Abstract
The structure of DNA, encoded on four bases, allows to generate a considerable number of unique markers, even considering very short sequences composed of n nucleotides leading to 4n different combinations. The possibility of synthesizing DNA sequences in vitro at low cost and in large quantities, coupled with well-known strategies of strand functionalization with groups having optical, magnetic or redox properties, allows to consider DNA not simply as a tool for detection of target nucleotide sequences but as versatile label in many biomolecular recognition event transduction schemes. This ability is strongly enhanced by modern DNA amplification approaches. Furthermore, iterative selection methods (SELEX) have achieved a high level of performance, reliability and sophistication, enabling the use of short DNA sequences also as selective binding element for the detection of an increasing number of analytes ranging from proteins to small organic molecules, such as pollutants and endocrine disruptors. This chapter highlights the progress made in the areas of analytical sciences through the use of nucleic acid sequences that act either only as an amplifiable label or both as a recognition element and as a marker.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Adams M, Jackson SR, Haselton FR et al (2012) Design, synthesis, and characterization of nucleic-acid-functionalized gold surfaces for biomarker detection. Langmuir 28:1068–1082
Akter F, Mie M, Kobatake E (2011) Immuno-rolling circle amplification using a multibinding fusion protein. Anal Biochem 416:174–179
Akter F, Mie M, Grimm S et al (2012) Detection of antigens using a protein−DNA chimera developed by enzymatic covalent bonding with phiX gene A. Anal Chem 84:5040–5046
Campolongo MJ, Tan SJ, Xu J et al (2010) DNA nanomedicine: engineering DNA as a polymer for therapeutic and diagnostic applications. Adv Drug Deliv Rev 62:606–616
Cao C, Dhumpa R, Bang DD et al (2010) Detection of avian influenza virus by fluorescent DNA barcode-based immunoassay with sensitivity comparable to PCR. Analyst 135:337–342
Cao ZJ, Peng QW, Qiu X et al (2011) Highly sensitive chemiluminescence technology for protein detection using aptamer-based rolling circle amplification platform. J Pharm Anal 1:159–165
Challier L, Mavre F, Moreau J et al (2012) Simple and highly enantioselective electrochemical aptamer-based binding assay for trace detection of chiral compounds. Anal Chem 84:5415–5420
Challier L, Miranda-Castro R, Marchal D et al (2013) Kinetic rotating droplet electrochemistry: a simple and versatile method for reaction progress kinetic analysis in microliter volumes. J Am Chem Soc 135:14215–14228
Chang TL, Tsai CY, Sun CC et al (2007) Ultrasensitive electrical detection of protein using nanogap electrodes and nanoparticle-based DNA amplification. Biosens Bioelectron 22:3139–3145
Chen HY, Zhuang HS (2009) Real-time immuno-PCR assay for detecting PCBs in soil samples. Anal Bioanal Chem 394:1205–1211
Cheng W, Yan F, Ding L et al (2010) Cascade signal amplification strategy for subattomolar protein detection by rolling circle amplification and quantum dots tagging. Anal Chem 82:3337–3342
Cheng W, Ding S, Li Q et al (2012) A simple electrochemical aptasensor for ultrasensitive protein detection using cyclic target-induced primer extension. Biosens Bioelectron 36:12–17
Cheng S, Zheng B, Wang M et al (2014a) A target-triggered strand displacement reaction cycle: the design and application in adenosine triphosphate sensing. Anal Biochem 446:69–75
Cheng S, Zheng B, Wang M et al (2014b) Determination of adenosine triphosphate by a target inhibited catalytic cycle based on a strand displacement reaction. Anal Lett 47:478–491
Cho EJ, Yang L, Levy M et al (2005) Using a deoxyribozyme ligase and rolling circle amplification to detect a non-nucleic acid analyte, ATP. J Am Chem Soc 127:2022–2023
Dirks RM, Pierce NA (2004) Triggered amplification by hybridization chain reaction. Proc Natl Acad Sci USA 101:15275–15278
Feng K, Kong R, Wang H et al (2012) A universal amplified strategy for aptasensors: enhancing sensitivity through allostery-triggered enzymatic recycling amplification. Biosens Bioelectron 38:121–125
Fire A, Xu SQ (1995) Rolling replication of short DNA circles. Proc Natl Acad Sci USA 92:4641–4645
Focke F, Haase I, Fischer M (2013) Loop-mediated isothermal amplification (LAMP): methods for plant species identification in food. J Agric Food Chem 61:2943–2949
Freeman R, Girsh J, Jou AF et al (2012) Optical aptasensors for the analysis of the vascular endothelial growth factor (VEGF). Anal Chem 84:6192–6198
Gerasimova YV, Kolpashchikov DM (2014) Enzyme-assisted target recycling (EATR) for nucleic acid detection. Chem Soc Rev 43:6405–6438
Goluch ED, Nam J-M, Georganopoulou DG et al (2006) A bio-barcode assay for on-chip attomolar-sensitivity protein detection. Lab Chip 6:1293–1299
Guo YC, Zhou YF, Zhang XE et al (2006) Phage display mediated immuno-PCR. Nucleic Acids Res 34:e62–e68
Heyduk T, Heyduk E (2002) Molecular beacons for detecting DNA binding proteins. Nat Biotechnol 20:171–176
Hill HD, Mirkin CA (2006) The bio-barcode assay for the detection of protein and nucleic acid targets using DTT-induced ligand exchange. Nat Protoc 1:324–336
Huang Y, Chen J, Zhao S et al (2013) Label-free colorimetric aptasensor based on nicking enzyme assisted signal amplification and DNAzyme amplification for highly sensitive detection of protein. Anal Chem 85:4423–4430
Huang J, He Y, Yang X et al (2014) Split aptazyme-based catalytic molecular beacons for amplified detection of adenosine. Analyst 139:2994–2997
Jiang X, Cheng S, Chen W et al (2012) Comparison of oligonucleotide-labeled antibody probe assays for prostate-specific antigen detection. Anal Biochem 424:1–7
Jung C, Ellington AD (2014) Diagnostic applications of nucleic acid circuits. Acc Chem Res 47:1825–1835
Klussmann S (2006) The aptamer handbook: functional oligonucleotides and their applications. Wiley, Hoboken, NJ
Kotia RB, Li L, McGown LB (2000) Separation of nontarget compounds by DNA aptamers. Anal Chem 72:827–831
Kuczius T, Becker K, Karch H et al (2009) High sensitivity detection of the glial fibrillary acidic protein as indicator for TSE risk material in meat products using an immuno-PCR. Mol Nutr Food Res 53:1329–1335
Lee J, Jeon CH, Ahn SJ et al (2014) Highly stable colorimetric aptamer sensors for detection of ochratoxin A through optimizing the sequence with the covalent conjugation of hemin. Analyst 139:1622–1627
Li Y, Ji X, Song W et al (2013) Design of a sensitive aptasensor based on magnetic microbeads-assisted strand displacement amplification and target recycling. Anal Chim Acta 770:147–152
Lin X, Cui L, Huang Y et al (2014) Carbon nanoparticle-protected aptamers for highly sensitive and selective detection of biomolecules based on nuclease-assisted target recycling signal amplification. Chem Commun 50:7646–7648
Linck L, Reiß E, Bier F et al (2012) Direct labeling rolling circle amplification as a straightforward signal amplification technique for biodetection formats. Anal Methods 4:1215–1220
Liu X, Freeman R, Willner I (2012) Amplified fluorescence aptamer-based sensors using exonuclease III for the regeneration of the analyte. Chem Eur J 18:2207–2211
Liu S, Wang Y, Zhang C et al (2013) Homogeneous electrochemical aptamer-based ATP assay with signal amplification by exonuclease III assisted target recycling. Chem Commun 49:2335–2337
Lu C-H, Li J, Lin M-H et al (2010) Amplified aptamer-based assay through catalytic recycling of the analyte. Angew Chem Int Ed 49:8454–8457
Lu L, Liu B, Zhao Z et al (2012) Ultrasensitive electrochemical immunosensor for HE4 based on rolling circle amplification. Biosens Bioelectron 33:216–221
Ma DL, Xu T, Chan DSH et al (2011) A highly selective, label-free, homogenous luminescent switch-on probe for the detection of nanomolar transcription factor NF-kappaB. Nucleic Acids Res 39:e67–e75
McManus SA, Li Y (2013) Turning a kinase deoxyribozyme into a sensor. J Am Chem Soc 135:7181–7186
Moreau J, Challier L, Lalaoui N et al (2014) Rational design of a redox-labeled chiral target for an enantioselective aptamer-based electrochemical binding assay. Chem Eur J 20:2953–2959
Mullenix MC, Sivakamasundari R, Feaver WJ et al (2002) Rolling circle amplification improves sensitivity in multiplex immunoassays on microspheres. Clin Chem 48:1855–1858
Nam J-M, Park S-J, Mirkin CA (2002) Bio-barcodes based on oligonucleotide-modified nanoparticles. J Am Chem Soc 124:3820–3821
Notomi T, Okayama H, Masubuchi H et al (2000) Loop-mediated isothermal amplification of DNA. Nucleic Acids Res 28:E63
Ou LJ, Liu SJ, Chu X et al (2009) DNA encapsulating liposome based rolling circle amplification immunoassay as a versatile platform for ultrasensitive detection of protein. Anal Chem 81:9664–9673
Pei X, Zhang B, Tang J et al (2013) Sandwich-type immunosensors and immunoassays exploiting nanostructure labels. Anal Chim Acta 758:1–18
Peng Q, Cao Z, Lau C et al (2011) Aptamer-barcode based immunoassay for the instantaneous derivatization chemiluminescence detection of IgE coupled to magnetic beads. Analyst 136:140–147
Peng K, Zhao H, Yuan Y et al (2014) Mediator-free triple-enzyme cascade electrocatalytic aptasensor with exonuclease-assisted target recycling and hybridization chain reaction amplification. Biosens Bioelectron 55:366–371
Pourhassan-Moghaddam M, Rahmati-Yamchi M, Akbarzadeh A et al (2013) Protein detection through different platforms of immuno-loop-mediated isothermal amplification. Nanoscale Res Lett 8:485–496
Qian L, Winfree E, Bruck J (2011) Neural network computation with DNA strand displacement cascades. Nature 475:368–372
Ravan H, Yazdanparast R (2012) Development and evaluation of a loop-mediated isothermal amplification method in conjunction with an enzyme-linked immunosorbent assay for specific detection of Salmonella serogroup D. Anal Chim Acta 733:64–70
Ravan H, Yazdanparast R (2013) Loop region-specific oligonucleotide probes for loop-mediated isothermal amplification-enzyme-linked immunosorbent assay truly minimize the instrument needed for detection process. Anal Biochem 439:102–108
Ruta J, Ravelet C, Baussanne I et al (2007) Aptamer-based enantioselective competitive binding assay for the trace enantiomer detection. Anal Chem 79:4716–4719
Ruta J, Perrier S, Ravelet C et al (2009) Noncompetitive fluorescence polarization aptamer-based assay for small molecule detection. Anal Chem 81:7468–7473
Sano T, Smith CL, Cantor CR (1992) Immuno-PCR: very sensitive antigen detection by means of specific antibody-DNA conjugates. Science 258:120–122
Song W, Zhu K, Cao Z et al (2012) Hybridization chain reaction-based aptameric system for the highly selective and sensitive detection of protein. Analyst 137:1396–1401
Stoeva SI, Lee JS, Smith JE et al (2006) Multiplexed detection of protein cancer markers with biobarcoded nanoparticle probes. J Am Chem Soc 128:8378–8379
Suess B (2010) Riboswitches: new aspects of an old story. RNA Biol 7:65–66
Tan Y, Guo Q, Zhao X et al (2014) Proximity-dependent protein detection based on enzyme-assisted fluorescence signal amplification. Biosens Bioelectron 51:255–260
Tang J, Hou L, Tang D et al (2012a) Hemin/G-quadruplex-based DNAzyme concatamers as electrocatalysts and biolabels for amplified electrochemical immunosensing of IgG1w. Chem Commun 48:8180–8182
Tang L, Liu Y, Ali MM et al (2012b) Colorimetric and ultrasensitive bioassay based on a dual-amplification system using aptamer and DNAzyme. Anal Chem 84:4711–4717
Tong P, Zhao WW, Zhang L et al (2012) Double-probe signal enhancing strategy for toxin aptasensing based on rolling circle amplification. Biosens Bioelectron 33:146–151
Travascio P, Lia Y, Sen D (1998) DNA-enhanced peroxidase activity of a DNA-aptamer-hemin complex. Chem Biol 5:505–517
Van Ness J, Van Ness LK, Galas DJ (2003) Isothermal reactions for the amplification of oligonucleotides. Proc Natl Acad Sci USA 100:4504–4509
Wang JK, Li TX, Guo XY et al (2005) Exonuclease III protection assay with FRET probe for detecting DNA-binding proteins. Nucleic Acids Res 33:e23
Wang F, Freage L, Ron Orbach R et al (2013a) Autonomous replication of nucleic acids by polymerization/nicking enzyme/DNAzyme cascades for the amplified detection of DNA and the aptamer−Cocaine Complex. Anal Chem 85:8196–8203
Wang Q, Zheng H, Gao X et al (2013b) A label-free ultrasensitive electrochemical aptameric recognition system for protein assay based on hyperbranched rolling circle amplification. Chem Commun 49:11418–11420
Wang F, Lu C-H, Willner I (2014) From cascaded catalytic nucleic acids to enzyme-DNA nanostructures: controlling reactivity, sensing, logic operations, and assembly of complex structures. Chem Rev 114:2881–2941
Willner I, Shlyahovsky B, Zayats M et al (2008) DNAzymes for sensing, nanobiotechnology and logic gate applications. Chem Soc Rev 37:1153–1165
Wu ZS, Zhou H, Zhang SB et al (2010) Electrochemical aptameric recognition system for a sensitive protein assay based on specific target binding-induced rolling circle amplification. Anal Chem 82:2282–2289
Xie S, Chai Y, Yuan Y et al (2014) Development of an electrochemical method for Ochratoxin A detection based on aptamer and loop-mediated isothermal amplification. Biosens Bioelectron 55:324–329
Xu J, Cai LL, Kong DM et al (2011) General sensor design strategy based on G-quadruplex-hemin DNAzymes. Anal Lett 44:2582–2592
Xue L, Zhou X, Xing D (2012a) Sensitive and homogeneous protein detection based on target-triggered aptamer hairpin switch and nicking enzyme assisted fluorescence signal amplification. Anal Chem 84:3507–3513
Xue Q, Wang L, Jiang W (2012b) A versatile platform for highly sensitive detection of protein: DNA enriching magnetic nanoparticles based rolling circle amplification immunoassay. Chem Commun 33:3897–4020
Xue Q, Wang Z, Wang L et al (2012c) Sensitive detection of proteins using assembled cascade fluorescent DNA nanotags based on rolling circle amplification. Bioconjug Chem 23:734–739
Xue Q, Zhang G, Wang L et al (2014) Aptamer-based exonuclease protection and enzymatic recycling cleavage amplification homogeneous assay for the highly sensitive detection of thrombin. Analyst 139:3167–3173
Yan J, Su S, He S et al (2012) Nano rolling-circle amplification for enhanced SERS hot spots in protein microarray analysis. Anal Chem 84:9139–9145
Yan L, Zhou J, Zheng Y et al (2014) Isothermal amplified detection of DNA and RNA. Mol BioSyst 10:970–1003
Yang L, Fung CW, Cho EJ et al (2007) Real-time rolling circle amplification for protein detection. Anal Chem 79:3320–3329
Yin P, Choi HMT, Calvert CR et al (2008) Programming biomolecular self-assembly pathways. Nature 451:318–322
Yin H-Q, Jia M-X, Shi L-J et al (2011) Nanoparticle-based bio-barcode assay for the detection of bluetongue virus. J Virol Methods 178:225–228
Yuan Y, Gou X, Yuana R et al (2011) Electrochemical aptasensor based on the dual-amplification of G-quadruplex horseradish peroxidase-mimicking DNAzyme and blocking reagent-horseradish peroxidase. Biosens Bioelectron 26:4236–4240
Yuan Y, Yuan R, Chai Y et al (2012) Hemin/G-quadruplex simultaneously acts as NADH oxidase and HRP-mimicking DNAzyme for simple, sensitive pseudobienzyme electrochemical detection of thrombin. Chem Commun 48:4621–4623
Yuan Y, Chai Y, Yuan R et al (2013) An ultrasensitive electrochemical aptasensor with autonomous assembly of hemin-G-quadruplex DNAzyme nanowires for pseudo triple-enzyme cascade electrocatalytic amplification. Chem Commun 49:7328–7330
Zhang DY, Turberfield AJ, Yurk B et al (2007a) Engineering entropy-driven reactions and networks catalyzed by DNA. Science 5883:1121–1125
Zhang D, Carr DJ, Alocilja EC (2009) Fluorescent bio-barcode DNA assay for the detection of Salmonella enterica serovar Enteritidis. Biosens Bioelectron 24:1377–1381
Zhang L, Ren J, Pan K et al (2010) Detection of gastric carcinoma-associated MG7-Ag by serum immuno-PCR assay in a high-risk Chinese population, with implication for screening. Int J Cancer 126:469–473
Zhang H, Fang C, Zhang S (2011) Ultrasensitive electrochemical analysis of two analytes by using an autonomous DNA machine that works in a two-cycle mode. Chem Eur J 17:7531–7537
Zhang B, Liu B, Tang D et al (2012a) DNA-based hybridization chain reaction for amplified bioelectronic signal and ultrasensitive detection of proteins. Anal Chem 84:5392–5399
Zhang Y, Hu J, Zhang C-Y (2012b) Sensitive detection of transcription factors by isothermal exponential amplification-based colorimetric assay. Anal Chem 84:9544–9549
Zhang J, Chai Y, Yuan R et al (2013) A novel electrochemical aptasensor for thrombin detection based on the hybridization chain reaction with hemin/G-quadruplex DNAzyme-signal amplification. Analyst 138:4558–4564
Zhao B, Yan J, Wang D et al (2013a) Carbon nanotubes multifunctionalized by rolling circle amplification and their application for highly sensitive detection of cancer markers. Small 15:2595–2601
Zhao M, Zhuo Y, Chai Y et al (2013b) Dual signal amplification strategy for the fabrication of an ultrasensitive electrochemiluminescence aptasensor. Analyst 138:6639–6644
Zheng AX, Wang JR, Li J et al (2012a) Enzyme-free fluorescence aptasensor for amplification detection of human thrombin via target-catalyzed hairpin assembly. Biosens Bioelectron 36:217–221
Zheng AX, Wang JR, Li J et al (2012b) Nicking enzyme based homogeneous aptasensors for amplification detection of protein. Chem Commun 48:374–376
Zheng J, Hu Y, Bai J et al (2014) Universal surface-enhanced Raman scattering amplification detector for ultrasensitive detection of multiple target analytes. Anal Chem 86:2205–2212
Zhou L, Ou LJ, Chu X et al (2007) Aptamer-based rolling circle amplification: a platform for electrochemical detection of protein. Anal Chem 79:7492–7500
Zhou J, Zhuang J, Tang J et al (2013) Dual-nanogold-linked bio-barcodes with superstructures for in situ amplified electronic detection of low-abundance proteins. Mol BioSyst 9:622–625
Zhou W, Gong X, Xiang Y et al (2014) Target-triggered quadratic amplification for label-free and sensitive visual detection of cytokines based on hairpin aptamer DNAzyme probes. Anal Chem 86:953–958
Zhuang HS, Zhou C (2009) Determination of anthracene by real-time immune-polymerase chain reaction assay. Anal Chim Acta 633:278–282
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer International Publishing Switzerland
About this chapter
Cite this chapter
Noel, V., Piro, B., Reisberg, S. (2015). DNA for Non-nucleic Acid Sensing. In: Erdmann, V., Jurga, S., Barciszewski, J. (eds) RNA and DNA Diagnostics. RNA Technologies. Springer, Cham. https://doi.org/10.1007/978-3-319-17305-4_4
Download citation
DOI: https://doi.org/10.1007/978-3-319-17305-4_4
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-17304-7
Online ISBN: 978-3-319-17305-4
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)