedGoogle Scholar
  18. 18.
    Zhang W, Cohenford M, Lentrichia B et al (2002) Detection of Chlamydia trachomatis by isothermal ramification amplification method: a feasibility study. J Clin Microbiol 40:128–132PubMedCrossRefGoogle Scholar
  19. 19.
    Yi J, Zhang W, Zhang DY (2006) Molecular Zipper: a fluorescent probe for real-time isothermal DNA amplification. Nucleic Acids Res 34:e81PubMedCrossRefGoogle Scholar
  20. 20.
    Li F, Zhao C, Zhang W et al (2005) Use of ramification amplification assay for detection of Escherichia coli O157:H7 and other E. coli Shiga toxin-producing strains. J Clin Microbiol 43:6086–6090PubMedCrossRefGoogle Scholar
  21. 21.
    Rector A, Tachezy R, Van Ranst M (2004) A sequence-independent strategy for detection and cloning of circular DNA virus genomes by using multiply primed rolling-circle amplification. J Virol 78:4993–4998PubMedCrossRefGoogle Scholar
  22. 22.
    Burtt NP (2011) Whole-genome amplification using Phi29 DNA polymerase. Cold Spring Harb Protoc 2011(1):pdb.prot5552PubMedCrossRefGoogle Scholar
  23. 23.
    Wharam SD, Marsh P, Lloyd JS et al (2001) Specific detection of DNA and RNA targets using a novel isothermal nucleic acid amplification assay based on the formation of a three-way junction structure. Nucleic Acids Res 29:E54-4PubMedCrossRefGoogle Scholar
  24. 24.
    Hall MJ, Wharam SD, Weston A, Cardy DL, Wilson WH (2002) Use of signal-mediated amplification of RNA technology (SMART) to detect marine cyanophage DNA. BioTechniques 32:604–606, 608–611Google Scholar
  25. 25.
    Wharam SD, Hall MJ, Wilson WH (2007) Detection of virus mRNA within infected host cells using an isothermal nucleic acid amplification assay: marine cyanophage gene expression within Synechococcus sp. Virol J 4:52PubMedCrossRefGoogle Scholar
  26. 26.
    Levi K, Bailey C, Bennett A, Marsh P, Cardy DL, Towner KJ (2003) Evaluation of an isothermal signal amplification method for rapid detection of methicillin-resistant Staphylococcus aureus from patient-screening swabs. J Clin Microbiol 41:3187–3191PubMedCrossRefGoogle Scholar
  27. 27.
    Lyamichev VI, Kaiser MW, Lyamicheva NE et al (2000) Experimental and theoretical analysis of the invasive signal amplification reaction. Biochemistry 39:9523–9532PubMedCrossRefGoogle Scholar
  28. 28.
    Wong DK, Yuen MF, Yuan H et al (2004) Quantitation of covalently closed circular hepatitis B virus DNA in chronic hepatitis B patients. Hepatology 40:727–737PubMedCrossRefGoogle Scholar
  29. 29.
    Kurtycz DF, Smith M, He R, Miyazaki K, Shalkham J (2010) Comparison of methods trial for high-risk HPV. Diagn Cytopathol 38:104–108PubMedGoogle Scholar
  30. 30.
    Stillman MJ, Day SP, Schutzbank TE (2009) A comparative review of laboratory-developed tests utilizing Invader HPV analyte-specific reagents for the detection of high-risk human papillomavirus. J Clin Virol 45(Suppl 1):S73–S77PubMedCrossRefGoogle Scholar
  31. 31.
    Cooksey RC, Holloway BP, Oldenburg MC, Listenbee S, Miller CW (2000) Evaluation of the invader assay, a linear signal amplification method, for identification of mutations associated with resistance to rifampin and isoniazid in Mycobacterium tuberculosis. Antimicrob Agents Chemother 44:1296–1301PubMedCrossRefGoogle Scholar
  32. 32.
    Deloukas P, Bentley D (2004) The HapMap project and its application to genetic studies of drug response. Pharmacogenomics J 4:88–90PubMedCrossRefGoogle Scholar
  33. 33.
    Schouten JP, McElgunn CJ, Waaijer R, Zwijnenburg D, Diepvens F, Pals G (2002) Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification. Nucleic Acids Res 30:e57PubMedCrossRefGoogle Scholar
  34. 34.
    Park YN, Abe K, Li H, Hsuih T, Thung SN, Zhang DY (1996) Detection of hepatitis C virus RNA using ligation-dependent polymerase chain reaction in formalin-fixed, paraffin-embedded liver tissues. Am J Pathol 149:1485–1491PubMedGoogle Scholar
  35. 35.
    Wu W, Tang YW (2009) Emerging molecular assays for detection and characterization of respiratory viruses. Clin Lab Med 29:673–693PubMedCrossRefGoogle Scholar
  36. 36.
    Bourdeaut F, Lequin D, Brugieres L et al (2011) Frequent hSNF5/INI1 germline mutations in patients with rhabdoid tumor. Clin Cancer Res 17:31–38PubMedCrossRefGoogle Scholar
  37. 37.
    Pristauz G, Petru E, Stacher E et al (2010) Androgen receptor expression in breast cancer patients tested for BRCA1 and BRCA2 mutations. Histopathology 57:877–884PubMedCrossRefGoogle Scholar
  38. 38.
    Damato B, Dopierala JA, Coupland SE (2010) Genotypic profiling of 452 choroidal melanomas with multiplex ligation-dependent probe amplification. Clin Cancer Res 16:6083–6092PubMedCrossRefGoogle Scholar
  39. 39.
    Bergval IL, Vijzelaar RN (2008) Dalla Costa ER, et al. Development of multiplex assay for rapid characterization of Mycobacterium tuberculosis. J Clin Microbiol 46:689–699PubMedCrossRefGoogle Scholar
  40. 40.
    Terefework Z, Pham CL, Prosperi AC et al (2008) MLPA diagnostics of complex microbial communities: relative quantification of bacterial species in oral biofilms. J Microbiol Methods 75:558–565PubMedCrossRefGoogle Scholar
  41. 41.
    Reijans M, Dingemans G, Klaassen CH et al (2008) RespiFinder: a new multiparameter test to differentially identify fifteen respiratory viruses. J Clin Microbiol 46:1232–1240PubMedCrossRefGoogle Scholar
  42. 42.
    Bekkaoui F, Poisson I, Crosby W, Cloney L, Duck P (1996) Cycling probe technology with RNase H attached to an oligonucleotide. Biotechniques 20:240–248PubMedGoogle Scholar
  43. 43.
    Dickinson Laing T, Mah DC, Poirier RT, Bekkaoui F, Lee WE, Bader DE (2004) Genomic DNA detection using cycling probe technology and capillary gel electrophoresis with laser-induced fluorescence. Mol Cell Probes 18:341–348PubMedCrossRefGoogle Scholar
  44. 44.
    Modrusan Z, Bekkaoui F, Duck P (1998) Spermine-mediated improvement of cycling probe reaction. Mol Cell Probes 12:107–116PubMedCrossRefGoogle Scholar
  45. 45.
    Fong WK, Modrusan Z, McNevin JP, Marostenmaki J, Zin B, Bekkaoui F (2000) Rapid solid-phase immunoassay for detection of methicillin-resistant Staphylococcus aureus using cycling probe technology. J Clin Microbiol 38:2525–2529PubMedGoogle Scholar
  46. 46.
    Jung C, Chung JW, Kim UO, Kim MH, Park HG (2010) Isothermal target and signaling probe amplification method, based on a combination of an isothermal chain amplification technique and a fluorescence resonance energy transfer cycling probe technology. Anal Chem 82:5937–5943PubMedCrossRefGoogle Scholar
  47. 47.
    Chu BC, Kramer FR, Orgel LE (1986) Synthesis of an amplifiable reporter RNA for bioassays. Nucleic Acids Res 14:5591–5603PubMedCrossRefGoogle Scholar
  48. 48.
    Gronowski AM, Copper S, Baorto D, Murray PR (2000) Reproducibility problems with the Abbott laboratories LCx assay for Chlamydia trachomatis and Neisseria gonorrhoeae. J Clin Microbiol 38:2416–2418PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  • Fei Ye
    • 1
  • Miao Cui
    • 1
  • Tao Feng
    • 1
  • Ivy Lee
    • 1
  • Josephine Wu
    • 1
  • Bingjiao Yin
    • 1
  • David Zhang
    • 1
  1. 1.Molecular Pathology Laboratory, Department of Pathology, Mount Sinai School of MedicineNew York UniversityNew YorkUSA

Personalised recommendations