Advances in aptamer screening and small molecule aptasensors

Advances in Biochemical Engineering/Biotechnology

Volumn 140, Issue , 2014, Pages 29-67

  Kim, Yeon Seok ^a   Gu, Man Bock ^b  

^a SK Telecom   (South Korea)

^b Korea University   (South Korea)

Author keywords

Aptamers; SELEX; Small molecule aptasensors

Indexed keywords

APTAMER;

CHEMISTRY; COMBINATORIAL CHEMISTRY; CONDUCTOMETRY; GENETIC PROCEDURES; GENETICS; HIGH THROUGHPUT SCREENING; IMMUNOASSAY; METHODOLOGY; MOLECULAR LIBRARY; REVIEW; SPECTROFLUOROMETRY; SYNTHESIS;

APTAMERS, NUCLEOTIDE; BIOSENSING TECHNIQUES; CONDUCTOMETRY; HIGH-THROUGHPUT SCREENING ASSAYS; IMMUNOASSAY; SELEX APTAMER TECHNIQUE; SMALL MOLECULE LIBRARIES; SPECTROMETRY, FLUORESCENCE;

EID: 84902662444     PISSN: 07246145     EISSN: None     Source Type: Book Series    
DOI: 10.1007/10_2013_225     Document Type: Article

References (183)

1. Ellington AD, Szostak JW (1990) In vitro selection of RNA molecules that bind specific ligands. Nature 346:818–822
2. Tuerk C, Gold L (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA-polymerase. Science 249:505–510
3. Jayasena SD (1999) Aptamers: an emerging class of molecules that rival antibodies in diagnostics. Clinic Chem 45:1628–1650
4. Patel DJ, Suri AK, Jiang F, Jiang LC, Fan F, Kumar RA, Nonin S (1997) Structure, recognition and adaptive binding in RNA aptamer complex. J Mol Biol 272:645–664
5. Hermann T, Patel DJ (2000) Adaptive recognition by nucleic acid aptamers. Science 87:820–825
6. Osborne SE, Ellington AE (1997) Nucleic acid selection and the challenge of combinatorial chemistry. Chem Rev 97:349–370
7. Jenison RD, Gill SC, Pardi A, Polisky B (1994) High-resolution molecular discrimination by RNA. Science 263:1425–1429
8. Geiger A, Burgstaller P, Von der Eltz H, Roeder A, Famulok M (1996) RNA aptamers that bind L-arginine with sub-micromolar dissociation constants and high enantioselectivity. Nucleic Acids Res 24:1029–1036
9. Niazi JH, Lee SJ, Kim YS, Gu MB (2008) ssDNA aptamers that selectively bind oxytetracycline. Bioorg Med Chem 16:1254–1261
10. You KM, Lee SH, Im A, Lee SB (2003) Aptamers as functional nucleic acids: in vitro selection and biotechnological applications. Biotech Bioprocess Eng 8:64–75
11. Tombelli S, Minunni M, Mascini M (2005) Analytical application of aptamers. Biosens Bioelectron 20:2424–2434
12. Baldrich E, Acero JL, Reekmans G, Laureyn W, O’Sullivan CK (2005) Displacement enzyme linked aptamer assay. Anal Chem 77:4774–4784
13. Robertson DL, Joyce GF (1990) Selection in vitro of an RNA enzyme that specifically cleaves single-stranded DNA. Nature 344:467–468
14. Ho SP, Britton DH, Stone BA, Behrens DL, Leffet LM, Hobbs FW, Miller JA, Trainor GL (1996) Potent antisense oligonucleotides to human multidrug resistance-1 mRNA are rationally selected by mapping RNA-accessible sites with oligonucleotide libraries. Nucleic Acids Res 24:1901–1907
15. Bock LC, Griffin LC, Latham JA, Vermaas EH, Toole JJ (1992) Selection of single-stranded DNA molecules that bind and inhibit human thrombin. Nature 355:564–566
16. Marshall KA, Ellington AD (2000) In vitro selection of RNA aptamers. Meth Enzymol 318:19–214
17. Sampson T (2003) Aptamers and SELEX: the technology. World Patent Inf 25:123–129
18. Harada K, Frankel AD (1995) Identification of two novel arginine binding DNAs. EMBO J 23:5798–5811
19. Hamula C, Guthrie J, Zhang H, Li XF, Le XC (2006) Selection and analytical applications of aptamers. Tr Anal Chem 25:681–691
20. Reinemann C, Stoltenburg R, Strehlitz B (2009) Investigations on the specificity of DNA aptamers binding to ethanolamine. Anal Chem 81:3973–3978
21. Berezovski M, Drabovich A, Krylova SM, Musheev M, Okhonin V, Petrov A, Krylov SN (2005) Nonequilibrium capillary electrophoresis of equilibrium mixtures: a universal tool for development of aptamers. J Am Chem Soc 127:3165–3171
22. White R, Rusconi C, Scardino E, Wolberg A, Lawson J, Hoffman M, Sullenger B (2001) Generation of species cross-reactive aptamers using “toggle” SELEX. Mol Ther 4:567–573
23. Shimada T, Fujita N, Maeda M, Ishihama A (2005) Systematic search for the Cra-binding promoters using genomic SELEX system. Genes Cells 10:907–917
24. Stoltenburg R, Reinemann C, Strehlitz B (2005) FluMag-SELEX as an advantageous method for DNA aptamer selection Anal. Bioanal Chem 383:83–91
25. Bianchini M, Radrizzani M, Brocardo MG, Reyes GB, Gonzalez SC, Santa-Coloma TA (2001) Specific oligobodies against ERK-2 that recognize both the native and the denatured state of the protein. J Immunol Methods 252:191–197
26. Theis MG, Knorre A, Kellersch B, Moelleken J, Wieland F, Kolanus W, Famulok M (2004) Discriminatory aptamer reveals serum response element transcription regulated by cytohesin-2. Proc Natl Acad Sci 101:11221–11226
27. Weiss S, Proske D, Neumann M, Groschup MH, Kretzschmar HA, Famulok M, Winnacker EL (1997) RNA aptamers specifically interact with the prion protein PrP. J Virol 71:8790–8797
28. Bridonneau P, Chang YF, Buvoli VB, O’Connell D, Parma D (1999) Site directed selection of oligonucleotide antagonists by competitive elution. Antisens. Nucleic A 9:1–11
29. Sefah K, Shangguan D, Xiong X, O’Donoghue MB, Tan W (2010) Development of DNA aptamers using cell-SELEX. Nat Protocol 5:1169–1185
30. Cadwell RC, Joyce GF (1994) Mutagenic PCR. PCR methods Appl 3:S136–S140
31. Bittker JA, Le BV, Liu DR (2002) Nucleic acids evolution and minimization by nonhomologous random recombination. Nat Biotechnol 20:1204–1209
32. Paul A, Avci-Adali M, Ziemer G, Wendel HP (2009) Streptavidin-coated magnetic beads for DNA strand separation implicate a multitude of problems udirng cell-SELEX. Oligonucleotides 19:243–254
33. Fitzwater T, Polisky B (1996) A SELEX primer Methods Enzymol 267:275–301
34. Naimuddin M, Kitamura K, Kinoshita Y, Honda-Takahashi Y, Murakami M, Ito M, Yamamoto K, Hanada K, Husimi Y, Nishigaki K (2007) Selection-by-function: efficient enrichment of cathepsin E inhibitors from a DNA library. J Mol Recognit 20:58–68
35. Wu LH, Curran JF (1999) An allosteric synthetic DNA. Nucleic Acids Res 27:1512–1516
36. Williams KP, Bartel DP (1995) PCR product with strands of unequal length. Nucleic Acids Res 23:4220–4221
37. Hendry P, Hannan G (1996) Detection and quantitation of unlabeled nucleic acids in polyacrylamide gels. Biotechniques 20:258–264
38. Niazi JH, Lee SJ, Gu MB (2008) Single stranded DNA aptamers specific for antibiotics tetracyclines. Bioorg Med Chem 16:7245–7253
39. Kim YS, Hyun CJ, Kim IA, Gu MB (2010) Isolation and characterization of enantioselective DNA aptamers for ibuprofen. Bioorg Med Chem 18:3467–3473
40. Shi H, Fan XC, Ni ZY, Lis JT (2002) Evolutionary dynamics and population control during in vitro selection and amplification with multiple targets. RNA 8:1461–1470
41. Beinoraviciute-Kellner R, Lipps G, Krauss G (2005) In vitro selection of DNA binding sites for ABF1 protein from Saccharomyces cerevisiae. FEBS Lett 579:4535–4540
42. Rhie A, Kirby L, Sayer N, Wellesley R, Disterer P, Sylvester I, Gill A, Hope J, James W, Tahiri-Alaoui A (2003) Characterization of 2’-fluoro-RNA aptamers that bind preferentially to disease-associated conformations of prion protein and inhibit conversion. J Biol Chem 278:39697–39705
43. Ellington AD, Szostak JW (1992) Selection in vitro of single-stranded DNA molecules that fold into specific ligand-binding structures. Nature 355:850–852
44. Wang W, Jia L (2009) Progress in aptamer screening methods. Chin J Anal Chem 37:454–460
45. Wang CL, Zhang M, Yang G, Zhang DJ, Ding HM, Wang HX, Fan M, Shen BF, Shao NS (2003) Single-stranded DNA aptamers that bind differentiated but not parental cells: subtractive systematic evolution of ligands by exponential enrichment. J Biotechnol 102:15–22
46. Shangguan D, Li Y, Tang Z, Cao ZC, Chen HW, Mallikaratchy P, Sefah K, Yang CZ, Tan W (2006) Aptamers evolved from live cells as effective molecular probes for cancer study. Proc Natl Acad Sci 103:11838–11843
47. Conrad RC, Baskerville S, Ellington AD (1995) In vitro selection methodologies to probe RNA function and structure. Mol Div 1:69–78
48. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680
49. Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD (2003) Multiple sequence alignment with the clustal series of programs. Nucleic Acids Res 31:3497–3500
50. Morgenstern B (2004) DIALIGN: multiple DNA and Protein Sequence Alignment at BiBiServ. Nucleic Acids Res 32:W33–W36
51. Morgenstern B, Prohaska SJ, Pöhler D, Stadler PF (2006) Multiple sequence alignment with user-defined anchor points. Algorithms Mol Boil 1:6
52. Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31:3406–3415
53. Horn WT, Convery MA, Stonehouse NJ, Adams CJ, Liljas L, Phillips SEV, Stockley PG (2004) The crystal structure of a high affinity RNA stem-loop complexed with the bacteriophage MS2 capsid: further challenges in the modeling of ligand-RNA interactions. RNA 10:1776–1782
54. Macaya RF, Schultze P, Smith FW, Roe JA, Feigon J (1993) Thrombin binding DNA aptamer forms a unimolecular quadruplex structure in solution. Proc Natl Acad Sci 90:3745–3749
55. Chaloin L, Lehmann MJ, Sczakiel G, Restle T (2002) Endogenous expression of a highaffinity pseudoknot RNA aptamer suppresses replication of HIV-1. Nucleic Acids Res 30:4001–4008
56. Bruno JG, Kiel JL (1999) In vitro selection of DNA aptamers to anthrax spores with electrochemiluminescence detection. Biosens Bioelectron 14:457–464
57. Ruff KM, Snyder TM, Liu DR (2010) Enhanced functional potential of nucleic acid aptamer library patterned to increase secondary structure. J Am Chem Soc 132:9453–9464
58. Wilson C, Keefe AD (2006) Building oligonucleotide therapeutics using non-natural chemistries. Curr Opin Chem Biol 10:607–614
59. Kusser W (2000) Chemically modified nucleic acid aptamers for in vitro selections: evolving evolution. J Biotechnol 74:27–38
60. Pieken W, Olsen DB, Benseler F, Aurup H, Eckstein HF (1991) Kinetic characterization of ribonuclease-resistant 20-modified hammerhead ribozymes. Science 253:314–317
61. Heidenreich O, Eckstein F (1992) Hammerhead ribozyme-mediated cleavage of the long terminal repeat RNA of human immunodeficiency virus type 1. J Biol Chem 267:1904–1909
62. Kubik MF, Bell C, Fitzwater T, Watson SR, Tasset DM (1997) Isolation and characterization of 2’-fluoro-, 2’-amino-, and 2’-fluoro-/amino- modified RNA ligands to human INF-gamma that inhibit receptor binding. J Immunol 159: 259–267
63. Prakash TP, Bhat B (2007) 2’-modified oligonucleitides for antisense therapeutics. Curr Top Med Chem 7:641–649
64. Koizumi M (2007) True antisense oligonucleotides with modified nucleotides restricted in the N-conformation. Curr Top Med Chem 7:661–665
65. Sawai H, Ozaki A, Satoh F, Ohbayashi T, Masud M, Ozaki H (2001) Expansion of structural and functional diversities of DNA using new 5-substituted deoxyuridinederivatives by PCR with superthermophilic KOD Dash DNA polymerase, Chem Commun 24:2604–2605
66. Kuwahara M, Hanawa K, Ohsawa K, Kitagata R, Ozaki H, Sawai H (2006) Direct PCR amplification of various modified DNAs having amino acids: convenient preparation of DNA libraries with high-potential activities for in vitro selection. Bioorg Med Chem 14:2518–2526
67. Keefe AD, Cload ST (2008) SELEX with modified nucleotides. Curr Opion Chem Biol 12:448–456
68. Golden MC, Collins BD, Willis MC, Koch TH (2000) Diagnostic potential of photoSELEXevolved ssDNA aptamers. J Biotechnol 81:167–178
69. Singer BS, Shtatland T, Brown D, Gold L (1997) Libraries for genomic SELEX. Nucleic Acids Res 25:781–786
70. Shtatland T, Gill SC, Javornik BE, Johansson HE, Singer BS, Uhlenbeck OC, Zichi DA, Gold L (2000) Interactions of Escherichia coli RNA with bacteriophage MS2 coat protein: genomic SELEX. Nucleic Acids Res 28:E93
71. Fischer NO, Tok J, Tarasow TM (2008) Massively parallel interrogation of aptamer sequence, structure and function. PLoS ONE 3:e2720
72. Katilius E, Flores C, Woodbury NW (2007) Exploring the sequence space of a DNA aptamer using microarrays. Nucleic Acids Res 35:7626–7635
73. Wen JD, Gray DM (2004) Selection of genomic sequences that bind tightly to Ff gene 5 protein: primer-free genomic SELEX. Nucleic Acids Res 32:e182
74. Pan WH, Xin P, Clawson GA (2008) Minimal primer and primer-free SELEX protocols for selection of aptamers from random DNA libraries. Biotechniques 44:351–360
75. Vater A, Jarosch F, Buchner K, Klussmann S (2003) Short bioactive Spiegelmers to migraine-associated calcitonin gene-related peptide rapidly identified by a novel approach: tailored-SELEX. Nucleic Acids Res 31:e130
76. Burke DH, Willis JH (1998) Recombination, RNA evolution, and bifunctional RNA molecules isolated through Chimeric SELEX. RNA 4:1165–1175
77. Deng Q, German I, Buchanan D, Kennedy RT (2001) Retention and separation of adenosine and analogues by affinity chromatography with an aptamer stationary phase. Anal Chem 73:5415–5421
78. Bruno JG, Kiel JL (2002) Use of magnetic beads in selection and detection of biotoxin aptamers by electrochemiluminescence and enzymatic methods. Biotechniques 32(178–180): 182–173
79. Tok JB, Fischer NO (2008) Single microbead SELEX for efficient ssDNA aptamer generation against botulinum neurotoxin. Chem Comm 16:1883–1885
80. Mendonsa SD, Bowser MT (2004) In vitro selection of high-affinity DNA ligands for human IgE using capillary electrophoresis. Anal Chem 76:5387–5392
81. Tang JJ, Xie JW, Shao NS, Yan Y (2006) The DNA aptamers that specifically recognize ricin toxin are selected by two in vitro selection methods. Electrophoresis 27:1303–1311
82. Drabovich AP, Berezovski M, Okhonin V, Krylov SN (2006) Selection of smart aptamers by methods of kinetic capillary electrophoresis. Anal Chem 78:3171–3178
83. Mosing RK, Mendonsa SD, Bowser MT (2005) Capillary electrophoresis-SELEX selection of aptamers with affinity for HIV-1 reverse transcriptase. Anal Chem 77:6107–6112
84. Cox JC, Rudolph P, Ellington AD (1998) Automated RNA selection. Biotechnol Prog 14:845–850
85. Cox JC, Ellington AD (2001) Automated selection of anti-protein aptamers. Bioorg Med Chem 9:2525–2531
86. Cox JC, Rajendran M, Riedel T, Davidson EA, Sooter LJ, Bayer TS, Schmitz BM, Ellington AD (2002) Automated acquisition of aptamer sequences. Comb Chem High Throughput Screening 5:289–299
87. Cox JC, Hayhurst A, Hesselberth J, Bayer TS, Georgiou G, Ellington AD (2002) Automated selection of aptamers against protein targets translated in vitro: from gene to aptamer. Nucleic Acids Res 30:e108
88. Hianik T, Ostatna V, Sonlajtnerova M, Grman I (2007) Influence of ionic strength, pH, and aptamer configuration for binding affinity to thrombin. Biochem 70:127–133
89. Eulberg D, Buchner K, Maasch C, Klussmann S (2005) Development of an automated in vitro selection protocol to obtain RNA-based aptamers: identification of a biostable substance P antagonist. Nucleic Acids Res 33:e45
90. Hybarger G, Bynum J, Williams RF, Valdes JJ, Chambers JP (2006) A microfluidic SELEX prototype. Anal Bioanal Chem 384:191–198
91. Park SM, Ahn JY, Jo MJ, Lee D, Lis JT, Craighead HG, Kim S (2009) Selection and elution of aptamers using nanoporous sol-gel arrays with integrated microheaters. Lab Chip 9:1206–1212
92. Lou X, Qian J, Xiao Y, Viel L, Gerdon AE, Lagally ET, Atzberger P, Tarasow TM, Heeger AJ, Soh HT (2009) Micromagnetic selection of aptamers in microfluidic channels. Proc Natl Acad Sci 106:2989–2994
93. Gian J, Lou X, Zhang Y, Xiao Y, Soh HT (2009) Generation of high specific aptamers via micromagnetic selection. Anal Chem 81:5490–5495
94. Ciesiolka J, Gorski J, Yarus M (1995) Selection of an RNA domain that binds Zn2+. RNA 1:538–550
95. Hofmann HP, Limmer S, Hornung V, Sprinzl M (1997) Ni2 ? -binding RNA motifs with an asymmetric purine-rich internal loop and a G-A base pair. RNA 3:1289–1300
96. Kim M, Um HJ, Bang S, Lee SH, Oh SJ, Han JH, Kim KW, Min J, Kim YH (2009) Arsenic removal from Vietnamese groundwater using the Arsenic-binding DNA aptamer. Environ Sci Technol 43:9335–9340
97. Mann D, Reinemann C, Stoltenburg R, Strehlitz B (2005) In vitro selection of DNA aptamers binding ethanolamine. Biochem Biophys Res Commun 338:1928–1934
98. Grate D, Wilson C (2001) Inducible regulation of the S-cerevisiae cell cycle mediated by an RNA aptamer-ligand complex. Bioorg Med Chem 9:2565–2570
99. Stojanovic MN, Landry DW (2002) Aptamer-based colorimetric probe for cocaine. J Am Chem Soc 124:9678–9679
100. Kato T, Takemura T, Yano K, Ikebukuro K, Karube I (2000) In vitro selection of DNA aptamers which bind to cholic acid. Biochim Biophys Acta 1493:12–18
101. Vianini E, Palumbo M, Gatto B (2001) In vitro selection of DNA aptamers that bind L-tyrosinamide. Bioorg Med Chem 9:2543–2548
102. Park JW, Tatavarty R, Kim DW, Jung HE, Gu MB (2012) Immobilization-free screening of aptamers assisted by graphene oxide. Chem Com 48:2071–2073
103. Wu M, Kempaiah R, Huang PJJ, Maheshwari V, Liu J (2011) Adsorption and desorption of DNA on graphene oxide studies by fluorescently labeled oligonucleotides. Langmuir 27:2731–2738
104. Nutiu R, Li YF (2005) In vitro selection of structure-switching signaling aptamers. Angew Chem Int Edit 44:1061–1065
105. Daniels DA, Chen H, Hicke BJ, Swiderek KM, Gold L (2003) A tenascin-C aptamer identified by tumor cell SELEX: systematic evolution of ligands by exponential enrichment. Proc Natl Acad Sci 100:15416–15421
106. Cerchia L, Duconge F, Pestourie C, Boulay J, Aissouni Y, Gombert K, Tavitian B, de Franciscis V, Libri D (2005) Neutralizing aptamers from whole-cell SELEX inhibit the RET receptor tyrosine kinase. PLoS Biol 3:697–704
107. Tang Z, Shangguan D, Wang K, Shi H, Sefah K, Mallikratchy P, Chen HW, Li Y, Tan W (2007) Selection of aptamers for molecular recognition and characterization of cancer cells. Anal Chem 79:4900–4907
108. Kim YS, Jung HS, Matsuura T, Lee HY, Kawai T, Gu MB (2007) Electrochemical detection of 17b-estradiol using DNA aptamer immobilized gold electrode chip. Biosens Bioelectron 22:2525–2531
109. Song S, Wang L, Li J, Zhao J, Fan C (2008) Aptamer-based biosensors. Trends Anal Chem 27:108–117
110. Li D, Song S, Fan C (2010) Target-responsive structural switching for nucleic acid-based sensors. Acc Chem Res 43:631–614
111. Yamamoto R, Baba T, Kumar PK (2000) Molecular beacon aptamer fluorescence in the presence of Tat protein of HIV-1. Genes Cells 5:389–396
112. Frauendorf CA, Jaschke A (2001) Detection of small organic analytes by fluorescing molecular switches. Bioorg Med Chem 9:2521–2524
113. Song Y, Zhao C, Ren J, Qu X (2009) Rapid and ultra-sensitive detection of AMP using a fluorescent and magnetic nano-silica sandwich complex. Chem Commun 15:1975–1977
114. Nutiu R, Li Y (2003) Structure-switching signaling aptamers. J Am Chem Soc 125:4771–4778
115. Cruz-Aguado JA, Penner G (2008) Fluorescence polarization based displacement assay for the determination of small molecules with aptamers. Anal Chem 80:8853–8855
116. Wu C, Yan L, Wang C, Lin H, Wang C, Chen X, Yang CJ (2010) A general excimer signaling approach for aptamer sensors. Biosens Bioelectron 25:2232–2237
117. Liu JW, Lee JH, Lu Y (2007) Quantum dot encoding of aptamer-linked nanostructures for one-pot simultaneous detection of multiple analytes. Anal Chem 79:4120–4125
118. Fan C, Wang S, Hong JW, Bazan GC, Plaxco KW, Heeger AJ (2003) Beyond superquenching: hyper-efficient energy transfer from conjugated polymers to gold nanoparticles. Proc Natl Acad Sci 100:6297–6301
119. Song S, Liang Z, Zhang J, Wang L, Li G, Fan C (2009) Gold-nanoparticle-based multicolor nanobeacons for sequence-specific DNA analysis. Angew Chem Int Ed 48:8670–8674
120. Zhang J, Wang L, Zhang H, Boey F, Song S, Fan C (2010) Aptamer-based multicolor fluorescent gold nanoparticles for multiplex detection in homogenous solution. Small 6:201–204
121. Kim YS, Jurng J (2011) Gold nanoparticle-based homogeneous fluorescent aptasensor for multiplex detection. Analyst 136:3720–3724
122. Yang R, Tang Z, Yan J, Kang H, Kim Y, Zhu Z, Tan W (2008) Noncovalent assembly of carbon nanotubes and single-stranded DNA: an effective sensing platform for probing biomolecular interactions. Anal Chem 80:7408–7413
123. Chang H, Tang L, Wang Y, Jiang J, Li J (2010) Graphene fluorescence resonance energy transfer aptasensor for the thrombin detection. Anal Chem 82:2341–2346
124. Sheng L, Ren J, Miao Y, Wang J, Wang E (2011) PVP-coated graphene oxide for selective determination of ochratoxin A via quenching fluorescence of free aptamer. Biosens Bioelectron 26:3494–3499
125. Stojanovic MN, de Prada P, Landry DW (2001) Aptamer-based folding fluorescent sensor for cocaine. J Am Chem Soc 123:4928–4931
126. Liu CW, Huang CC, Chang HT (2009) Highly selective DNA-based sensor for lead(II) and mercury(II) ions. Anal Chem 81:2383–2387
127. Ozaki H, Nishihira A, Wakabayashi M, Kuwahara M, Sawai H (2006) Biomolecular sensor based on fluorescence-labeled aptamer. Bioorg Med Chem Lett 16:4381–4384
128. Xiang Y, Tong A, Lu Y (2009) Abasic site-containing DNAzyme and aptamer for label-free fluorescent detection of Pb2 ? and adenosine with high sensitivity, selectivity, and tunable dynamic range. J Am Chem Soc 131:15352–15357
129. Xiang Y, Wang Z, Xing H, Wong NY, Lu Y (2010) Label-free fluorescent functional DNA sensors using unmodified DNA: a vacant site approach. Anal Chem 82:4122–4129
130. Xu Z, Morita K, Sato Y, Dai Q, Nishizawa S, Teramae N (2009) Label-free aptamer-based sensor using abasic site-containing DNA and a nucleobase-specific fluorescent ligand. Chem Commun 42:6445–6447
131. Li B, Qin C, Li T, Wang L, Dong S (2009) Fluorescent switch constructed based on heminsensitive anionic conjugated polymer and its applications in DNA-related sensors. Anal Chem 81:3544–3550
132. Zhang CY, Johnson LW (2009) Single quantum-dot-based aptameric nanosensor for cocaine. Anal Chem 81:3051–3055
133. Zhu Z, Yang C, Zhou X, Qin J (2011) Label-free aptamer-based sensors for L-argininamide by using nucleic acid minor groove binding dyes. Chem Commun 47:3192–3194
134. Xu W, Lu Y (2010) Label-free fluorescent aptamer sensor based on regulation of malachite green fluorescence. Anal Chem 82:574–578
135. Babendure JR, Adams SR, Tsien RY (2003) Aptamers switch on fluorescence of triphenylmethane dyes. J Am Chem Soc 125:14716–14717
136. Sando S, Narita A, Hayami M, Aoyama Y (2008) Transcription monitoring using fused RNA with a dyebinding light-up aptamer as a tag: a blue fluorescent RNA. Chem Commun 33:3858–3860
137. Furutani C, Shinomiya K, Aoyama Y, Yamada K, Sando S (2010) Modular blue fluorescent RNA sensors for label-free detection of target molecules. Mol BioSyst 6:1569–1571
138. Shi Y, Huang WT, Luo HQ, Li NB (2011) A label-free DNA reduced graphene oxide-based fluorescent sensor for highly sensitive and selective detection of hemin. Chem Commun 47:4676–4678
139. Huang CC, Chang HT (2008) Aptamer-based fluorescence sensor for rapid detection of potassium ions in urine. Chem Commun 12:1461–1463
140. Rotaru A, Dutta S, Jentzsch E, Gothelf K, Mokhir A (2010) Selective dsDNA-templated formation of copper nanoparticles in solution. Angew Chem Int Ed 49:5665–5667
141. Liu J, Lu Y (2003) A colorimetric lead biosensor using DNAzyme-directed assembly of gold nanoparticles. J Am Chem Soc 125:6642–6643
142. Liu J, Lu Y (2007) A DNAzyme catalytic beacon sensor for paramagnetic Cu2 ? ions in aqueous solution with high sensitivity and selectivity. J Am Chem Soc 129:9838–9839
143. Zhang J, Wang L, Pan D, Song S, Boey F, Zhang H, Fan C (2008) Visual cocaine detection with gold nanoparticles and rationally engineered aptamer structures. Small 4:1196–1200
144. Liu J, Lu Y (2006) Fast colorimetric sensing of adenosine and cocaine based on a general sensor design involving aptamers and nanoparticles. Angew Chem Int Ed 45:90–94
145. Liu J, Mazumdar D, Lu Y (2006) A simple and sensitive “dipstick” test in serum based on lateral flow separation of aptamer-linked nanostructures. Angew Chem Int Ed 45: 7955–7959
146. Zhao WA, Chiuman W, Brook MA, Li YF (2007) Simple and rapid colorimetric biosensors based on DNA aptamer and noncrosslinking gold nanoparticle aggregation. ChemBioChem 8:727–731
147. Huang CC, Huang YF, Cao Z, Tan W, Chang HT (2005) Aptamer-modified gold nanoparticles for colorimetric determination of platelet-derived growth factors and their receptors. Anal Chem 77:5735–5741
148. Ono A, Torigou H, Tanaka Y, Okamoto I (2011) Binding of metal ions by pyrimidine base pairs in DNA duplexes. Chem Soc Rev 40:5855–5866
149. Lee JS, Han MS, Mirkin CA (2007) Colorimetric detection of mercuric ion (Hg2+) in aqueous media using DNA-functionalized gold nanoparticles. Angew Chem Int Ed 46:4093–4096
150. Xu H, Wang Y, Huang X, Li Y, Zhang H, Zhong X (2012) Hg2+ -mediated aggregation of gold nanoparticles for colorimetric screening of biothiols. Analyst 137:924–931
151. Li B, Du Y, Dong S (2009) DNA based gold nanoparticles colorimetric sensors for sensitive and selective detection of Ag(I) ions. Anal Chimi Acta 644:78–82
152. Li H, Rothberg L (2004) Colorimetric detection of DNA sequences based on electrostatic interactions with unmodified gold nanoparticles. Proc Natl Acad Sci 101:14036–14039
153. Wei H, Li B, Li J, Dong S, Wang E (2008) DNAzyme-based colorimetric sensing of lead (Pb2 +) using unmodified gold nanoparticle probes. Nanotechnology 19:1–5
154. Wang L, Liu X, Hu X, Song S, Fan C (2006) Unmodified gold nanoparticles as a colorimetric probe for potassium DNA aptamers. Chem Commun 28:3780–3782
155. Liu CW, Hsieh YT, Huang CC, Lin ZH, Chang HT (2008) Detection of mercury(II) based on Hg2 ? –DNA complexes inducing the aggregation of gold nanoparticles. Chem Commun ***2242–2244
156. Kim YS, Kim JH, Kim IA, Lee SJ, Jurng J, Gu MB (2010) A novel colorimetric aptasensor using gold nanoparticle for a highly sensitive and specific detection of oxytetracycline. Biosens Bioelectron 26:1644–1649
157. Kim YS, Kim JH, Kim IA, Lee SJ, Gu MB (2011) The affinity ratio—Its pivotal role in gold nanoparticle-based competitive colorimetric aptasensor. Biosens Bioelectron 26:4058–4063
158. Wang J, Wang L, Liu X, Liang Z, Song S, Li W, Li G, Fan W (2007) A gold nanoparticlebased aptamer target binding readout for ATP assay. Adv Mater 19:3943–3946
159. Lee J, Kim HJ, Kim J (2008) Polydiacetylene liposome arrays for selective potassium detection. J Am Chem Soc 130:5010–5011
160. Lee J, Seo S, Kim J (2012) Colorimetric detection of warfare gases by polydiacetylenes toward equipment-free detection. Adv Func Mater 22:1632–1638
161. Liu X, Tang Y, Wang L, Zhang J, Song S, Fan C, Wang S (2007) Optical detection of mercury(II) in aqueous solutions by using conjugated polymers and label-free oligonucleotides. Adv Mater 19:1471–1474
162. Rodriguez MC, Kawde AN, Wang J (2005) Aptamer biosensor for label-free impedance spectroscopy detection of proteins based on recognition-induced switching of the surface charge. Chem Commun 2005:4267–4269
163. Radi AE, Sanchez JLA, Baldrich E, O’Sullivan CK (2005) Reusable impedimetric aptasensor. Anal Chem 77:6320–6323
164. Xu Y, Yang L, Ye XY, He PA, Fang YZ (2006) An aptamer-based protein biosensor by detecting the amplified impedance signal. Electroanal 18:1449–1456
165. Kim YS, Niazi JH, Gu MB (2009) Sepecific detection of oxytetracycline using DNA aptamer-immobilized interdigitated array electrode chip. Anal Chim Acta 634:250–254
166. Kim YJ, Kim YS, Niazi JH, Gu MB (2010) Electrochemical aptasensor for tetracycline detection. Bioprocess Biosyst Eng 33:31–37
167. Xiao Y, Lubin AA, Heeger AJ, Plaxco KW (2005) Label-free electronic detection of thrombin in blood serum by using an aptamer-based sensor. Angew Chem Int Ed 44:5456–5459
168. Baker BR, Lai RY, Wood MS, Doctor EH, Heeger AJ, Plaxco KW (2006) An electronic, aptamer-based small-molecule sensor for the rapid, label-free detection of cocaine in adulterated samples and biological fluids. J Am Chem Soc 128:3138–3139
169. Zuo X, Song S, Zhang J, Pan D, Wang L, Fan C (2007) A target-responsive electrochemical aptamer switch (TREAS) for reagentless detection of nanomolar ATP. J Am Chem Soc 129:1042–1043
170. Li X, Qi H, Shen L, Gao Q, Zhang C (2008) Electrochemical aptasensor for the determination of cocaine incorporating gold nanoparticles modification. Electroanalysis 13:1475–1482
171. Xiao Y, Piorek BD, Plaxco KW, Heeger AJ (2005) A reagentless signal-on architecture for electronic, aptamer-based sensors via target-induced strand displacement. J Am Chem Soc 127:17990–17991
172. Xiao Y, Rowe AA, Plaxco KW (2007) Electrochemical detection of parts-per-billion lead via an electrode-bound DNAzyme assembly. J Am Chem Soc 129:262–263
173. Lu Y, Li X, Zhang L, Yu P, Su L, Mao L (2008) Aptamer-based electrochemical sensors with aptamer-complementary DNA oligonucleotides as probe. Anal Chem 80:1883–1890
174. Wu Z, Guo M, Zhang S, Chen C, Jiang J, Shen G, Yu R (2007) Reusable electrochemical sensing platform for highly sensitive detection of small molecules based on structureswitching signaling aptamers. Anal Chem 79:2933–2939
175. Du Y, Li B, Wei H, Wang Y, Wang E (2008) Multifunctional label-free electrochemical biosensor based on an integrated aptamer. Anal Chem 80:5110–5117
176. Feng K, Sun C, Kang Y, Chen J, Jiang J, Shen G, Yu R (2008) Label-free electrochemical detection of nanomolar adenosine based on target-induced aptamer displacement. Electrochem Comm 10:531–535
177. Zhu Z, Su Y, Li J, Li D, Zhang J, Song S, Zhao Y, Li G, Fan C (2009) Highly sensitive electrochemical sensor for mercury(II) ions by using a mercury-specific oligonucleotide probe and gold nanoparticle-based amplification. Anal Chem 81:7660–7666
178. Ferapontova EE, Olsen EM, Gothelf KV (2008) An RNA aptamer-based electrochemical biosensor for detection of theophylline in resum. J Am Chem Soc 130:4256–4258
179. Feng K, Sun C, Kang Y, Chen J, Jiang JH, Shen GL, Yu RQ (2008) Electrochem Commun 10:531–535
180. Li X, Qi HL, Shen LH, Gao Q, Zhang CX (2008) Electrochemical aptasensor for the determination of cocaine incorporating gold nanoparticles modification. Electroanalysis 20:1475–1482
181. Wang X, Dong P, He PG, Fang YZ (2010) A solid-state electrochemiluminescence sensing platform for detection of adenosine based on ferrocene-labeled structure-switching signaling aptamer. Anal Chim Acta 658:128–132
182. Shen L, Chen Z, Li Y, Jing P, Xie S, He S, He P, Shao Y (2007) A chronocoulometric aptamer sensor for adenosine monophosphate. Chem Commun 21:2169–2171.
183. Du Y, Li B, Wang F, Dong S (2009) Au nanoparticles grafted sandwich platform used amplified small molecules electrochemical aptasensor. Biosens Bioelectron 24:1979–1983