Advertisement

Springer Nature is making SARS-CoV-2 and COVID-19 research free. View research | View latest news | Sign up for updates

Nucleic acid tool enzymes-aided signal amplification strategy for biochemical analysis: status and challenges

Abstract

Owing to their highly efficient catalytic effects and substrate specificity, the nucleic acid tool enzymes are applied as ‘nano-tools’ for manipulating different nucleic acid substrates both in the test-tube and in living organisms. In addition to the function as molecular scissors and molecular glue in genetic engineering, the application of nucleic acid tool enzymes in biochemical analysis has also been extensively developed in the past few decades. Used as amplifying labels for biorecognition events, the nucleic acid tool enzymes are mainly applied in nucleic acids amplification sensing, as well as the amplification sensing of biorelated variations of nucleic acids. With the introduction of aptamers, which can bind different target molecules, the nucleic acid tool enzymes-aided signal amplification strategies can also be used to sense non-nucleic targets (e.g., ions, small molecules, proteins, and cells). This review describes and discusses the amplification strategies of nucleic acid tool enzymes-aided biosensors for biochemical analysis applications. Various analytes, including nucleic acids, ions, small molecules, proteins, and cells, are reviewed briefly. This work also addresses the future trends and outlooks for signal amplification in nucleic acid tool enzymes-aided biosensors.

Nucleic acid tool enzymes-aided signal amplification sensing

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

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9
Fig. 10
Fig. 11
Fig. 12

References

  1. 1.

    Berdis AJ. Mechanisms of DNA polymerases. Chem Rev. 2009;109:2862–79.

  2. 2.

    Barany F. Genetic disease detection and DNA amplification using cloned thermostable ligase. Proc Natl Acad Sci U S A. 1991;88:189–93.

  3. 3.

    Rhyu MS. Telomeres, telomerase, and immortality. J Natl Cancer Inst. 1995;87:884–94.

  4. 4.

    Roberts RJ, Murray K. Restriction endonuclease. Crit Rev Biochem Mol. 1976;4:123–64.

  5. 5.

    Zheleznaya LA, Kachalova GS, Artyukh RI, Yunusova AK, Perevyazova TA, Matvienko NI. Nicking endonucleases. Biochemistry. 2009;74:1457–66.

  6. 6.

    Shagin DA, Rebrikov DV, Kozhemyako VB, Altshuler IM, Shcheglov AS, Zhulidov PA, et al. A novel method for SNP detection using a new duplex-specific nuclease from crab hepatopancreas. Genome Res. 2002;12:1935–42.

  7. 7.

    Lee JE, Frank BC, Cooper TA. RNase H-mediated degradation of toxic RNA in myotonic dystrophy type 1. Proc Natl Acad Sci U S A. 2012;109:4221–6.

  8. 8.

    Sayers JR, Schmidt W, Eckstein F. 5′-3′ Exonucleases in phosphorothioate-based oligonucleotide-directed mutagenesis. Nucleic Acids Res. 1988;16:791–802.

  9. 9.

    Shevelev IV, Hübscher U. The 3′-5′ Exonucleases. Nat Rev Mol Cell Biol. 2002;3:364–76.

  10. 10.

    Zhang H, Wang S, Fang G. Applications and recent developments of multi-analyte simultaneous analysis by enzyme-linked immunosorbent assays. J Immunol Methods. 2011;368:1–23.

  11. 11.

    Haab BB. Applications of antibody array platforms. Trends Biotechnol. 2006;17:415–21.

  12. 12.

    Niemeyer CM, Adler MR. Immuno-PCR: high sensitivity detection of proteins by nucleic acid amplification. Trends Biotechnol. 2005;23:208–16.

  13. 13.

    Chiang CK, Chen WT, Chang HT. Nanoparticle-based mass spectrometry for the analysis of biomolecules. Chem Soc Rev. 2011;40:1269–81.

  14. 14.

    Lei JP, Ju HX. Signal amplification using functional nanomaterials for biosensing. Chem Soc Rev. 2012;41:2122–34.

  15. 15.

    Taniguchi K, Kajiyama T, Kambara H. Quantitative analysis of gene expression in a single cell by qPCR. Nat Methods. 2009;6:503–6.

  16. 16.

    Miao P, Tang Y, Wang B, Yin J, Ning L. Signal amplification by enzymatic tools for nucleic acids. TrAC Trends Anal Chem. 2015;67:1–15.

  17. 17.

    Gerasimova YV, Kolpashchikov DM. Enzyme-assisted target recycling (EATR) for nucleic acid detection. Chem Soc Rev. 2014;43:6405–38.

  18. 18.

    Willner I, Shlyahovsky B, Zayats M, Willner B. DNAzymes for sensing, nanobiotechnology and logic gate applications. Chem Soc Rev. 2008;37:1153–65.

  19. 19.

    Scharf P, Müller J. Nucleic acids with metal-mediated base pairs and their applications. ChemPlusChem. 2013;78:20–34.

  20. 20.

    Hamula CLA, Guthrie JW, Zhang HQ, Li XF, Le CX. Selection and analytical applications of aptamers. TrAC Trends Anal Chem. 2006;25:681–91.

  21. 21.

    Cho EJ, Lee JW, Ellington AD. Applications of aptamers as sensors. Annu Rev Anal Chem. 2009;2:241–64.

  22. 22.

    Lubin AA, Plaxco KW. Folding-based electrochemical biosensors: the case for responsive nucleic acid architectures. Acc Chem Res. 2010;43:496–505.

  23. 23.

    Li D, Song SP, Fan CH. Target-responsive structural switching for nucleic acid-based sensors. Acc Chem Res. 2010;43:631–41.

  24. 24.

    Wang F, Elbaz J, Orbach R, Magen N, Willner I. Amplified analysis of DNA by the autonomous assembly of polymers consisting of DNAzyme wires. J Am Chem Soc. 2011;133:17149–51.

  25. 25.

    Andras SC, Power JB, Cocking EC, Davey MR. Strategies for signal amplification in nucleic acid detection. Mol Biotechnol. 2001;19:29–44.

  26. 26.

    Lie YS, Petropoulos CJ. Advances in quantitative PCR technology: 5′ nuclease assays. Curr Opin Biotechnol. 1998;9:43–8.

  27. 27.

    Wassenegger M. Advantages and disadvantages of using PCR techniques to characterize transgenic plants. Mol Biotechnol. 2001;17:73–82.

  28. 28.

    Saghatelian A, Guckian KM, Thayer DA, Thayer DA, Ghadiri MR. DNA detection and signal amplification via an engineered allosteric enzyme. J Am Chem Soc. 2003;125:344–5.

  29. 29.

    Liu J, Lu Y. Accelerated color change of gold nanoparticles assembled by DNAzymes for simple and fast colorimetric Pb2+ detection. J Am Chem Soc. 2004;126:12298–305.

  30. 30.

    Guo X, Liu P, Yang X, Wang K, Wang Q, Guo Q, et al. A multiple amplification strategy for nucleic acid detection based on host-guest interaction between the β-cyclodextrin polymer and pyrene. Analyst. 2015;140:2016–22.

  31. 31.

    Wu L, Xiong E, Zhang X, Zhang X, Chen J. Nanomaterials as signal amplification elements in DNA-based electrochemical sensing. Nano Today. 2014;9:197–211.

  32. 32.

    Wang J, Liu G, Jan MR. Ultrasensitive electrical biosensing of proteins and DNA: carbon-nanotube derived amplification of the recognition and transduction events. J Am Chem Soc. 2004;126:3010–1.

  33. 33.

    Wang J. Carbon-nanotube based electrochemical biosensors: a review. Electroanalysis. 2005;17:7–14.

  34. 34.

    Tian Y, Mao C. DNAzyme amplification of molecular beacon signal. Talanta. 2005;67:532–7.

  35. 35.

    Weizmann Y, Patolsky F, Katz E, Willner I. Amplified DNA sensing and immunosensing by the rotation of functional magnetic particles. J Am Chem Soc. 2003;125:3452–4.

  36. 36.

    Lu J, Paulsen IT, Jin D. Application of exonuclease III-aided target recycling in flow cytometry: DNA detection sensitivity enhanced by orders of magnitude. Anal Chem. 2013;85:8240–5.

  37. 37.

    Xu W, Xue X, Li T, Zeng H, Liu X. Ultrasensitive and selective colorimetric DNA detection by nicking endonuclease assisted nanoparticle amplification. Angew Chem Int Ed. 2009;48:6849–52.

  38. 38.

    Bi S, Li L, Cui Y. Exonuclease-assisted cascaded recycling amplification for label-free detection of DNA. Chem Commun. 2012;48:1018–20.

  39. 39.

    Xu W, Xie X, Li D, Yang Z, Li T, Liu X. Ultrasensitive colorimetric DNA detection using a combination of rolling circle amplification and nicking endonuclease-assisted nanoparticle amplification (NEANA). Small. 2012;8:1846–50.

  40. 40.

    Shen W, Deng H, Gao Z. Gold nanoparticle-enabled real-time ligation chain reaction for ultrasensitive detection of DNA. J Am Chem Soc. 2012;134:14678–81.

  41. 41.

    Xing Y, Wang P, Zang Y, Ge Y, Jin Q, Zhao J, et al. A colorimetric method for H1N1 DNA detection using rolling circle amplification. Analyst. 2013;138:3457–62.

  42. 42.

    Li JJ, Chu Y, Lee BYH, Xie XS. Enzymatic signal amplification of molecular beacons for sensitive DNA detection. Nucleic Acids Res. 2008;36:e36.

  43. 43.

    Zou B, Ma Y, Wu H, Zhou G. Ultrasensitive DNA detection by cascade enzymatic signal amplification based on Afu flap endonuclease coupled with nicking endonuclease. Angew Chem Int Ed. 2011;50:7395–8.

  44. 44.

    Gao F, Lei J, Ju H. Assistant DNA recycling with nicking endonuclease and molecular beacon for signal amplification using a target-complementary arched structure. Chem Commun. 2013;49:4006–8.

  45. 45.

    Wang HB, Ou LJ, Huang KJ, Wen XG, Wang LL, Liu YM. A sensitive biosensing strategy for DNA detection based on graphene oxide and T7 exonuclease assisted target recycling amplification. Can J Chem. 2013;91:1266–71.

  46. 46.

    Liu L, Lei J, Gao F, Ju H. A DNA machine for sensitive and homogeneous DNA detection via lambda exonuclease assisted amplification. Talanta. 2013;115:819–22.

  47. 47.

    Zuo X, Xia F, Xiao Y, Plaxco KW. Sensitive and selective amplified fluorescence DNA detection based on exonuclease III-aided target recycling. J Am Chem Soc. 2010;132:1816–8.

  48. 48.

    Yang CJ, Liang C, Huang J, Ling Y, Lin X, Wang C, et al. Linear molecular beacons for highly sensitive bioanalysis based on cyclic Exo III enzymatic amplification. Biosens Bioelectron. 2011;27:119–24.

  49. 49.

    Zhang M, Guan YM, Ye BC. Ultrasensitive fluorescence polarization DNA detection by target assisted exonuclease III-catalyzed signal amplification. Chem Commun. 2011;47:3478–80.

  50. 50.

    Cai Z, Chen Y, Lin C, Wu Y, Yang CJ, Wang Y, et al. A dual-signal amplification method for the dna detection based on exonuclease III. Biosens Bioelectron. 2014;61:370–3.

  51. 51.

    Zhou F, Li B. Exonuclease III-assisted target recycling amplification coupled with liposome-assisted amplification: one-step and dual-amplification strategy for highly sensitive fluorescence detection of DNA. Anal Chem. 2015;87:7156–62.

  52. 52.

    Wang Q, Yang L, Yang X, Wang K, He L, Zhu J, et al. An electrochemical DNA biosensor based on the “Y” junction structure and restriction endonuclease-aided target recycling strategy. Chem Commun. 2012;48:2982–4.

  53. 53.

    Ji H, Yan F, Lei J, Ju H. Ultrasensitive electrochemical detection of nucleic acids by template enhanced hybridization followed with rolling circle amplification. Anal Chem. 2012;84:7166–71.

  54. 54.

    Liu S, Wang C, Zhang C, Wang Y, Tang B. Label-free and ultrasensitive electrochemical detection of nucleic acids based on autocatalytic and exonuclease III-assisted target recycling strategy. Anal Chem. 2013;85:2282–8.

  55. 55.

    Liu S, Lin Y, Wang L, Liu T, Cheng C, Wei W, et al. Exonuclease III-aided autocatalytic DNA biosensing platform for immobilization-free and ultrasensitive electrochemical detection of nucleic acid and protein. Anal Chem. 2014;86:4008–15.

  56. 56.

    Tao C, Yan Y, Xiang H, Zhu D, Cheng W, Ju H, et al. A new mode for highly sensitive and specific detection of DNA based on exonuclease III-assisted target recycling amplification and mismatched catalytic hairpin assembly. Chem Commun. 2015;51:4220–2.

  57. 57.

    Xiong E, Zhang X, Liu Y, Zhou J, Yu P, Li X, et al. Ultrasensitive electrochemical detection of nucleic acids based on the dual-signaling electrochemical ratiometric method and exonuclease III-assisted target recycling amplification strategy. Anal Chem. 2015;87:7291–6.

  58. 58.

    Xia F, Zuo X, Yang R, Xiao Y, Kang D, Vallée-Bélisle A, et al. Colorimetric detection of DNA, small molecules, proteins, and ions using unmodified gold nanoparticles and conjugated polyelectrolytes. Proc Natl Acad Sci U S A. 2010;107:10837–41.

  59. 59.

    Lodeiro C, Capelo JL, Mejuto JC, Oliveira E, Santos HM, Pedras B, et al. Light and colour as analytical detection tools: a journey into the periodic table using polyamines to bio-inspired systems as chemosensors. Chem Soc Rev. 2010;39:2948–76.

  60. 60.

    Tansil NC, Gao Z. Nanoparticles in biomolecular detection. Nano Today. 2006;1:28–37.

  61. 61.

    Rosi NL, Mirkin CA. Nanostructures in biodiagnostics. Chem Rev. 2005;105:1547–62.

  62. 62.

    Link S, El-Sayed MA. Spectral properties and relaxation dynamics of surface plasmon electronic oscillations in gold and silver nanodots and nanorods. J Phys Chem B. 1999;103:8410–26.

  63. 63.

    Yang Z, Sismour AM, Benner SA. Nucleoside alpha-thiotriphosphates, polymerases, and the exonuclease III analysis of oligonucleotides containing phosphorothioate linkages. Nucleic Acids Res. 2007;35:3118–27.

  64. 64.

    Ronkainen NJ, Halsall HB, Heineman WR. Electrochemical biosensors. Chem Soc Rev. 2010;39:1747–63.

  65. 65.

    Chang BY, Park SM. Electrochemical impedance spectroscopy. Annu Rev Anal Chem. 2010;3:207–29.

  66. 66.

    Wu D, Yin BC, Ye BC. A label-free electrochemical DNA sensor based on exonuclease III-aided target recycling strategy for sequence-specific detection of femtomolar DNA. Biosens Bioelectron. 2011;28:232–8.

  67. 67.

    Yu P, Zhou J, Wu L, Xiong E, Zhang X, Chen J. A ratiometric electrochemical aptasensor for sensitive detection of protein based on aptamer-target-aptamer sandwich structure. J Electroanal Chem. 2014;732:61–5.

  68. 68.

    Yan D, Byung Joon L, Bingling L, Yu Sherry J, Sessler JL, Ellington AD. Reagentless ratiometric electrochemical DNA sensors with improved robustness and reproducibility. Anal Chem. 2014;86:8010–6.

  69. 69.

    He L, Hannon GJ. MicroRNAs: small RNAs with a big role in gene regulation. Nat Rev Genet. 2004;5:22–531.

  70. 70.

    Sawyers CL. The cancer biomarker problem. Nature. 2008;452:548–52.

  71. 71.

    Tricoli JV, Jacobson JW. MicroRNA: potential for cancer detection, diagnosis, and prognosis. Cancer Res. 2007;67:4553–5.

  72. 72.

    Mitchell PS, Parkin RK, Kroh EM, Fritz BR, Wyman SK, Pogosova-Agadjanyan EL, et al. Circulating microRNAs as stable blood-based markers for cancer detection. Proc Natl Acad Sci U S A. 2008;105:10513–8.

  73. 73.

    Cissell KA, Shrestha S, Deo SK. MicroRNA detection: challenges for the analytical chemist. Anal Chem. 2007;79:4754–61.

  74. 74.

    Válóczi A, Hornyik C, Varga N, Burgyán J, Kauppinen S, Havelda Z. Sensitive and specific detection of microRNAs by northern blot analysis using LNA-modified oligonucleotide probes. Nucleic Acids Res. 2004;32:e175.

  75. 75.

    Lee I, Ajay SS, Chen H, Maruyama A, Wang N, McInnis MG, et al. Discriminating single-base difference miRNA expressions using microarray Probe Design Guru (ProDeG). Nucleic Acids Res. 2008;36:e27.

  76. 76.

    Fang S, Lee HJ, Wark AW, Corn RM. Attomole microarray detection of microRNAs by nanoparticle-amplified SPR imaging measurements of surface polyadenylation reactions. J Am Chem Soc. 2006;128:14044–6.

  77. 77.

    Qiu X, Zhang H, Yu H, Jiang T, Luo Y. Duplex-specific nuclease-mediated bioanalysis. Trends Biotechnol. 2015;33:180–8.

  78. 78.

    Xu F, Shi H, He X, Wang K, He D, Guo Q, et al. Concatemeric dsDNA-templated copper nanoparticles strategy with improved sensitivity and stability based on rolling circle replication and its application in microRNA detection. Anal Chem. 2014;86:6976–82.

  79. 79.

    Yin BC, Liu YQ, Ye BC. Sensitive detection of microRNA in complex biological samples via enzymatic signal amplification using DNA polymerase coupled with nicking endonuclease. Anal Chem. 2013;85:11487–93.

  80. 80.

    Ge J, Zhang LL, Liu SJ, Yu RQ, Chu X. A highly sensitive target-primed rolling circle amplification (TPRCA) method for fluorescent in situ hybridization detection of microRNA in tumor cells. Anal Chem. 2014;86:1808–15.

  81. 81.

    Duan R, Zuo X, Wang S, Quan X, Chen D, Chen Z, et al. Quadratic isothermal amplification for the detection of microRNA. Nat Protoc. 2014;9:597–607.

  82. 82.

    Guo X, Yang X, Liu P, Wang K, Wang Q, Guo Q, et al. Multiple amplification detection of microRNA based on the host–guest interaction between β-cyclodextrin polymer and pyrene. Analyst. 2015;140:4291–7.

  83. 83.

    Yin BC, Liu YQ, Ye BC. One-step multiplexed fluorescence detection of microRNAs based on duplex-specific nuclease signal amplification. J Am Chem Soc. 2012;134:5064–7.

  84. 84.

    Lin X, Zhang C, Huang Y, Zhu Z, Chen X, Yang C. Backbone-modified molecular beacons for highly sensitive and selective detection of microRNAs based on duplex specific nuclease signal amplification. Chem Commun. 2013;49:7243–5.

  85. 85.

    Cui L, Zhu Z, Lin N, Zhang H, Guan Z, Yang C. A T7 exonuclease-assisted cyclic enzymatic amplification method coupled with rolling circle amplification: a dual-amplification strategy for sensitive and selective microRNA detection. Chem Commun. 2014;13:1576–8.

  86. 86.

    Xie Y, Lin X, Huang Y, Pan R, Zhu Z, Zhou L, et al. Highly sensitive and selective detection of miRNA: DNase I-assisted target recycling using DNA probes protected by polydopamine nanospheres. Chem Commun. 2015;51:2156–8.

  87. 87.

    Ching ADA, Caldwell KS, Jung M, Dolan M, Smith OS, Tingey S, et al. SNP frequency, haplotype structure, and linkage disequilibrium in elite maize inbred line. BMC Genet. 2002;3:19–33.

  88. 88.

    Mehta AM, Jordanova ES, Corver WE, van Wezel T, Uh HW, Kenter GG, et al. Single nucleotide polymorphisms in antigen processing machinery component ERAP1 significantly associate with clinical outcome in cervical carcinoma. Genes Chromosom Cancer. 2009;48:410–8.

  89. 89.

    Nam RK, Zhang WW, Trachtenberg J, Seth A, Klotz LH, Stanimirovic A, et al. Utility of incorporating genetic variants for the early detection of prostate cancer. Clin Cancer Res. 2009;15:1787–93.

  90. 90.

    Lichtenstein A, Willner I. Detection of single-base DNA mutations by enzyme-amplified electronic transduction. Nat Biotechnol. 2001;19:253–7.

  91. 91.

    Wei W, Ni Q, Pu Y, Yin L, Liu S. Electrochemical biosensor for DNA damage detection based on exonuclease III digestions. J Electroanal Chem. 2014;714:25–9.

  92. 92.

    Wu T, Xiao X, Zhang Z, Zhao M. Enzyme-mediated single-nucleotide variation detection at room temperature with high discrimination factor. Chem Sci. 2015;6:1206–11.

  93. 93.

    Zou Z, Qing Z, He X, Wang K, He D, Shi H, et al. Ligation-rolling circle amplification combined with γ-cyclodextrin mediated stemless molecular beacon for sensitive and specific genotyping of single-nucleotide polymorphism. Talanta. 2014;125:306–12.

  94. 94.

    Liu M, Yuan M, Lou X, Mao H, Zheng D, Zou R, et al. Label-free optical detection of single-base mismatches by the combination of nuclease and gold nanoparticles. Biosens Bioelectron. 2011;26:4294–300.

  95. 95.

    Till BJ, Burtner C, Comai L, Henikoff S. Mismatch cleavage by single-strand specific nucleases. Nucleic Acids Res. 2004;32:2632–41.

  96. 96.

    Wu S, Liang P, Yu H, Xu X, Liu Y, Lou X, et al. Amplified single base-pair mismatch detection via aggregation of exonuclease-sheared gold nanoparticles. Anal Chem. 2014;86:3461–7.

  97. 97.

    Reik W, Walter J. Genomic imprinting: parental influence on the genome. Nat Rev Genet. 2001;2:21–32.

  98. 98.

    Okano M, Bell DW, Haber DA, Li E. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell. 1999;99:247–57.

  99. 99.

    Palmer BR, Marinus MG. The DAM and DCM strains of Escherichia coli—a review. Gene. 1994;143:1–12.

  100. 100.

    Robertson KD, Wolffe AP. DNA methylation in health and disease. Nat Rev Genet. 2000;1:11–9.

  101. 101.

    Laird PW, Jaenisch R. The role of DNA methylation in cancer genetics and epigenetics. Annu Rev Genet. 1996;30:441–64.

  102. 102.

    McCabe MT, Low JA, Daignault S, Imperiale MJ, Wojno KJ, Day ML. Inhibition of DNA methyltransferase activity prevents tumorigenesis in a mouse model of prostate cancer. Cancer Res. 2006;66:385–92.

  103. 103.

    Kurita R, Niwa O. DNA methylation analysis triggered by bulge specific immuno-recognition. Anal Chem. 2012;84:7533–8.

  104. 104.

    Ma L, Su M, Li T, Wang Z. Microarray-based resonance light scattering assay for detecting DNA methylation and human DNA methyltransferase simultaneously with high sensitivity. Analyst. 2014;139:3537–40.

  105. 105.

    Ehrich M, Zoll S, Sur S, Van Den Boom D. A new method for accurate assessment of DNA quality after bisulfite treatment. Nucleic Acids Res. 2007;35:e29.

  106. 106.

    Wang Y, Wee EJH, Trau M. Highly sensitive DNA methylation analysis at CpG resolution by surface-enhanced raman scattering via ligase chain reaction (LCR). Chem Commun. 2015;51:10953–6.

  107. 107.

    Hong T, Wang T, He Z, Ma J, Xiao H, Huang J, et al. Qualitative and quantitative detection of methylation at CpG sites using the fluorescein-dGTP incorporated asymmetric PCR assay strategy. Chem Commun. 2014;50:6653–5.

  108. 108.

    Gao C, Li H, Liu Y, Wei W, Zhang Y, Liu S. Label-free fluorescence detection of DNA methylation and methyltransferase activity based on restriction endonuclease Hpa II and exonuclease III. Analyst. 2014;139:6387–92.

  109. 109.

    Zhu G, Yang K, Zhang C. Sensitive detection of methylated DNA using the short linear quencher–fluorophore probe and two-stage isothermal amplification assay. Biosens Bioelectron. 2013;49:170–5.

  110. 110.

    Su F, Wang L, Sun Y, Liu C, Duan X, Li Z. Highly sensitive detection of CpG methylation in genomic DNA by AuNP-based colorimetric assay with ligase chain reaction. Chem Commun. 2015;51:3371–4.

  111. 111.

    Li W, Wu P, Zhang H, Cai C. Signal amplification of graphene oxide combining with restriction endonuclease for site-specific determination of DNA methylation and assay of methyltransferase activity. Anal Chem. 2012;84:7583–90.

  112. 112.

    Zhang H, Li M, Fan M, Gu J, Wu P, Cai C. Electrochemiluminescence signal amplification combined with a conformation-switched hairpin DNA probe for determining the methylation level and position in the Hsp53 tumor suppressor gene. Chem Commun. 2014;50:2932–4.

  113. 113.

    Mutze K, Langer R, Schumacher F, Becker K, Ott K, Novotny A, et al. DNA methyltransferase 1 as a predictive biomarker and potential therapeutic target for chemotherapy in gastric cancer. Eur J Cancer. 2011;47:1817–25.

  114. 114.

    Zhu C, Wen Y, Peng H, Long Y, He Y, Huang Q, et al. A methylation-stimulated DNA machine: an autonomous isothermal route to methyltransferase activity and inhibition analysis. Anal Bioanal Chem. 2011;399:3459–64.

  115. 115.

    Liu P, Yang XH, Wang Q, Huang J, Liu JB, Zhu Y, et al. Sensitive detection of DNA methyltransferase activity based on rolling circle amplification technology. Chin Chem Lett. 2014;25:1047–51.

  116. 116.

    Zeng Y, Hu J, Long Y, Zhang CY. Sensitive detection of DNA methyltransferase using hairpin probe-based primer generation rolling circle amplification-induced chemiluminescence. Anal Chem. 2013;85:6143–50.

  117. 117.

    Xue Q, Lv Y, Xu S, Zhang Y, Wang L, Li R, et al. Highly sensitive fluorescence assay of DNA methyltransferase activity by methylation-sensitive cleavage-based primer generation exponential isothermal amplification-induced G-quadruplex formation. Biosens Bioelectron. 2015;66:547–53.

  118. 118.

    Xue Q, Wang L, Jiang W. Label-free molecular beacon-based quadratic isothermal exponential amplification: a simple and sensitive one-pot method to detect DNA methyltransferase activity. Chem Commun. 2015;51:13538–41.

  119. 119.

    He X, Su J, Wang Y, Wang K, Ni X, Chen Z. A sensitive signal-on electrochemical assay for MTase activity using AuNPs amplification. Biosens Bioelectron. 2011;28:298–303.

  120. 120.

    Su J, He X, Wang Y, Wang K, Chen Z, Yan G. A sensitive signal-on assay for MTase activity based on methylation-responsive hairpin-capture DNA probe. Biosens Bioelectron. 2012;36:123–8.

  121. 121.

    Wang Y, He X, Wang K, Su J, Chen Z, Yan G, et al. A label-free electrochemical assay for methyltransferase activity detection based on the controllable assembly of single wall carbon nanotubes. Biosens Bioelectron. 2013;41:238–43.

  122. 122.

    Zhang Y, Xu W, Zeng Y, Zhang C. Sensitive detection of DNA methyltransferase activity by transcription-mediated duplex-specific nuclease-assisted cyclic signal amplification. Chem Commun. 2015;51:13968–71.

  123. 123.

    Watson JD, Crick FH. Letters to nature: molecular structure of nucleic acid. Nature. 1953;171:738.

  124. 124.

    Ding W, Xu M, Zhu H, Liang H. Mechanism of the hairpin folding transformation of thymine-cytosine-rich oligonucleotides induced by Hg (II) and Ag (I) ions. Eur Phys J E. 2013;36:1–8.

  125. 125.

    Fortino M, Marino T, Russo N. Theoretical study of silver-ion-mediated base pairs: the case of C-Ag-C and C-Ag-A systems. J Phys Chem A. 2014;119:5153–7.

  126. 126.

    He X, Qing Z, Wang K, Zou Z, Shi H, Huang J. Engineering a unimolecular multifunctional DNA probe for analysis of Hg2+ and Ag+. Anal Methods. 2012;4:345–7.

  127. 127.

    Tortolini C, Bollella P, Antonelli ML, Antiochia R, Mazzei F, Favero G. DNA-based biosensors for Hg2+ determination by polythymine-methylene blue modified electrodes. Biosens Bioelectron. 2015;67:524–31.

  128. 128.

    Xuan F, Luo X, Hsing IM. Conformation-dependent exonuclease III activity mediated by metal ions reshuffling on thymine-rich DNA duplexes for an ultrasensitive electrochemical method for Hg2+ detection. Anal Chem. 2013;85:4586–93.

  129. 129.

    Chen J, Zhou S, Wen J. Disposable strip biosensor for visual detection of Hg2+ based on Hg2+-triggered toehold binding and exonuclease III-assisted signal amplification. Anal Chem. 2014;86:3108–14.

  130. 130.

    Yin J, He X, Jia X, Wang K, Xu F. Highly sensitive label-free fluorescent detection of Hg2+ ions by DNA molecular machine-based Ag nanoclusters. Analyst. 2013;138:2350–6.

  131. 131.

    Xu G, Wang G, He X, Zhu Y, Chen L, Zhang X. An ultrasensitive electrochemical method for detection of Ag+ based on cyclic amplification of exonuclease III activity on cytosine-Ag+-cytosine. Analyst. 2013;138:6900–6.

  132. 132.

    Zhou Y, Xing XJ, Pang DW, Tang HW. An exonuclease III-aided “turn-on” fluorescence assay for mercury ions based on graphene oxide and metal-mediated “molecular beacon”. RSC Adv. 2015;5:12994–9.

  133. 133.

    Zhao W, Lam JCF, Chiuman W, Brook MA, Li Y. Enzymatic cleavage of nucleic acids on gold nanoparticles: a generic platform for facile colorimetric biosensors. Small. 2008;4:810–6.

  134. 134.

    Shen L, Chen Z, Li Y, He S, Xie S, Xu X, et al. Electrochemical DNAzyme sensor for lead based on amplification of DNA-Au Bio-Bar codes. Anal Chem. 2008;80:6323–8.

  135. 135.

    Tang S, Tong P, Li H, Tang J, Zhang L. Ultrasensitive electrochemical detection of Pb2+ based on rolling circle amplification and quantum dots tagging. Biosens Bioelectron. 2013;42:608–11.

  136. 136.

    Peng Y, Li L, Yi X, Guo L. Label-free picomolar detection of Pb2+ using atypical icosahedra gold nanoparticles and rolling circle amplification. Biosens Bioelectron. 2014;59:314–20.

  137. 137.

    He JL, Zhu SL, Wu P, Li PP, Li T, Cao Z. Enzymatic cascade based fluorescent DNAzyme machines for the ultrasensitive detection of Cu (II) ions. Biosens Bioelectron. 2014;60:112–7.

  138. 138.

    Ellington AD, Szostak JW. In vitro selection of RNA molecules that bind specific ligands. Nature. 1990;346:818–22.

  139. 139.

    Tuerk C, Gold L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science. 1990;249:505–10.

  140. 140.

    Liu J, Cao Z, Lu Y. Functional nucleic acid sensors. Chem Rev. 2009;109:1948–98.

  141. 141.

    Cho EJ, Yang L, Levy M, Ellington AD. Using a deoxyribozyme ligase and rolling circle amplification to detect a non-nucleic acid analyte, ATP. J Am Chem Soc. 2005;127:2022–3.

  142. 142.

    Shi H, He X, Wang K, Wu X, Ye X, Guo Q, et al. Activatable aptamer probe for contrast-enhanced in vivo cancer imaging based on cell membrane protein-triggered conformation alteration. Proc Natl Acad Sci U S A. 2011;108:3900–5.

  143. 143.

    Lu CH, Wang F, Willner I. Amplified optical aptasensors through the endonuclease-stimulated regeneration of the analyte. Chem Sci. 2012;3:2616–22.

  144. 144.

    Li F, Zhang H, Wang Z, Newbigging AM, Reid MS, Li XF, et al. Aptamers facilitating amplified detection of biomolecules. Anal Chem. 2014;87:274–92.

  145. 145.

    Yin J, He X, Wang K, Xu F, Shangguan J, He D, et al. Label-free and turn-on aptamer strategy for cancer cells detection based on a DNA-silver nanocluster fluorescence upon recognition-induced hybridization. Anal Chem. 2013;85:12011–9.

  146. 146.

    Tan W, Donovan MJ, Jiang J. Aptamers from cell-based selection for bioanalytical applications. Chem Rev. 2013;113:2842–62.

  147. 147.

    Holm RH, Kennepohl P, Solomon EI. Structural and functional aspects of metal sites in biology. Chem Rev. 1996;96:2239–314.

  148. 148.

    Deng B, Lin Y, Wang C, Li F, Wang Z, Zhang H, et al. Aptamer binding assays for proteins: the thrombin example-a review. Anal Chim Acta. 2014;837:1–15.

  149. 149.

    Feng C, Dai S, Wang L. Optical aptasensors for quantitative detection of small biomolecules: A review. Biosens Bioelectron. 2014;59:64–74.

  150. 150.

    Huang Y, Chen J, Zhao S, Shi M, Chen ZF, Liang H. Label-free colorimetric aptasensor based on nicking enzyme assisted signal amplification and DNAzyme amplification for highly sensitive detection of protein. Anal Chem. 2013;85:4423–30.

  151. 151.

    Liu S, Wang Y, Zhang C, Lin Y, Li F. Homogeneous electrochemical aptamer-based ATP assay with signal amplification by exonuclease III assisted target recycling. Chem Commun. 2013;49:2335–7.

  152. 152.

    Huang Y, Liu X, Zhang L, Hu K, Zhao S, Fang B, et al. Nicking enzyme and graphene oxide-based dual signal amplification for ultrasensitive aptamer-based fluorescence polarization assays. Biosens Bioelectron. 2015;63:178–84.

  153. 153.

    Xue L, Zhou X, Xing D. Sensitive and homogeneous protein detection based on target-triggered aptamer hairpin switch and nicking enzyme assisted fluorescence signal amplification. Anal Chem. 2012;84:3507–13.

  154. 154.

    Gao T, Ning L, Li C, Wang H, Li G. A colorimetric method for protein assay via exonuclease III-assisted signal attenuation strategy and specific DNA–protein interaction. Anal Chim Acta. 2013;788:171–6.

  155. 155.

    Zheng AX, Wang JR, Li J, Song XR, Chen GN, Yang HH. Nicking enzyme based homogeneous aptasensors for amplification detection of protein. Chem Commun. 2011;48:374–6.

  156. 156.

    Li L, Wang Q, Feng J, Tong L, Tang B. Highly sensitive and homogeneous detection of membrane protein on a single living cell by aptamer and nicking enzyme assisted signal amplification based on microfluidic droplets. Anal Chem. 2014;86(10):5101–7.

  157. 157.

    Liu X, Freeman R, Willner I. Amplified fluorescence aptamer-based sensors using exonuclease III for the regeneration of the analyte. Chem Eur J. 2012;18:2207–11.

  158. 158.

    Freeman R, Girsh J, Fang-ju Jou A, Ho JAA, Hug T, Dernedde J, Willner I. Optical aptasensors for the analysis of the vascular endothelial growth factor (VEGF). Anal Chem. 2012;84:6192–6198.

  159. 159.

    Tan Y, Guo Q, Zhao X, Yang X, Wang K, Huang J, et al. Proximity-dependent protein detection based on enzyme-assisted fluorescence signal amplification. Biosens Bioelectron. 2014;51:255–60.

  160. 160.

    Song J, Lv F, Yang G, Liu L, Yang Q, Wang S. Aptamer-based polymerase chain reaction for ultrasensitive cell detection. Chem Commun. 2012;48:7465–7.

  161. 161.

    Bamrungsap S, Chen T, Shukoor MI, Chen Z, Sefah K, Chen Y, et al. Pattern recognition of cancer cells using aptamer-conjugated magnetic nanoparticles. ACS Nano. 2012;6:3974–81.

  162. 162.

    Herr JK, Smith JE, Medley CD, Shangguan D, Tan W. Aptamer-conjugated nanoparticles for selective collection and detection of cancer cells. Anal Chem. 2006;78:2918–24.

  163. 163.

    Zhang X, Xiao K, Cheng L, Chen H, Liu B, Zhang S, et al. Visual and highly sensitive detection of cancer cells by a colorimetric aptasensor based on cell-triggered cyclic enzymatic signal amplification. Anal Chem. 2014;86:5567–72.

  164. 164.

    Ding C, Liu H, Wang N, Wang Z. Cascade signal amplification strategy for the detection of cancer cells by rolling circle amplification and nanoparticles tagging. Chem Commun. 2012;48:5019–21.

  165. 165.

    Zhao J, Zhang L, Chen C, Jiang J, Yu R. A novel sensing platform using aptamer and RNA polymerase-based amplification for detection of cancer cells. Anal Chim Acta. 2012;745:106–11.

  166. 166.

    Li Y, Zeng Y, Ji X, Li X, Ren R. Cascade signal amplification for sensitive detection of cancer cell based on self-assembly of DNA scaffold and rolling circle amplification. Sensors Actuators B Chem. 2012;171:361–6.

  167. 167.

    Sheng Q, Cheng N, Bai W, Zheng J. Ultrasensitive electrochemical detection of breast cancer cells based on DNA-rolling-circle-amplification-directed enzyme-catalyzed polymerization. Chem Commun. 2015;51:2114–7.

  168. 168.

    Li W, Liu X, Hou T, Li H, Li F. Ultrasensitive homogeneous electrochemical strategy for DNA methyltransferase activity assay based on autonomous exonuclease III-assisted isothermal cycling signal amplification. Biosens Bioelectron. 2015;70:304–9.

  169. 169.

    Joneja A, Huang X. Linear nicking endonuclease-mediated strand-displacement DNA amplification. Anal Biochem. 2011;414:58–69.

Download references

Acknowledgments

This work was supported by the Key Project of Natural Science Foundation of China (grant no. 21175039, 21322509, 21305035, 21190044, and 21221003), Research Fund for the Doctoral Program of Higher Education of China (grant no. 20110161110016), and the project supported by Hunan Provincial Innovation Foundation for Postgraduate (grant no. CX2015B072).

Author information

Correspondence to Xiaoxiao He or Kemin Wang.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Additional information

Published in the topical collection featuring Young Investigators in Analytical and Bioanalytical Science with guest editors S. Daunert, A. Baeumner, S. Deo, J. Ruiz Encinar, and L. Zhang.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Qing, T., He, D., He, X. et al. Nucleic acid tool enzymes-aided signal amplification strategy for biochemical analysis: status and challenges. Anal Bioanal Chem 408, 2793–2811 (2016). https://doi.org/10.1007/s00216-015-9240-y

Download citation

Keywords

  • Nucleic acid tool enzymes
  • Signal amplification
  • Nucleic acid
  • Aptamer
  • Sensing