Alessandra Vinelli, Manuele Onofri and Giampaolo Zuccheri
8.5 CONCLUSIONS AND PERSPECTIVES
Many are the possible strategies towards signal amplification for nucleic acids biosensors. Some can leverage commercial lab kits for nucleic acids amplification, others exploit technology and solutions coming from ELISA or similar techniques. Full automation and ease of use are still somewhat to come, but it is nowadays clear that PCR is not the only solution at making sensitive nucleic acids detection, even though it will power a number of applications also in the future.
In the arenas of medical diagnostics and environmental testing, the winner strategies will have to put together high-volumes of assays, low-cost, high-reliability, high-sensitivity, high simplicity, at least.
Likely, one solution will not satisfy all the needs and all the tasks and many strategies in addition to the ones mentioned in this chapter will emerge and will have a chance to play a role in empowering biosensors even more and participate in the decentralization of bioanalytics.
REFERENCES
Alfonta L., Bardea A., Khersonsky O., Katz E. and Willner I. (2001). Chronopotentiometry and Faradaic impedance spectroscopy as signal transduction methods for the biocatalytic precipitation of an insoluble product on electrode supports: routes for enzyme sensors, immunosensors and DNA sensors. Biosensors and Bioelectronics,16(9–12), 675–687.
Alivisatos A. P., Johnsson K. P., Peng X., Wilson T. E., Loweth C. J., Bruchez M. P. and Schultz P. G. (1996).
Organization of‘nanocrystal molecules’using DNA.Nature,382(6592), 609–611.
Bachmann L. H., Johnson R. E., Cheng H., Markowitz L., Papp J. R., Palella F. J. and Hook E. W. (2010). Nucleic acid amplification tests for diagnosis of neisseria gonorrhoeae and chlamydia trachomatis rectal infections.Journal of Clinical Microbiology,48(5), 1827–1832.
Baeumner A. J., Cohen R. N., Miksic V. and Min J. (2003). RNA biosensor for the rapid detection of viableEscherichia coliin drinking water.Biosensors & Bioelectronics,18(4), 405–413.
Baeumner A. J., Leonard B., McElwee J. and Montagna R. A. (2004). A rapid biosensor for viableB. anthracisspore.
Analytical and Bioanalytical Chemistry,380(1), 15–23.
Baeumner A. J., Pretz J. and Fang S. (2004). A universal nucleic acid sequence biosensor with nanomolar detection limits.Analytical Chemistry,76(4), 888–894.
Bath J. and Turberfield A. J. (2007). DNA nanomachines.Nature Nanotechnology,2(5), 275–284.
Carter D. J. and Cary R. B. (2007). Lateral flow microarrays: a novel platform for rapid nucleic acid detection based on miniaturized lateral flow chromatography.Nucleic Acid Research,35(10), e74.
Cheglakov Z., Weizmann Y., Basnar B. and Willner I. (2007). Diagnosing viruses by the rolling circle amplified synthesis of DNAzymes.Organic & Biomolecular Chemistry,5(2), 223–225.
Chelliserrykattil J., Nelson N. C., Lyakhov D., Carlson J., Phelps S. S., Kaminsky M. B., Gordon P., Hashima S., Ngo T., Blazie S. and Brentano S. (2009). Development of a quantitative real-time transcription-mediated amplification
assay for simultaneous detection of multiple nucleic acid analytes. Journal of Molecular Diagnostics, 11(6), 680–680.
Chen J., Zhang J., Yang H., Fu F. and Chen G. (2010). A strategy for development of electrochemical DNA biosensor based on site-specific DNA cleavage of restriction endonuclease.Biosensors & Bioelectronics,26(1), 144–148.
Chen Q. H., Bian Z. H., Chen M., Hua X., Yao C. Y., Xia H., Kuang H., Zhang X., Huang J. F., Cai G. R. and Fu W. L.
(2009). Real-time monitoring of the strand displacement amplification (SDA) of human cytomegalovirus by a new SDA-piezoelectric DNA sensor system.Biosensors & Bioelectronics,24(12), 3412–3418.
Choi Y. S. and Park D. H. (2004). Electrochemical gene detection using multielectrode array DNA chip.Journal of the Korean Physical Society,44(6), 1556–1559.
Chow D. C., Lee W. K., Zauscher S. and Chilkoti A. (2005). Enzymatic fabrication of DNA nanostructures: extension of a self-assembled oligonucleotide monolayer on gold arrays.Journal of the American Chemical Society,127(41), 14122–14123.
Collins M. L., Irvine B., Tyner D., Fine E., Zayati C., Chang C. A., Horn T., Ahle D., Detmer J., Shen L. P., Kolberg J., Bushnell S., Urdea M. S. and Ho D. D. (1997). A branched DNA signal amplification assay for quantification of nucleic acid targets below 100 molecules/ml.Nucleic Acids Research,25(15), 2979–2984.
Demers L. M., Mirkin C. A., Mucic R. C., Reynolds R. A., Letsinger R. L., Elghanian R. and Viswanadham G. (2000). A fluorescence-based method for determining the surface coverage and hybridization efficiency of thiol-capped oligonucleotides bound to gold thin films and nanoparticles.Analytical Chemistry,72(22), 5535–5541.
Dirks R. M. and Pierce N. A. (2004). Triggered amplification by hybridization chain reaction.Proceedings of the National Academy of Sciences of the United States of America,101(43), 15275–15278.
Edman C. and Nerember M. I. (2006). Electronically Mediated Nucleic Acid Amplification in NASBA.
Nanogen/Becton Dickinson Partnership, USA. US7070961.
Edwards K. A. and Baeumner A. J. (2006). Liposomes in analyses.Talanta,68(5), 1421–1431.
Elsholz B., Nitsche A., Achenbach J., Ellerbrok H., Blohm L., Albers J., Pauli G., Hintsche R. and Woerl R. (2009).
Electrical microarrays for highly sensitive detection of multiplex PCR products from biological agents.
Biosensors & Bioelectronics,24(6), 1737–1743.
Elsholz B., Wörl R., Blohm L., Albers J., Feucht H., Grunwald T., Jürgen B., Schweder T. and Hintsche R. (2006).
Automated detection and quantitation of bacterial RNA by using electrical microarrays.Analytical Chemistry, 78(14), 4794–4802.
Esch M. B., Baeumner A. J. and Durst R. A. (2001). Detection of cryptosporidium parvum using oligonucleotide-tagged liposomes in a competitive assay format.Analytical Chemistry,73(13), 3162–3167.
Gerion D., Chen F., Kannan B., Fu A., Parak W. J., Chen D. J., Majumdar A. and Alivisatos A. P. (2003).
Room-temperature single-nucleotide polymorphism and multiallele DNA detection using fluorescent nanocrystals and microarrays.Analytical Chemistry,75(18), 4766–4772.
Giraud G., Schulze H., Bachmann T., Campbell C., Mount A., Ghazal P., Khondoker M., Ross A., Ember S., Ciani I., Tlili C., Walton A., Terry J. and Crain J. (2009). Fluorescence lifetime imaging of quantum dot labeled DNA microarrays.Internation Journal of Molecular Science,10(4), 1930–1941.
Goodman R. P., Heilemann M., Doose S., Erben C. M., Kapanidis A. N. and Turberfield A. J. (2008). Reconfigurable, braced, three-dimensional DNA nanostructures.Nature Nanotechnology,3(2), 93–96.
Goodrich T. T., Lee H. J. and Corn R. M. (2004). Enzymatically amplified surface plasmon resonance imaging method using RNase H and RNA microarrays for the ultrasensitive detection of nucleic acids.Analytical Chemistry,76(21), 6173–6178.
Guatelli J. C., Whitfield K. M., Kwoh D. Y., Barringer K. J., Richman D. D. and Gingeras T. R. (1990). Isothermal, in vitroamplification of nucleic acids by a multienzyme reaction modeled after retroviral replication.Proceedings of the National Academy of Sciences of the United States of America,87(5), 1874–1878.
Hill C. (2001). Molecular diagnostic testing for infectious diseases using TMA technology.Expert Review of Molecular Diagnostic,1(4), 445–455.
Hwang S., Kim E. and Kwak J. (2005). Electrochemical detection of DNA hybridization using biometallization.
Analytical Chemistry,77(2), 579–584.
Biochemical and nanotechnological strategies for signal enhancement 131
Inomata A., Kishida N., Momoda T., Akiba M., Izumiyama S., Yagita K. and Endo T. (2009). Development and evaluation of a reverse transcription-loop-mediated isothermal amplification assay for rapid and high-sensitive detection of Cryptosporidium in water samples.Water Science and Technology,60(8), 2167–2172.
Jin D., Qi H., Chen S., Zeng T., Liu Q. and Wang S. (2008). Simultaneous detection of six human diarrheal pathogens by using DNA microarray combined with tyramide signal amplification.Journal of Microbiological Methods,75(2), 365–368.
Joo C., Balci H., Ishitsuka Y., Buranachai C. and Ha T. (2008). Advances in single-molecule fluorescence methods for molecular biology.Annual Review of Biochemistry,77, 51–76.
Joung H.-A., Lee N.-R., Lee S. K., Ahn J., Shin Y. B., Choi H.-S., Lee C.-S., Kim S. and Kim M.-G. (2008). High sensitivity detection of 16s rRNA using peptide nucleic acid probes and a surface plasmon resonance biosensor.
Analytica Chimica Acta,630(2), 168–173.
Kern D., Collins M., Fultz T., Detmer J., Hamren S., Peterkin J. J., Sheridan P., Urdea M., White R., Yeghiazarian T. and Todd J. (1996). An enhanced-sensitivity branched-DNA assay for quantification of human immunodeficiency virus type 1 RNA in plasma.Journal of Clinical Microbiology,34(12), 3196–3202.
Liang R.-Q., Li W., Li Y., Tan C.-Y., Li J.-X., Jin Y.-X. and Ruan K.-C. (2005). An oligonucleotide microarray for microRNA expression analysis based on labeling RNA with quantum dot and nanogold probe.Nucleic Acid Research,33(2), e17.
Liu J. and Lu Y. (2003). A colorimetric lead biosensor using DNAzyme-directed assembly of gold nanoparticles.
Journal of the American Chemical Society,125(22), 6642–6643.
Lizardi P. M., Huang X. H., Zhu Z. R., Bray-Ward P., Thomas D. C. and Ward D. C. (1998). Mutation detection and single-molecule counting using isothermal rolling-circle amplification.Nature Genetics,19(3), 225–232.
Lubrich D., Green S. J. and Turberfield A. J. (2009). Kinetically controlled self-assembly of DNA oligomers.Journal of the American Chemical Society,131(7), 2422–2423.
Maruyama F., Kenzaka T., Yamaguchi N., Tani K. and Nasu M. (2003). Detection of bacteria carrying the stx2 gene by in situ loop-mediated isothermal amplification.Applied and Environmental Microbiology,69(8), 5023–5028.
Mirkin C. A., Letsinger R. L., Mucic R. C. and Storhoff J. J. (1996). A DNA-based method for rationally assembling nanoparticles into macroscopic materials.Nature,382(6592), 607–609.
Munge B., Liu G., Collins G. and Wang J. (2005). Multiple enzyme layers on carbon nanotubes for electrochemical detection down to 80 DNA copies.Analytical Chemistry,77(14), 4662–4666.
Nam J.-M., Stoeva S. I. and Mirkin C. A. (2004). Bio-bar-code-based DNA detection with PCR-like sensitivity.Journal of the American Chemical Society,126(19), 5932–5933.
Nam J.-M., Thaxton C. S. and Mirkin C. A. (2003). Nanoparticle-based bio-bar codes for the ultrasensitive detection of proteins.Science,301(5641), 1884–1886.
Niu S. Y., Jiang Y. and Zhang S. S. (2010). Fluorescence detection for DNA using hybridization chain reaction with enzyme-amplification.Chemical Communications,46(18), 3089–3091.
Notomi T., Okayama H., Masubuchi H., Yonekawa T., Watanabe K., Amino N. and Hase T. (2000). Loop-mediated isothermal amplification of DNA.Nucleic Acid Research,28(12), e63.
Ostroff R. M., Hopkins D., Haeberli A. B., Baouchi W. and Polisky B. (1999). Thin film biosensor for rapid visual detection of nucleic acid targets.Clinical Chemistry,45, 1659–1664.
Parab H. J., Jung C., Lee J.-H. and Park H. G. (2010). A gold nanorod-based optical DNA biosensor for the diagnosis of pathogens.Biosensors and Bioelectronics,26(2), 667–673.
Patolsky F., Katz E. and Willner I. (2002). Amplified DNA detection by electrogenerated biochemiluminescence and by the catalyzed precipitation of an insoluble product on electrodes in the presence of the doxorubicin intercalator.
Angewandte Chemie,114(18), 3548–3552.
Polsky R., Gill R., Kaganovsky L. and Willner I. (2006). Nucleic acid-functionalized Pt nanoparticles: Catalytic labels for the amplified electrochemical detection of biomolecules.Analytical Chemistry,78(7), 2268–2271.
Rao V., Fabrizi F., Pennell P., Schiff E., de Medina M., Lane J. R., Martin P. and Ivor L. (2010). Improved detection of hepatitis C virus infection by transcription-mediated amplification technology in dialysis population. Renal Failure,32(6), 721–726.
Sando S., Sasaki T., Kanatani K. and Aoyama Y. (2003). Amplified nucleic acid sensing using programmed self-cleaving DNAzyme.Journal of the American Chemical Society,125(51), 15720–15721.
Scheler O., Glynn B., Parkel S., Palta P., Toome K., Kaplinski L., Remm M., Maher M. and Kurg A. (2009). Fluorescent labeling of NASBA amplified tmRNA molecules for microarray applications.BMC Biotechnology,9(1), 45.
Schienle M., Frey A., Hofmann F., Holzapfl B., Paulus C., Schindler-Bauer P. and Thewes R. (2004). A fully electronic DNA sensor with 128 positions and in-pixel A/D conversion. Solid-State Circuits Conference, 2004. Digest of Technical Papers. ISSCC. 2004 IEEE International, San Francisco, CA, U.S.A.
Smolina I., Lee C. and Frank-Kamenetskii M. (2007). Detection of low-copy-number genomic DNA sequences in individual bacterial cells by using peptide nucleic acid-assisted rolling-circle amplification and fluorescence in situ hybridization.Applied and Environmental Microbiology,73(7), 2324–2328.
Stamm S. and Brosius J. (1991). Sanchored PCR–PCR with cDNA coupled to a solid-phase.Nucleic Acids Research, 19(6), 1350–1350.
Storhoff J. J., Lazarides A. A., Mucic R. C., Mirkin C. A., Letsinger R. L. and Schatz G. C. (2000). What controls the optical properties of DNA-linked gold nanoparticle assemblies? Journal of the American Chemical Society, 122(19), 4640–4650.
Storhoff J. J., Lucas A. D., Garimella V., Bao Y. P. and Muller U. R. (2004). Homogeneous detection of unamplified genomic DNA sequences based on colorimetric scatter of gold nanoparticle probes.Nature Biotechnology,22(7), 883–887.
Taton T. A., Mirkin C. A. and Letsinger R. L. (2000). Scanometric DNA Array detection with nanoparticle probes.
Science,289(5485), 1757–1760.
Tian Y., He Y. and Mao C. (2006). Cascade signal amplification for DNA detection.ChemBioChem,7(12), 1862–1864.
Tsongalis G. J. (2006). Branched DNA technology in molecular diagnostics.American Journal of Clinical Pathology, 126(3), 448–453.
Walker G. T., Fraiser M. S., Schram J. L., Little M. C., Nadeau J. G. and Malinowski D. P. (1992). Strand displacement amplification: an isothermal, in vitro DNA amplification technique.Nucleic Acid Research,20(7), 1691–1696.
Walker G. T., Little M. C., Nadeau J. G. and Shank D. D. (1992). Isothermalin vitroamplification of DNA by a restriction enzyme/DNA polymerase system.Proceedings of the National Academy of Sciences of the United States of America,89(1), 392–396.
Walter A., Wu J., Flechsig G. U., Haake D. A. and Wang J. (2011). Redox cycling amplified electrochemical detection of DNA hybridization: application to pathogenE. coilbacterial RNA.Analytica Chimica Acta,689(1), 29–33.
Walter N. G., Huang C.-Y., Manzo A. J. and Sobhy M. A. (2008). Do-it-yourself guide: how to use the modern single-molecule toolkit.Nature Methods,5(6), 475–489.
Xie H., Zhang C. and Gao Z. (2004). Amperometric detection of nucleic acid at femtomolar levels with a nucleic acid/electrochemical activator bilayer on gold electrode.Analytical Chemistry,76(6), 1611–1617.
Yang J. L., Ma G. P., Yang R., Yang S. Q., Fu L. Z., Cheng A. C., Wang M. S., Zhang S. H., Shen K. F., Jia R. Y., Deng S. X. and Xu Z. Y. (2010). Simple and rapid detection of Salmonella serovar Enteritidis under field conditions by loop-mediated isothermal amplification.Journal of Applied Microbiology,109(5), 1715–1723.
Yu Chang S.-S., Lee C.-L. and Wang C. R. C. (1997). Gold nanorods: electrochemical synthesis and optical properties.
The Journal of Physical Chemistry B,101(34), 6661–6664.
Zajac A., Song D., Qian W. and Zhukov T. (2007). Protein microarrays and quantum dot probes for early cancer detection.Colloids and Surfaces B: Biointerfaces,58(2), 309–314.
Zaytseva N. V., Goral V. N., Montagna R. A. and Baeumner A. J. (2005). Development of a microfluidic biosensor module for pathogen detection.Lab on a Chip,5(8), 805–811.
Zhang C.-Y., Yeh H.-C., Kuroki M. T. and Wang T.-H. (2005). Single-quantum-dot-based DNA nanosensor.Nature Materials,4(11), 826–831.
Zhang D., Carr D. J. and Alocilja E. C. (2009). Fluorescent bio-barcode DNA assay for the detection ofSalmonella entericaserovarEnteritidis.Biosensors and Bioelectronics,24(5), 1377–1381.
Zhao X., Tapec-Dytioco R. and Tan W. (2003). Ultrasensitive DNA detection using highly fluorescent bioconjugated nanoparticles.Journal of the American Chemical Society,125(38), 11474–11475.
Biochemical and nanotechnological strategies for signal enhancement 133
Zheleznaya L. A., Kopein D. S., Rogulin E. A., Gubanov S. I. and Matvienko N. I. (2006). Significant enhancement of fluorescence on hybridization of a molecular beacon to a target DNA in the presence of a site-specific DNA nickase.
Analytical Biochemistry,348(1), 123–126.
Zheng Y., Li Y., Lu N. and Deng Z. (2011). Surface-initiated DNA self-assembly as an enzyme-free and nanoparticle-free strategy towards signal amplification of an electrochemical DNA sensor. Analyst, 136(3), 459–462.