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Emerging techniques employed in aptamer-based diagnostic tests

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References

  • Ellington AD, Szostak JW. In vitro selection of RNA molecules that bind specific ligands. Nature 346(6287), 818–822 (1990).
  • Tuerk C, Gold L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249(4968), 505–510 (1990).
  • Lauridsen LH, Veedu RN. Nucleic acid aptamers against biotoxins: a new paradigm toward the treatment and diagnostic approach. Nucleic Acid Ther. 22(6), 371–379 (2012).
  • Burnett JC, Rossi JJ. RNA-based therapeutics: current progress and future prospects. Chem. Biol. 19(1), 60–71 (2012).
  • Ikebukuro K, Kiyohara C, Sode K. Novel electrochemical sensor system for protein using the aptamers in sandwich manner. Biosens. Bioelectron. 20(10), 2168–2172 (2005).
  • Ikebukuro K, Kiyohara C, Sode K. Electrochemical detection of protein using a double aptamer sandwich. Anal. Lett. 37(14), 2901–2909 (2004).
  • Tombelli S, Minunni M, Luzi E, Mascini M. Aptamer-based biosensors for the detection of HIV-1 Tat protein. Bioelectrochemistry 67(2), 135–141 (2005).
  • Miyachi Y, Shimizu N, Ogino C, Kondo A. Selection of DNA aptamers using atomic force microscopy. Nucl. Acids Res. 38(4), e21 (2010).
  • Maehashi K, Katsura T, Kerman K, Takamura Y, Matsumoto K, Tamiya E. Label-free protein biosensor based on aptamer-modified carbon nanotube field-effect transistors. Anal. Chem. 79(2), 782–787 (2007).
  • Estrela P, Paul D, Song Q et al. Label-free sub-picomolar protein detection with field-effect transistors. Anal. Chem. 82(9), 3531–3536 (2010).
  • Hermann T, Patel DJ. Adaptive recognition by nucleic acid aptamers. Science 287(5454), 820–825 (2000).
  • Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucl. Acids Res. 31(13), 3406–3415 (2003).
  • Jhaveri SD, Kirby R, Conrad R et al. Designed signaling aptamers that transduce molecular recognition to changes in fluorescence intensity. J. Am. Chem. Soc. 122(11), 2469–2473 (2000).
  • Jhaveri S, Rajendran M, Ellington AD. In vitro selection of signaling aptamers. Nat. Biotechnol. 18(12), 1293–1297 (2000).
  • Yamamoto R, Baba T, Kumar PK. Molecular beacon aptamer fluoresces in the presence of Tat protein of HIV-1. Genes Cells 5(5), 389–396 (2000).
  • Stojanovic MN, De Prada P, Landry DW. Fluorescent sensors based on aptamer self-assembly. J. Am. Chem. Soc. 122(46), 11547–11548 (2000).
  • Hamaguchi N, Ellington A, Stanton M. Aptamer beacons for the direct detection of proteins. Anal. Biochem. 294(2), 126–131 (2001).
  • Stojanovic MN, De Prada P, Landry DW. Aptamer-based folding fluorescent sensor for cocaine. J. Am. Chem. Soc. 123(21), 4928–4931 (2001).
  • Nutiu R, Li Y. Structure-switching signaling aptamers. J. Am. Chem. Soc. 125(16), 4771–4778 (2003).
  • Yoshida W, Yokobayashi Y. Photonic Boolean logic gates based on DNA aptamers. Chem. Commun. (2), 195–197 (2007).
  • Ho H-A, Leclerc M. Optical sensors based on hybrid aptamer/conjugated polymer complexes. J. Am. Chem. Soc. 126(5), 1384–1387 (2004).
  • Stojanovic MN, Kolpashchikov DM. Modular aptameric sensors. J. Am. Chem. Soc. 126(30), 9266–9270 (2004).
  • Abe K, Ogasawara D, Yoshida W, Sode K, Ikebukuro K. Aptameric sensors based on structural change for diagnosis. Faraday Discuss. 149, 93–105, discussion 137–157 (2011).
  • Ogasawara D, Hachiya NS, Kaneko K, Sode K, Ikebukuro K. Detection system based on the conformational change in an aptamer and its application to simple bound/free separation. Biosens. Bioelectron. 24(5), 1372–1376 (2009).
  • Xiao Y, Lubin AA, Heeger AJ, Plaxco KW. Label-free electronic detection of thrombin in blood serum by using an aptamer-based sensor. Angew. Chem. Int. Ed. Engl. 44(34), 5456–5459 (2005).
  • Xiao Y, Piorek BD, Plaxco KW, Heeger AJ. A reagentless signal-on architecture for electronic, aptamer-based sensors via target-induced strand displacement. J. Am. Chem. Soc. 127(51), 17990–17991 (2005).
  • Swensen JS, Xiao Y, Ferguson BS et al. Continuous, real-time monitoring of cocaine in undiluted blood serum via a microfluidic, electrochemical aptamer-based sensor. J. Am. Chem. Soc. 131(12), 4262–4266 (2009).
  • Frauendorf C, Jaschke A. Detection of small organic analytes by fluorescing molecular switches. Bioorg. Med. Chem. 9(10), 2521–2524 (2001).
  • Li T, Wang E, Dong S. G-quadruplex-based DNAzyme for facile colorimetric detection of thrombin. Chem. Commun. (31), 3654–3656 (2008).
  • Liu X, Freeman R, Golub E, Willner I. Chemiluminescence and chemiluminescence resonance energy transfer (CRET) aptamer sensors using catalytic hemin/G-quadruplexes. ACS Nano 5(9), 7648–7655 (2011).
  • Pelossof G, Tel-Vered R, Elbaz J, Willner I. Amplified biosensing using the horseradish peroxidase-mimicking DNAzyme as an electrocatalyst. Anal. Chem. 82(11), 4396–4402 (2010).
  • Travascio P, Bennet AJ, Wang DY, Sen D. A ribozyme and a catalytic DNA with peroxidase activity: active sites versus cofactor-binding sites. Chem. Biol. 6(11), 779–787 (1999).
  • Elghanian R. Selective colorimetric detection of polynucleotides based on the distance-dependent optical properties of gold nanoparticles. Science 277(5329), 1078–1081 (1997).
  • Liu J, Lu Y. Adenosine-dependent assembly of aptazyme-functionalized gold nanoparticles and its application as a colorimetric biosensor. Anal. Chem. 76(6), 1627–1632 (2004).
  • Liu J, Lu Y. Fast colorimetric sensing of adenosine and cocaine based on a general sensor design involving aptamers and nanoparticles. Angew. Chem. Int. Ed. 45(1), 90–94 (2006).
  • Yoshida W, Sode K, Ikebukuro K. Aptameric enzyme subunit for biosensing based on enzymatic activity measurement. Anal. Chem. 78(10), 3296–3303 (2006).
  • Yoshida W, Sode K, Ikebukuro K. Label-free homogeneous detection of immunoglobulin E by an aptameric enzyme subunit. Biotechnol. Lett. 30(3), 421–425 (2008).
  • Yoshida W, Mochizuki E, Takase M et al. Selection of DNA aptamers against insulin and construction of an aptameric enzyme subunit for insulin sensing. Biosens. Bioelectron. 24(5), 1116–1120 (2009).
  • Yoshida W, Sode K, Ikebukuro K. Homogeneous DNA sensing using enzyme-inhibiting DNA aptamers. Biochem. Biophys. Res. Commun. 348(1), 245–252 (2006).
  • Ikebukuro K, Yoshida W, Sode K. Aptameric enzyme subunit for homogeneous DNA sensing. Biotechnol. Lett. 30(2), 243–252 (2008).
  • Ferri S, Kojima K, Sode K. Review of glucose oxidases and glucose dehydrogenases: a bird’s eye view of glucose sensing enzymes. J. Diabetes Sci. Technol. 5(5), 1068–1076 (2011).
  • Abe K, Hasegawa H, Ikebukuro K. Electrochemical detection of vascular endothelial growth factor by an aptamer-based bound/free separation system. Electrochemistry 80(5), 348–352 (2012).
  • Abe K, Kiyohara C, Saito Y, Sode K, Ikebukuro K. Electrochemical SNP detection using glucose dehydrogenase. Electrochemistry 80(5), 345–347 (2012).
  • Fukasawa M, Yoshida W, Yamazaki H, Sode K, Ikebukuro K. An aptamer-based bound/free separation system for protein detection. Electroanalysis 21(11), 1297–1302 (2009).
  • Nonaka Y, Abe K, Ikebukuro K. Electrochemical detection of vascular endothelial growth factor with aptamer sandwich. Electrochemistry 80(5), 363–366 (2012).
  • Yamazaki T, Okuda-Shimazaki J, Sakata C, Tsuya T, Sode K. Construction and characterization of direct electron transfer-type continuous glucose monitoring system employing thermostable glucose dehydrogenase complex. Anal. Lett. 41(13), 2363–2373 (2008).
  • Morita Y, Yoshida W, Savory N et al. Development of a novel biosensing system based on the structural change of a polymerized guanine-quadruplex DNA nanostructure. Biosens. Bioelectron. 26(12), 4837–4841 (2011).
  • Xiang Y, Lu Y. Using personal glucose meters and functional DNA sensors to quantify a variety of analytical targets. Nat. Chem. 3(9), 697–703 (2011).
  • Zhu Z, Wu C, Liu H et al. An aptamer cross-linked hydrogel as a colorimetric platform for visual detection. Angew. Chem. Int. Ed. Engl. 49(6), 1052–1056 (2010).
  • Yan L, Zhu Z, Zou Y et al. Target-responsive “Sweet” hydrogel with glucometer readout for portable and quantitative detection of non-glucose targets. J. Am. Chem. Soc. 135(10), 3748–3751 (2013).
  • Sano T, Smith CL, Cantor CR. Immuno-PCR: very sensitive antigen detection by means of specific antibody-DNA conjugates. Science 258(5079), 120–122 (1992).
  • Pinto A, Bermudo Redondo MC, Ozalp VC, O’sullivan CK. Real-time apta-PCR for 20 000-fold improvement in detection limit. Mol. Biosyst. 5(5), 548–553 (2009).
  • Zhou L, Ou LJ, Chu X, Shen GL, Yu RQ. Aptamer-based rolling circle amplification: a platform for electrochemical detection of protein. Anal. Chem. 79(19), 7492–7500 (2007).
  • Fredriksson S, Gullberg M, Jarvius J et al. Protein detection using proximity-dependent DNA ligation assays. Nat. Biotechnol. 20(5), 473–477 (2002).
  • Wang X-L, Li F, Su Y-H et al. Ultrasensitive detection of protein using an aptamer-based exonuclease protection assay. Anal. Chem. 76(19), 5605–5610 (2004).
  • Yang L, Ellington AD. Real-time PCR detection of protein analytes with conformation-switching aptamers. Anal. Biochem. 380(2), 164–173 (2008).
  • Yang L, Fung CW, Cho EJ, Ellington AD. Real-time rolling circle amplification for protein detection. Anal. Chem. 79(9), 3320–3329 (2007).
  • Pinto A, Lennarz S, Rodrigues-Correia A, Heckel A, Sullivan CK, Mayer G. Functional detection of proteins by caged aptamers. ACS Chem. Biol. 7(2), 360–366 (2012).
  • Shlyahovsky B, Li D, Weizmann Y, Nowarski R, Kotler M, Willner I. Spotlighting of cocaine by an autonomous aptamer-based machine. J. Am. Chem. Soc. 129(13), 3814–3815 (2007).
  • Jensen KB, Atkinson BL, Willis MC, Koch TH, Gold L. Using in vitro selection to direct the covalent attachment of human immunodeficiency virus type 1 Rev protein to high-affinity RNA ligands. Proc. Natl Acad. Sci. USA 92(26), 12220–12224 (1995).
  • Bock C, Coleman M, Collins B et al. Photoaptamer arrays applied to multiplexed proteomic analysis. Proteomics 4(3), 609–618 (2004).
  • Cho EJ, Collett JR, Szafranska AE, Ellington AD. Optimization of aptamer microarray technology for multiple protein targets. Anal. Chim. Acta 564(1), 82–90 (2006).
  • Gold L, Ayers D, Bertino J et al. Aptamer-based multiplexed proteomic technology for biomarker discovery. PLoS ONE 5(12), e15004 (2010).
  • Liu L, Li Y, Li S et al. Comparison of next-generation sequencing systems. J. Biomed. Biotechnol. 2012, 251364 (2012).
  • Cho M, Xiao Y, Nie J et al. Quantitative selection of DNA aptamers through microfluidic selection and high-throughput sequencing. Proc. Natl Acad. Sci. USA 107(35), 15373–15378 (2010).
  • Turner DJ, Tuytten R, Janssen KPF et al. Toward clinical proteomics on a next-generation sequencing platform. Anal. Chem. 83(3), 666–670 (2011).
  • Rotem D, Jayasinghe L, Salichou M, Bayley H. Protein detection by nanopores equipped with aptamers. J. Am. Chem. Soc. 134(5), 2781–2787 (2012).
  • Kimoto M, Yamashige R, Matsunaga K, Yokoyama S, Hirao I. Generation of high-affinity DNA aptamers using an expanded genetic alphabet. Nat. Biotechnol. 31(5), 453–457 (2013).
  • Polz MF, Cavanaugh CM. Bias in template-to-product ratios in multitemplate PCR. Appl. Environ. Microbiol. 64(10), 3724–3730 (1998).
  • Kanagawa T. Bias and artifacts in multitemplate polymerase chain reactions (PCR). J. Biosci. Bioeng. 96(4), 317–323 (2003).
  • Klug SJ, Famulok M. All you wanted to know about SELEX. Mol. Biol. Rep. 20(2), 97–107 (1994).
  • Chushak Y, Stone MO. In silico selection of RNA aptamers. Nucl. Acids Res. 37(12), e87 (2009).
  • Breaker RR. Prospects for riboswitch discovery and analysis. Mol. Cell. 43(6), 867–879 (2011).
  • Matylla-Kulinska K, Boots JL, Zimmermann B, Schroeder R. Finding aptamers and small ribozymes in unexpected places. Wiley Interdiscip. Rev. RNA 3(1), 73–91 (2012).
  • Weinberg Z, Wang JX, Bogue J et al. Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes. Genome Biol. 11(3), R31 (2010).
  • Bochman ML, Paeschke K, Zakian VA. DNA secondary structures: stability and function of G-quadruplex structures. Nat. Rev. Genet. 13(11), 770–780 (2012).
  • Yoshida W, Saito T, Yokoyama T, Ferri S, Ikebukuro K. Aptamer selection based on g4-forming promoter region. PLoS ONE 8(6), e65497 (2013).

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