Emerging applications of aptamers to micro- and nanoscale biosensing

Microfluidics and Nanofluidics

Volumn 6, Issue 3, 2009, Pages 347-362

  Nguyen, ThaiHuu ^a   Hilton, John P ^a   Lin, Qiao ^a  

^a Fu Foundation School of Engineering and Applied Science   (United States)

Author keywords

Affinity binding; Aptamer; Aptasensor; Biosensor; Microfluidics; Nanotechnology

Indexed keywords

BACTERIOPHAGES; DNA; GENES; MOLECULAR BIOLOGY; MOLECULAR RECOGNITION; NANOSTRUCTURED MATERIALS; NUCLEIC ACIDS; OLIGONUCLEOTIDES; RNA; SIGNAL TRANSDUCTION;

AFFINITY BINDING; AFFINITY LIGANDS; ANALYTES; APTAMER; APTAMERS; APTASENSOR; APTASENSORS; BIO-SENSING; BIOLOGICAL RECEPTORS; BIOMOLECULAR RECOGNITION; BIOSENSOR; DNA SYNTHESIS; ELECTROANALYTICAL TECHNIQUES; EMERGING APPLICATIONS; HIGH AFFINITIES; IMMUNORECEPTORS; IN-VITRO; MASS CHANGES; MOLECULAR RECOGNITION ELEMENTS; NANO FABRICATIONS; NANO-SCALE; OPTICAL TRANSDUCTIONS;

BIOSENSORS;

EID: 62649141314     PISSN: 16134982     EISSN: 16134990     Source Type: Journal    
DOI: 10.1007/s10404-008-0400-7     Document Type: Review

References (145)

1. Aberem MB et al (2006) Protein detecting arrays based on cationic polythiophene-DNA-aptamer complexes. Adv Mater 18(20):2703-2705
2. Bagalkot V et al (2007) Quantum dot-aptamer conjugates for synchronous cancer imaging, therapy, and sensing of drug delivery based on bi-fluorescence resonance energy transfer. Nano Lett 7(10):3065-3070
3. Baker BR et al (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(10):3138-3139
4. Balamurugan S et al (2006) Designing highly specific biosensing surfaces using aptamer monolayers on gold. Langmuir 22(14):6446-6453
5. Berezovski M, Krylov SN (2005) Thermochemistry of protein-DNA interaction studied with temperature-controlled nonequilibrium capillary electrophoresis of equilibrium mixtures. Anal Chem 77(5):1526-1529
6. Bock C et al (2004) Photoaptamer arrays applied to multiplexed proteomic analysis. Proteomics 4(3):609-618
7. Brody EN et al (1999) The use of aptamers in large arrays for molecular diagnostics. Mol Diagn 4(4):381-388
8. Brown D, Gold L (1995) Template recognition by an RNA-dependent RNA-polymerase: Identification and characterization of two RNA binding sites on Q beta replicase. Biochemistry 34(45):14765-14774
9. Brumbt A et al (2005) Chiral stationary phase based on a biostable L-RNA aptamer. Anal Chem 77(7):1993-1998
10. Cha M et al (2008) Biomolecular detection with a thin membrane transducer. Lab Chip 8(6):932-937
11. Chen XC et al (2008) Quantum dot-labeled aptamer nanoprobes specifically targeting glioma cells. Nanotechnology 19(23)
12. Cheng AKH, Ge B, Yu HZ (2007) Aptamer-based biosensors for label-free voltammetric detection of lysozyme. Anal Chem 79(14):5158-5164
13. Cho S et al (2004) Microbead-based affinity chromatography chip using RNA aptamer modified with photocleavable linker. Electrophoresis 25(21-22):3730-3739
14. Cho EJ et al (2006) Optimization of aptamer microarray technology for multiple protein targets. Anal Chim Acta 564(1):82-90
15. Choi JH, Chen KH, Strano MS (2006) Aptamer-capped nanocrystal quantum dots: A new method for label-free protein detection. J Am Chem Soc 128(49):15584-15585
16. Christodoulides N et al (2002) A microchip-based multianalyte assay system for the assessment of cardiac risk. Anal Chem 74(13):3030-3036
17. Chung WJ et al (2005) Microaffinity purification of proteins based on photolytic elution: Toward an efficient microbead affinity chromatography on a chip. Electrophoresis 26(3):694-702
18. Clark SL, Remcho VT (2003) Electrochromatographic retention studies on a flavin-binding RNA aptamer sorbent. Anal Chem 75(21):5692-5696
19. Cole JR et al (2007) affinity capture and detection of immunoglobulin E in human serum using an aptamer-modified surface in matrix-assisted laser desorption/ionization mass spectrometry. Anal Chem 79(1):273-279
20. Collett JR, Cho EJ, Ellington AD (2005) Production and processing of aptamer microarrays. Methods 37(1):4-15
21. Connor AC, McGown LB (2006) Aptamer stationary phase for protein capture in affinity capillary chromatography. J Chromatogr A 1111(2):115-119
22. Crevillen AG et al (2007) Real sample analysis on microfluidic devices. Talanta 74(3):342-357
23. Dangerfield JA et al (2006) Enhancement of the StreptoTag method for isolation of endogenously expressed proteins with complex RNA binding targets. Electrophoresis 27(10):1874-1877
24. Degefa TH, Kwak J (2008) Label-free aptasensor for platelet-derived growth factor (PDGF) protein. Anal Chim Acta 613(2):163-168
25. de-los-Santos-Alvarez N et al (2008) Aptamers as recognition elements for label-free analytical devices. Trac-Trends Anal Chem 27(5):437-446
26. Deng Q et al (2001) Retention and separation of adenosine and analogues by affinity chromatography with an aptamer stationary phase. Anal Chem 73(22):5415-5421
27. Deng Q, Watson CJ, Kennedy RT (2003) Aptamer affinity chromatography for rapid assay of adenosine in microdialysis samples collected in vivo. J Chromatogr A 1005(1-2):123-130
28. Dick LW, McGown LB (2004) Aptamer-enhanced laser desorption/ionization for affinity mass spectrometry. Anal Chem 76(11):3037-3041
29. Dittrich PS, Tachikawa K, Manz A (2006) Micro total analysis systems latest advancements and trends. Anal Chem 78(12):3887-3907
30. Drabovich AP et al (2006) Selection of smart aptamers by methods of kinetic capillary electrophoresis. Anal Chem 78(9):3171-3178
31. Du Y et al (2008) Multifunctional label-free electrochemical biosensor based on an integrated aptamer. Anal Chem 80(13):5110-5117
32. Dwarakanath S et al (2004) Quantum dot-antibody and aptamer conjugates shift fluorescence upon binding bacteria. Biochem Biophys Res Commun 325(3):739-743
33. Dwarakanath S et al (2005) Quantum dot-antibody and aptamer conjugates shift fluorescence upon binding bacteria (vol 325, p 739, 2004). Biochem Biophys Res Commun 329(1):416-416
34. Ellington AD, Szostak JW (1990) Invitro selection of RNA molecules that bind specific ligands. Nature 346(6287):818-822
35. Ellington AD, Szostak JW (1992) Selection invitro of single-stranded-dna molecules that fold into specific ligand-binding structures. Nature 355(6363):850-852
36. Farokhzad OC et al (2005) Microfluidic system for studying the interaction of nanoparticles and microparticles with cells. Anal Chem 77(17):5453-5459
37. Fehr M et al (2005) Development and use of fluorescent nanosensors for metabolite imaging in living cells. Biochem Soc Trans 33:287-290
38. Feigon J, Dieckmann T, Smith FW (1996) Aptamer structures from A to zeta. Chem Biol 3(8):611-617
39. Fischer NO, Tarasow TM, Tok JBH (2007) Aptasensors for biosecurity applications. Curr Opin Chem Biol 11(3):316-328
40. Furtado LM et al (1999) Interactions of HIV-1 TAR RNA with Tat-derived peptides discriminated by on-line acoustic wave detector. Anal Chem 71(6):1167-1175
41. Gebhardt K et al (2000) RNA aptamers to S -adenosylhomocysteine: Kinetic properties, divalent cation dependency, and comparison with anti- S -adenosylhomocysteine antibody. Biochemistry 39(24):7255-7265
42. Geiger A et al (1996) RNA aptamers that bind l - arginine with sub-micromolar dissociation constants and high enantioselectivity. Nucleic Acids Res 24(6):1029-1036
43. German I, Buchanan DD, Kennedy RT (1998) Aptamers as ligands in affinity probe capillary electrophoresis. Anal Chem 70(21):4540-4545
44. Gram H et al (1992) Invitro selection and affinity maturation of antibodies from a naive combinatorial immunoglobulin library. Proc Natl Acad Sci USA 89(8):3576-3580
45. Hansen JA et al (2006) Quantum-dot/aptamer-based ultrasensitive multi-analyte electrochemical biosensor. J Am Chem Soc 128(7):2228-2229
46. Hayashi G et al (2007) Reversible regulation of binding between a photoresponsive peptide and its RNA aptamer. Nucleic Acids Symp Ser (Oxf) (51):93-94
47. He P et al (2007) Ultrasensitive electrochemical detection of proteins by amplification of aptamer-nanoparticle bio bar codes. Anal Chem 79(21):8024-8029
48. Hermann T, Patel DJ (2000) Adaptive recognition by nucleic acid aptamers. Science 287:820-825
49. Herr JK et al (2006) Aptamer-conjugated nanoparticles for selective collection and detection of cancer cells. Anal Chem 78(9):2918-2924
50. Huang YF, Chang HT, Tan WH (2008) Cancer cell targeting using multiple aptamers conjugated on nanorods. Anal Chem 80:567-572
51. Hwang J, Nishikawa S (2006) Novel approach to analyzing RNA aptamer-protein interactions: Toward further applications of aptamers. J Biomol Screen 11(6):599-605
52. Ikanovic M et al (2007) Fluorescence assay based on aptamer-quantum dot binding to Bacillus thuringiensis spores. J Fluoresc 17(2):193-199
53. Jayasena SD (1999) Aptamers: An emerging class of molecules that rival antibodies in diagnostics. Clin Chem 45(9):1628-1650
54. Jung A et al (2007) Biofunctional structural design of SAW sensor chip surfaces in a microfluidic sensor system. Sens Actuators B Chem 124(1):46-52
55. Kase D et al (2004) Affinity selection of peptide phage libraries against single-wall carbon nanohorns identifies a peptide aptamer with conformational variability. Langmuir 20(20):8939-8941
56. Kirby R et al (2004) Aptamer-based sensor arrays for the detection and quantitation of proteins. Anal Chem 76(14):4066-4075
57. Langer P, Waldrop A, Ward D (1981) Enzymatic synthesis of biotin-labeled polynucleotides: Novel nucleic acid affinity probes. Proc Natl Acad Sci 78:6633-6637
58. LaVan DA, McGuire T, Langer R (2003) Small-scale systems for in vivo drug delivery. Nat Biotechnol 21(10):1184-1191
59. Lee M, Walt DR (2000) A fiber-optic microarray biosensor using aptamers as receptors. Anal Biochem 282(1):142-146
60. Lee JA et al (2008) An electrochemical impedance biosensor with aptamer-modified pyrolyzed carbon electrode for label-free protein detection. Sens Actuators B Chem 129:372-379
61. Levy M, Cater SF, Ellington AD (2005) Quantum-dot aptamer beacons for the detection of proteins. ChemBioChem 6(12):2163-2166
62. Li Y, Lee HJ, Corn RM (2006) Fabrication and characterization of RNA aptamer microarrays for the study of protein-aptamer interactions with SPR imaging. Nucleic Acids Res 34(22):6416-6424
63. Li Y-Y et al (2007a) Ultrasensitive densitometry detection of cytokines with nanoparticle-modified aptamers. Clin Chem 53(6):1061-1066
64. Li Y, Lee HJ, Corn RM (2007b) Detection of protein biomarkers using RNA aptamer microarrays and enzymatically amplified surface plasmon resonance imaging. Anal Chem 79(3):1082-1088
65. Li Y et al (2007c) Electrogenerated chemiluminescence aptamer-based biosensor for the determination of cocaine. Electrochem Commun 9(10):2571-2575
66. Li X et al (2008) Electrochemical impedance spectroscopy for study of aptamer-thrombin interfacial interactions. Biosens Bioelectron 23(11):1624-1630
67. Liss M et al (2002) An aptamer-based quartz crystal protein biosensor. Anal Chem 74(17):4488-4495
68. 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 Edit 45(1):90-94
69. 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 Edit 45(47):7955-7959
70. 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
71. Lohndorf M et al (2005) Microfabricated high-performance microwave impedance biosensors for detection of aptamer-protein interactions. Appl Phys Lett 87(24)
72. Lupold SE et al (2002) Identification and characterization of nuclease-stabilized RNA molecules that bind human prostate cancer cells via the prostate-specific membrane antigen. Cancer Res 62(14):4029-4033
73. Maehashi K et al (2007) Label-free protein biosensor based on aptamer-modified carbon nanotube field-effect transistors. Anal Chem 79(2):782-787
74. Marrack JR (1938) The chemistry of antigens and antibodies. H.M. Stationery Office, London
75. Mascini M (2008) Aptamers and their applications. Anal Bioanal Chem 390(4):987-988
76. Mascini M et al (2007) Colorimetric microarray detection system for ghrelin using aptamer-technology. Anal Lett 40(7):1386-1399
77. McCauley TG, Hamaguchi N, Stanton M (2003) Aptamer-based biosensor arrays for detection and quantification of biological macromolecules. Anal Biochem 319(2):244-250
78. Mendonsa SD, Bowser MT (2004) In vitro selection of high-affinity DNA ligands for human IgE using capillary electrophoresis. Anal Chem 76(18):5387-5392
79. Michaud M et al (2003) A DNA aptamer as a new target-specific chiral selector for HPLC. J Am Chem Soc 125(28):8672-8679
80. Michaud M et al (2004) Immobilized DNA aptamers as target-specific chiral stationary phases for resolution of nucleoside and amino acid derivative enantiomers. Anal Chem 76(4):1015-1020
81. Mir M, Katakis I (2007) Aptamers as elements of bioelectronic devices. Mol Biosyst 3(9):620-622
82. Morimoto K et al (2007) Electrochemical microsystem with porous matrix packed-beds for enzyme analysis. Sens Actuators B Chem 124(2):477-485
83. Mosing RK, Mendonsa SD, Bowser MT (2005) Capillary electrophoresis-SELEX selection of aptamers with affinity for HIV-1 reverse transcriptase. Anal Chem 77(19):6107-6112
84. Nguyen T et al (2009) An aptamer-based microfluidic device for thermally controlled affinity extraction. Microfluid Nanofluidics (in press)
85. Nguyen T et al, An integrated microfluidic system for affinity extraction and concentration of biomolecules coupled to MALDI-MS (in preparation)
86. Nguyen T et al, Highly selective concentration and thermally activated release of analytes on a microchip (in preparation)
87. Nieuwlandt D, Wecker M, Gold L (1995) In vitro selection of RNA ligands to substance-P. Biochemistry 34(16):5651-5659
88. Nimjee SM et al (2005) The potential of aptamers as anticoagulants. Trends cardiovasc med 15(1):41-45
89. Numnuam A et al (2008) Aptamer-based potentiometric measurements of proteins using ion-selective microelectrodes. Anal Chem 80:707-712
90. Nutiu R, Li Y (2003) Structure-switching signaling aptamers. J Am Chem Soc 125(16):4771-4778
91. Ozaki H et al (2006) Biomolecular sensor based on fluorescence-labeled aptamer. Bioorg Med Chem Lett 16(16):4381-4384
92. Patolsky F et al (2004) Electrical detection of single viruses. Proc Natl Acad Sci USA 101(39):14017-14022
93. Pavlov V et al (2004) Aptamer-functionalized au nanoparticles for the amplified optical detection of thrombin. J Am Chem Soc 126(38):11768-11769
94. Polsky R et al (2006) Nucleic acid-functionalized Pt nanoparticles: catalytic labels for the amplified electrochemical detection of biomolecules. Anal Chem 78(7):2268-2271
95. Potyrailo RA et al (1998) Adapting selected nucleic acid ligands (aptamers) to biosensors. Anal Chem 70(16):3419-3425
96. Radi AE, O'Sullivan CK (2006) Aptamer conformational switch as sensitive electrochemical biosensor for potassium ion recognition. Chem Commun (32):3432-3434
97. Radi AE et al (2006) Reagentless, reusable, ultrasensitive electrochemical molecular beacon aptasensor. J Am Chem Soc 128(1):117-124
98. Ravelet C, Grosset C, Peyrin E (2006) Liquid chromatography, electrochromatography and capillary electrophoresis applications of DNA and RNA aptamers. J Chromatogr A 1117(1):1-10
99. Revesz E, Lai EPC, DeRosa MC (2007) Towards a FRET-based ATP biosensor using quantum dot/aptamer-based complexes. J Biomol Struct Dyn 24(6):645-645
100. 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 (34):4267-4269
101. Romig TS, Bell C, Drolet DW (1999) Aptamer affinity chromatography: combinatorial chemistry applied to protein purification. J Chromatogr B Anal Technol Biomed Life Sci 731(2):275-284
102. Ruta J et al (2007) Chiral resolution of histidine using an anti- d -histidine L-RNA aptamer microbore column. J Chromatogr B Anal Technol Biomed Life Sci 845(2):186-190
103. Savran CA et al (2002) Fabrication and characterization of a micromechanical sensor for differential detection of nanoscale motions. J Microelectromech Syst 11(6):703-708
104. Savran CA et al (2003) Microfabricated mechanical biosensor with inherently differential readout. Appl Phys Lett 83(8):1659-1661
105. Savran CA et al (2004) Micromechanical detection of proteins using aptamer-based receptor molecules. Anal Chem 76(11):3194-3198
106. Schasfoort RBM et al (1990) Possibilities and limitations of direct detection of protein charges by means of an immunological field-effect transistor. Anal Chim Acta 238(2):323-329
107. Schlensog MD et al (2004) A Love-wave biosensor using nucleic acids as ligands. Sens Actuators B Chem 101(3):308-315
108. Schurer H et al (2001) Aptamers that bind to the antibiotic moenomycin A. Bioorg Med Chem 9(10):2557-2563
109. Shamah SM, Healy JM, Cload ST (2008) Complex target SELEX. Acc Chem Res 41:130-138
110. Shen L et al (2007) A chronocoulometric aptamer sensor for adenosine monophosphate. Chem Commun (21):2169-2171
111. Shekhawat G, Tark SH, Dravid VP (2006) MOSFET-embedded microcantilevers for measuring deflection in biomolecular sensors. Science 311(5767):1592-1595
112. Smith JE et al (2007) Aptamer-conjugated nanoparticles for the collection and detection of multiple cancer cells. Anal Chem 79(8):3075-3082
113. So HM et al (2005) Single-walled carbon nanotube biosensors using aptamers as molecular recognition elements. J Am Chem Soc 127(34):11906-11907
114. So HM et al (2008) Detection and titer estimation of Escherichia coli using aptamer-functionalized single-walled carbon-nanotube field-effect transistors. Small 4(2):197-201
115. Stadtherr K, Wolf H, Lindner P (2005) An aptamer-based protein biochip. Anal Chem 77(11):3437-3443
116. Star A et al (2003) Electronic detection of specific protein binding using nanotube FET devices. Nano Lett 3(4):459-463
117. Stemmer WPC (1994) Rapid evolution of a protein in-vitro by DNA shuffling. Nature 370(6488):389-391
118. Stojanovic MN, Kolpashchikov DM (2004) Modular aptameric sensors. J Am Chem Soc 126(30):9266-9270
119. Stojanovic MN, Landry DW (2002) Aptamer-based colorimetric probe for cocaine. J Am Chem Soc 124(33):9678-9679
120. Stojanovic MN, de Prada P, Landry DW (2001) Aptamer-based folding fluorescent sensor for cocaine. J Am Chem Soc 123(21):4928-4931
121. Tombelli S et al (2005) Aptamer-based biosensors for the detection of HIV-1 Tat protein. Bioelectrochemistry 67(2):135-141
122. Triroj N et al (2006) Microfluidic three-electrode cell array for low-current electrochemical detection. Sens J IEEE 6(6):1395-1402
123. Tuerk C, Gold L (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249:505-510
124. Turney K et al (2004) Functionalized nanoparticles for liquid atmospheric pressure matrix-assisted laser desorption/ionization peptide analysis. Rapid Commun Mass Spectrom 18(20):2367-2374
125. Tyagi S, Bratu DP, Kramer FR (1998) Multicolor molecular beacons for allele discrimination. Nat Biotech 16(1):49-53
126. Wang WU et al (2005) Label-free detection of small-molecule-protein interactions by using nanowire nanosensors. Proc Natl Acad Sci USA 102(9):3208-3212
127. Wang H et al (2006a) Identification of proteins bound to a thioaptamer probe on a proteomics array. Biochem Biophys Res Commun 347(3):586-593
128. Wang LH et al (2006b) Unmodified gold nanoparticles as a colorimetric probe for potassium DNA aptamers. Chem Commun (36):3780-3782
129. Wang ZZ et al (2007a) Surface plasmon resonance imaging for affinity analysis of aptamer-protein interactions with PDMS microfluidic chips. Anal Bioanal Chem 389:819-825
130. Wang X et al (2007b) Detection of thrombin using electrogenerated chemiluminescence based on Ru(bpy)32 + -doped silica nanoparticle aptasensor via target protein-induced strand displacement. Anal Chim Acta 598(2):242-248
131. Wei H et al (2007) Simple and sensitive aptamer-based colorimetric sensing of protein using unmodified gold nanoparticle probes. Chem Commun (36):3735-3737
132. Wernette DP et al (2008) Functional-DNA-based nanoscale materials and devices for sensing trace contaminants in water. MRS Bull 33(1):34-41
133. White R et al (2001) Generation of species cross-reactive aptamers using "Toggle" SELEX. Mol Ther 4(6):567-573
134. Willey MJ, West AC (2006) A microfluidic device to measure electrode response to changes in electrolyte composition. Electrochem Solid State Lett 9(7):E17-E21
135. Xiao Y et al (2005a) Label-free electronic detection of thrombin in blood serum by using an aptamer-based sensor. Angew Chem Int Edit 44(34):5456-5459
136. Xiao Y et al (2005b) A reagentless signal-on architecture for electronic, aptamer-based sensors via target-induced strand displacement. J Am Chem Soc 127(51):17990-17991
137. Xu D et al (2005) Label-free electrochemical detection for aptamer-based array electrodes. Anal Chem 77(16):5107-5113
138. Xu Y et al (2006) An aptamer-based protein biosensor by detecting the amplified impedance signal. Electroanalysis 18(15):1449-1456
139. Yamamoto R, Kumar PKR (2000) Molecular beacon aptamer fluoresces in the presence of Tat protein of HIV-1. Genes Cells 5(5):389-396
140. Yang RH et al (2008) Noncovalent assembly of carbon nanotubes and single-stranded DNA: An effective sensing platform for probing biomolecular interactions. Anal Chem 80(19):7408-7413
141. Yoon H et al (2008) A novel sensor platform based on aptamer-conjugated polypyrrole nanotubes for label-free electrochemical protein detection. Chembiochem 9(4):634-641
142. Zhao W et al (2007) Simple and rapid colorimetric biosensors based on DNA aptamer and noncrosslinking gold nanoparticle aggregation. ChemBioChem 8(7):727-731
143. Zhao Q, Li XF, Le XC (2008) Aptamer-modified monolithic capillary chromatography for protein separation and detection. Anal Chem 80(10):3915-3920
144. Zhu HY et al (2006) Aptamer based microsphere biosensor for thrombin detection. Sensors 6(8):785-795
145. Zuo X et al (2007) A target-responsive electrochemical aptamer switch (TREAS) for reagentless detection of nanomolar ATP. J Am Chem Soc 129(5):1042-1043