Aptasensors for biosecurity applications

Current Opinion in Chemical Biology

Volumn 11, Issue 3, 2007, Pages 316-328

  Fischer, Nicholas O ^a   Tarasow, Theodore M ^a   Tok, Jeffrey B H ^a  

^a Chemistry   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

APTAMER; NANOPARTICLE; NUCLEIC ACID;

BACILLUS ANTHRACIS; BACTERIAL SPORE; BIOETHICS; BIOSENSOR; FRANCISELLA; INFLUENZA VIRUS; MICROFLUIDIC ANALYSIS; MICROORGANISM DETECTION; NONHUMAN; ORGANIZATION AND MANAGEMENT; PROTOZOON; REVIEW; SALMONELLA TYPHI; TULAREMIA;

APTAMERS, NUCLEOTIDE; BASE SEQUENCE; BIOSENSING TECHNIQUES; LIGANDS; NUCLEIC ACID CONFORMATION; SECURITY MEASURES;

EID: 34250692157     PISSN: 13675931     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cbpa.2007.05.017     Document Type: Review

References (65)

1. Cook-Deegan R.M., Berkelman R., Davidson E.M., Finder S., Heitman E., Kelley M.C., King N.M., Moseley R., Thomas J.C., Tilden S.J., et al. Issues in biosecurity and biosafety. Science 308 (2005) 1867-1868
2. Watkins R.E., Eagleson S., Hall R.G., Dailey L., and Plant A.J. Approaches to the evaluation of outbreak detection methods. BMC Public Health 6 (2006) 263
3. Lim D.V., Simpson J.M., Kearns E.A., and Kramer M.F. Current and developing technologies for monitoring agents of bioterrorism and biowarfare. Clin Microbiol Rev 18 (2005) 583-607. An exhaustive review paper that provides readers an excellent understanding of the various advances in monitoring biowarfare agents.
4. Durodie B. Facing the possibility of bioterrorism. Curr Opin Biotechnol 15 (2004) 264-268
5. Ellington A.D., and Szostak J.W. In vitro selection of RNA molecules that bind specific ligands. Nature 346 (1990) 818-822
6. Tuerk C., and Gold L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249 (1990) 505-510
7. Bunka D.H., and Stockley P.G. Aptamers come of age - at last. Nat Rev Microbiol 4 (2006) 588-596
8. Jayasena S.D. Aptamers: an emerging class of molecules that rival antibodies in diagnostics. Clin Chem 45 (1999) 1628-1650
9. Bruno J.G., and Kiel J.L. In vitro selection of DNA aptamers to anthrax spores with electrochemiluminescence detection. Biosens Bioelectron 14 (1999) 457-464
10. Zhen B., Song Y.J., Guo Z.B., Wang J., Zhang M.L., Yu S.Y., and Yang R.F. In vitro selection and affinity function of the aptamers to Bacillus anthracis spores by SELEX. Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai) 34 (2002) 635-642
11. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31 (2003) 3406-3415
12. Perez D.R., Sorrell E.M., and Donis R.O. Avian influenza: an omnipresent pandemic threat. Pediatr Infect Dis J 24 (2005) S208-S216
13. Misono T.S., and Kumar P.K. Selection of RNA aptamers against human influenza virus hemagglutinin using surface plasmon resonance. Anal Biochem 342 (2005) 312-317
14. Gopinath S.C., Misono T.S., Kawasaki K., Mizuno T., Imai M., Odagiri T., and Kumar P.K. An RNA aptamer that distinguishes between closely related human influenza viruses and inhibits haemagglutinin-mediated membrane fusion. J Gen Virol 87 (2006) 479-487. The article describes the generation of RNA aptamers against whole viruses. The RNA aptamer analyzed have remarkable affinity (as it is ∼15-fold higher that monoclonal antibody) and selectivity (able to differentiate the same protein [HA] from different viral strains). The aptamer is also observed to be able to prevent the binding of the virus to targeted cells in vitro.
15. Gopinath S.C., Sakamaki Y., Kawasaki K., and Kumar P.K. An efficient RNA aptamer against human influenza B virus hemagglutinin. J Biochem (Tokyo) 139 (2006) 837-846
16. Jeon S.H., Kayhan B., Ben-Yedidia T., and Arnon R. A DNA aptamer prevents influenza infection by blocking the receptor binding region of the viral hemagglutinin. J Biol Chem 279 (2004) 48410-48419
17. Vivekananda J., and Kiel J.L. Anti-Francisella tularensis DNA aptamers detect tularemia antigen from different subspecies by Aptamer-Linked Immobilized Sorbent Assay. Lab Invest 86 (2006) 610-618
18. Hesselberth J.R., Miller D., Robertus J., and Ellington A.D. In vitro selection of RNA molecules that inhibit the activity of ricin A-chain. J Biol Chem 275 (2000) 4937-4942
19. Tang J., Xie J., Shao N., and Yan Y. The DNA aptamers that specifically recognize ricin toxin are selected by two in vitro selection methods. Electrophoresis 27 (2006) 1303-1311. This article describes the application of two approaches, namely CE and affinity chromatography, to generate DNA aptamers against whole ricin protein. Through the CE approach, it was observed that the aptamers generated have higher affinities against the ricin target and are faster to generate.
20. Mosing R.K., Mendonsa S.D., and Bowser M.T. Capillary electrophoresis-SELEX selection of aptamers with affinity for HIV-1 reverse transcriptase. Anal Chem 77 (2005) 6107-6112
21. Goringer H.U., Homann M., Zacharias M., and Adler A. RNA aptamers as potential pharmaceuticals against infections with African trypanosomes. Handb Exp Pharmacol 173 (2006) 375-393
22. Goringer H.U., Homann M., and Lorger M. In vitro selection of high-affinity nucleic acid ligands to parasite target molecules. Int J Parasitol 33 (2003) 1309-1317
23. Homann M., and Goringer H.U. Combinatorial selection of high affinity RNA ligands to live African trypanosomes. Nucleic Acids Res 27 (1999) 2006-2014
24. 2 modified RNA aptamers against live trypanosome protozoa. The aptamers are observed to be stable in human serum for over 30 hours, highlighting their structural robustness and their potential application as molecular recognition elements in sensing system.
25. Ulrich H., Magdesian M.H., Alves M.J., and Colli W. In vitro selection of RNA aptamers that bind to cell adhesion receptors of Trypanosoma cruzi and inhibit cell invasion. J Biol Chem 277 (2002) 20756-20762
26. Goldschmidt M.C. The use of biosensor and microarray techniques in the rapid detection and identification of salmonellae. J AOAC Int 89 (2006) 530-537
27. Zhang X.L., Tsui I.S., Yip C.M., Fung A.W., Wong D.K., Dai X., Yang Y., Hackett J., and Morris C. Salmonella enterica serovar typhi uses type IVB pili to enter human intestinal epithelial cells. Infect Immun 68 (2000) 3067-3073
28. Pan Q., Zhang X.L., Wu H.Y., He P.W., Wang F., Zhang M.S., Hu J.M., Xia B., and Wu J. Aptamers that preferentially bind type IVB pili and inhibit human monocytic-cell invasion by Salmonella enterica serovar typhi. Antimicrob Agents Chemother 49 (2005) 4052-4060
29. MacBeath G., and Schreiber S.L. Printing proteins as microarrays for high-throughput function determination. Science 289 (2000) 1760-1763
30. Lee H.J., Wark A.W., Li Y., and Corn R.M. Fabricating RNA microarrays with RNA-DNA surface ligation chemistry. Anal Chem 77 (2005) 7832-7837
31. Stadtherr K., Wolf H., and Lindner P. An aptamer-based protein biochip. Anal Chem 77 (2005) 3437-3443
32. Bock C., Coleman M., Collins B., Davis J., Foulds G., Gold L., Greef C., Heil J., Heilig J.S., Hicke B., et al. Photoaptamer arrays applied to multiplexed proteomic analysis. Proteomics 4 (2004) 609-618
33. Cox J.C., Rajendran M., Riedel T., Davidson E.A., Sooter L.J., Bayer T.S., Schmitz-Brown M., and Ellington A.D. Automated acquisition of aptamer sequences. Comb Chem High Throughput Screen 5 (2002) 289-299
34. Cox J.C., Hayhurst A., Hesselberth J., Bayer T.S., Georgiou G., and Ellington A.D. Automated selection of aptamers against protein targets translated in vitro: from gene to aptamer. Nucleic Acids Res 30 (2002) e108
35. Kirby R., Cho E.J., Gehrke B., Bayer T., Park Y.S., Neikirk D.P., McDevitt J.T., and Ellington A.D. Aptamer-based sensor arrays for the detection and quantitation of proteins. Anal Chem 76 (2004) 4066-4075
36. Hu X., Bessette P.H., Qian J., Meinhart C.D., Daugherty P.S., and Soh H.T. Marker-specific sorting of rare cells using dielectrophoresis. Proc Natl Acad Sci USA 102 (2005) 15757-15761
37. Paegel B.M., Grover W.H., Skelley A.M., Mathies R.A., and Joyce G.F. Microfluidic serial dilution circuit. Anal Chem 78 (2006) 7522-7527
38. Wilson R., Cossins A.R., and Spiller D.G. Encoded microcarriers for high-throughput multiplexed detection. Angew Chem Int Ed Engl 45 (2006) 6104-6117. An overall concise, yet comprehensive, review paper detailing the latest advances in encoded particles. Enhancing information derived from these encoded particles would greatly facilitate the detection and characterization of numerous targets simultaneously, that is, multiplex-interrogation capability.
39. McBride M.T., Masquelier D., Hindson B.J., Makarewicz A.J., Brown S., Burris K., Metz T., Langlois R.G., Tsang K.W., Bryan R., et al. Autonomous detection of aerosolized Bacillus anthracis and Yersinia pestis. Anal Chem 75 (2003) 5293-5299
40. Porschewski P., Grattinger M.A., Klenzke K., Erpenbach A., Blind M.R., and Schafer F. Using aptamers as capture reagents in bead-based assay systems for diagnostics and hit identification. J Biomol Screen 11 (2006) 773-781
41. Zhu H.Y., Suter J.D., White I.M., and Fan X.D. Aptamer based microsphere biosensor for thrombin detection. Sensors 6 (2006) 785-795
42. Liu J., and Lu Y. Fast colorimetric sensing of adenosine and cocaine based on a general sensor design involving aptamers and nanoparticles. Angew Chem Int Ed Engl 45 (2006) 90-94. The article describes the application of AuNP-aggregates, by way of aptamer and complementary oligonucleotides, for small molecule detection. The de-aggregation process, due to displacement of 'linking' complementary oligonucleotides, results in visible colorimetric changes.
43. Huang C.C., Huang Y.F., Cao Z., Tan W., and Chang H.T. Aptamer-modified gold nanoparticles for colorimetric determination of platelet-derived growth factors and their receptors. Anal Chem 77 (2005) 5735-5741
44. Levy M., Cater S.F., and Ellington A.D. Quantum-dot aptamer beacons for the detection of proteins. ChemBioChem 6 (2005) 2163-2166
45. Pavlov V., Xiao Y., Shlyahovsky B., and Willner I. Aptamer-functionalized Au nanoparticles for the amplified optical detection of thrombin. J Am Chem Soc 126 (2004) 11768-11769
46. Zayats M., Huang Y., Gill R., Ma C.A., and Willner I. Label-free and reagentless aptamer-based sensors for small molecules. J Am Chem Soc 128 (2006) 13666-13667
47. Rodriguez M.C., Kawde A.N., and Wang J. Aptamer biosensor for label-free impedance spectroscopy detection of proteins based on recognition-induced switching of the surface charge. Chem Commun (Camb) 34 (2005) 4267-4269
48. Hansen J.A., Wang J., Kawde A.N., Xiang Y., Gothelf K.V., and Collins G. Quantum-dot/aptamer-based ultrasensitive multi-analyte electrochemical biosensor. J Am Chem Soc 128 (2006) 2228-2229
49. Xiao Y., Lubin A.A., Heeger A.J., and Plaxco K.W. Label-free electronic detection of thrombin in blood serum by using an aptamer-based sensor. Angew Chem Int Ed Engl 44 (2005) 5456-5459. The article describes the development of the electronic aptamer-based (EAB) sensing system based on the displacement of complementary oligonucleotides. The attachment of a redox probe at the end of the aptamer enables electron transfer upon structural rearrangement.
50. Xiao Y., Piorek B.D., Plaxco K.W., and Heeger A.J. A reagentless signal-on architecture for electronic, aptamer-based sensors via target-induced strand displacement. J Am Chem Soc 127 (2005) 17990-17991
51. Baker B.R., Lai R.Y., Wood M.S., Doctor E.H., Heeger A.J., and Plaxco K.W. 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 (2006) 3138-3139
52. Baldrich E., Acero J.L., Reekmans G., Laureyn W., and O'Sullivan C.K. Displacement enzyme linked aptamer assay. Anal Chem 77 (2005) 4774-4784
53. Yang C.J., Jockusch S., Vicens M., Turro N.J., and Tan W. Light-switching excimer probes for rapid protein monitoring in complex biological fluids. Proc Natl Acad Sci USA 102 (2005) 17278-17283. The article describes the novel design of a pyrene end-labeled aptamer that is able to shift its fluorescence emission upon target binding through excimer formation. The excimer's long fluorescence lifetime suppresses the background signal, making the assay adaptable for most test mediums.
54. Nutiu R., and Li Y. Structure-switching signaling aptamers. J Am Chem Soc 125 (2003) 4771-4778
55. Rupcich N., Chiuman W., Nutiu R., Mei S., Flora K.K., Li Y., and Brennan J.D. Quenching of fluorophore-labeled DNA oligonucleotides by divalent metal ions: implications for selection, design, and applications of signaling aptamers and signaling deoxyribozymes. J Am Chem Soc 128 (2006) 780-790
56. Stojanovic M.N., and Kolpashchikov D.M. Modular aptameric sensors. J Am Chem Soc 126 (2004) 9266-9270
57. Katilius E., Katiliene Z., and Woodbury N.W. Signaling aptamers created using fluorescent nucleotide analogues. Anal Chem 78 (2006) 6484-6489. The article describes the strategic incorporation of fluorescent nucleotide analogs to existing signaling aptamers such that fluorescence enhancement up to 30-fold can be achieved upon target binding.
58. Wang X.L., Li F., Su Y.H., Sun X., Li X.B., Schluesener H.J., Tang F., and Xu S.Q. Ultrasensitive detection of protein using an aptamer-based exonuclease protection assay. Anal Chem 76 (2004) 5605-5610
59. Berezovski M., Musheev M., Drabovich A., and Krylov S.N. Non-SELEX selection of aptamers. J Am Chem Soc 128 (2006) 1410-1411
60. Zhang H., Wang Z., Li X.F., and Le X.C. Ultrasensitive detection of proteins by amplification of affinity aptamers. Angew Chem Int Ed Engl 45 (2006) 1576-1580. The article describes the application of CE to isolate target bound reporter DNA aptamers. Subsequent PCR amplification of the reporter aptamer enables ultrasensitive detection of target protein.
61. Haes A.J., Giordano B.C., and Collins G.E. Aptamer-based detection and quantitative analysis of ricin using affinity probe capillary electrophoresis. Anal Chem 78 (2006) 3758-3764
62. Lane H.C., Montagne J.L., and Fauci A.S. Bioterrorism: a clear and present danger. Nat Med 7 (2001) 1271-1273
63. Gopinath S.C., Shikamoto Y., Mizuno H., and Kumar P.K. A potent anti-coagulant RNA aptamer inhibits blood coagulation by specifically blocking the extrinsic clotting pathway. Thromb Haemost 95 (2006) 767-771
64. Jager S., Rasched G., Kornreich-Leshem H., Engeser M., Thum O., and Famulok M. A versatile toolbox for variable DNA functionalization at high density. J Am Chem Soc 127 (2005) 15071-15082
65. Tarasow T.M., and Eaton B.E. Dressed for success: Realizing the catalytic potential of RNA. Biopolymers 48 (1998) 29-37