Ultrasensitive protein-DNA binding assays

Current Opinion in Biotechnology

Volumn 14, Issue 1, 2003, Pages 65-73

  Pavski, Victor ^a   Le, X Chris ^a  

^a UNIVERSITY OF ALBERTA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

APTAMER; OLIGONUCLEOTIDE; SYNTHETIC DNA;

AFFINITY CHROMATOGRAPHY; ANALYTIC METHOD; BINDING AFFINITY; BIOSENSOR; CAPILLARY ELECTROPHORESIS; DNA DAMAGE; DNA DETERMINATION; ELECTROPHORETIC MOBILITY; FLUORESCENCE ANALYSIS; FLUORESCENCE POLARIZATION; PRIORITY JOURNAL; PROTEIN DNA BINDING; REVIEW; STOICHIOMETRY;

EID: 0037309123     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0958-1669(02)00016-2     Document Type: Review

References (36)

1. Le X.C., Wan Q.H., Lam M.T. Fluorescence polarization detection for affinity capillary electrophoresis. Electrophoresis. 23:2002;903-908 This paper reviews the principle of CE-LIFP and demonstrates its application to protein-DNA interactions and immunoassays. Interactions between single-stranded DNA and its binding protein SSB and immunoassay for cyclosporine were used as two examples.
2. Uphoff K.W., Bell S.D., Ellington A.D. In vitro selection of aptamers: the dearth of pure reason. Curr. Opin. Struct. Biol. 6:1996;281-288.
3. Tuerk C., Gold L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science. 249:1990;505-510.
4. Ellington A.D., Szostak J.W. In vitro selection of RNA molecules that bind specific ligands. Nature. 346:1990;818-822.
5. Famulok M. Molecular recognition of amino acids by RNA-aptamers: an L-citrulline binding RNA motif and its evolution into an L-arginine binder. J. Am. Chem. Soc. 116:1994;1698-1706.
6. Jenison R.D., Gill S.C., Pardi A., Polisky B. High-resolution molecular discrimination by RNA. Science. 263:1994;1425-1429.
7. Tuerk C., MacDougal S., Gold L. RNA pseudoknots that inhibit human immunodeficiency virus type 1 reverse transcriptase. Proc. Natl. Acad. Sci. USA. 89:1992;6988-6992.
8. Sooter L.J., Riedel T., Davidson E.A., Levy M., Cox J.C. Toward automated nucleic acid enzyme selection. Biol. Chem. 382:2001;1327-1334.
9. Clark S.L., Remcho V.T. Aptamers as analytical reagents. Electrophoresis. 23:2002;1335-1340.
10. Kumar N.V., Bernstein L.R. A new analytical scale DNA affinity binding assay for analyses of specific protein-DNA interactions. Anal. Biochem. 299:2001;203-210.
11. Wan Q.-H., Le X.C. Fluorescence polarization studies of affinity interactions in capillary electrophoresis. Anal. Chem. 71:1999;4183-4189.
12. 18 and single-stranded M13 DNA.
13. Krauss G., Sindermann H., Schomburg U., Maass G. Escherichia coli single-strand deoxyribonucleic acid binding protein: stability, specificity, and kinetics of complexes with oligonucleotides and deoxyribonucleic acid. Biochemistry. 20:1981;5346-5352.
14. Chase J.W., Rabin B.A., Murphy J.B., Stone K.L., Williams K.R. Escherichia coli exonuclease VII. Cloning and sequencing of the gene encoding the large subunit (xseA). J. Biol. Chem. 261:1986;14929-14935.
15. Carnelley T.J., Barker S., Wang H., Tan W.G., Weinfeld M., Le X.C. Synthesis, characterization, and applications of a fluorescent probe of DNA damage. Chem. Res. Toxicol. 14:2001;1513-1522.
16. Tan W.G., Carnelley T.J., Murphy P., Wang H., Lee J., Barker S., Weinfeld M., Le X.C. Detection of DNA adducts of benzo[a]pyrene using immunoelectrophoresis with laser-induced fluorescence analysis of A549 cells. J. Chromatogr. A. 924:2001;377-386.
17. Wang H., Xing J., Tan W., Lam M., Carnelley T., Weinfeld M., Le X.C. Binding stoichiometry of DNA adducts with antibody studied by capillary electrophoresis and laser-induced fluorescence. Anal. Chem. 74:2002;3714-3719 The authors examine the binding stoichiometry between single-stranded DNA (fluorescently labeled BPDE-16-mer and BPDE-90-mer) and the antibody (mouse IgG) used to bind to the DNA-damaged site. Complexes of 1:1 and 1:2 stoichiometry formed. It was possible to obtain two calibration curves for the 1:2 complex that correspond to the competition and redistribution of the ligands.
18. LeCaptain D.J., Michel M.A., Van Orden A. Characterization of DNA-protein complexes by capillary electrophoresis-single molecule fluorescence correlation spectroscopy. Analyst. 126:2001;1279-1284.
19. LeCaptain D.J., Van Orden A. Two-beam fluorescence cross-correlation spectroscopy in an electrophoretic mobility shift assay. Anal. Chem. 74:2002;1171-1176.
20. German I., Buchanan D.D., Kennedy R.T. Aptamers as ligands in affinity probe capillary electrophoresis. Anal. Chem. 70:1998;4540-4545.
21. Pavski V., Le X.C. Detection of human immunodeficiency virus type 1 reverse transcriptase using aptamers as probes in affinity capillary electrophoresis. Anal. Chem. 73:2001;6070-6076 The first direct assay for HIV-1 RT is described. Using DNA aptamers, the authors describe a CE assay that is much faster and simpler than current PCR-based HIV-1 RT assays. Used in conjunction with additional tests to determine HIV-1 viral load from HIV-1 RT activity, the assay could have potential use for determining HIV-1 viral load.
22. Schneider D.J., Feignon J., Hostomsky Z., Gold L. High-affinity ssDNA inhibitors of the reverse transcriptase of type 1 human immunodeficiency virus. Biochemistry. 34:1995;9599-9610.
23. Lee M.H., Sano K., Morales F.E., Imagawa D.T. Sensitive reverse transcriptase assay to detect and quantify the human immunodeficieny virus. J. Clin. Microbiol. 25:1987;1717-1721.
24. Rehder M.A., McGown L.B. Open-tubular capillary electrochromatography of bovine β-lactoglobulin variants A and B using an aptamer stationary phase. Electrophoresis. 22:2001;3759-3764.
25. Charles J.A.M., McGown L.B. Separation of Trp-Arg and Arg-Trp using G-quartet-forming DNA oligonucleotides in open-tubular capillary electrochromatography. Electrophoresis. 23:2002;1599-1604.
26. Kotia R.B., Li L., McGown L.B. Separation of nontarget compounds by DNA aptamers. Anal. Chem. 72:2000;827-831 The authors describe the first use of immobilized DNA aptamers in CEC for the determination of non-target compounds.
27. 2 were found to aid binding.
28. Li J.J., Fang X., Tan W. Molecular aptamer beacons for real-time protein recognition. Biochem. Biophys. Res. Commun. 292:2002;31-40 An aptamer molecular beacon (MB) was used for the detection of thrombin with high sensitivity (112 pM). Ratiometric imaging of binding reactions in microwell arrays demonstrated the potential for application to real-time protein quantification in living specimens.
29. Fang X., Li J.J., Tan W. Using molecular beacons to probe molecular interactions between lactate dehydrogenase and single-stranded DNA. Anal. Chem. 72:2000;3280-3285.
30. Fang X., Cao Z., Beck T., Tan W. Molecular aptamer for real-time oncoprotein platelet-derived growth factor monitoring by fluorescence anisotropy. Anal. Chem. 73:2001;5752-5757 The authors describe a simple assay for the real-time detection of PDGF in the subnanomolar range in homogenous solution without the need for separation. The assay is sensitive enough for potential application to human serum samples with a linear dynamic range (up to 1.25 nM PDGF).
31. -19 M. The aptamers provide improvements in terms of sensitivity and selectivity over immuno-PCR and are sensitive enough to be used for real samples (human serum).
32. Liss M., Petersen B., Wolf H., Prohaska E. An aptamer-based quartz crystal protein biosensor. Anal. Chem. 74:2002;4488-4495 The authors describe a QCM biosensor for the detection of IgE. The aptamer-immobilized QCM is regenerable, while a corresponding antibody QCM is not. The method is capable of detection of 0.5 nmol/L of IgE. Little non-specific binding was observed in solutions containing other proteins in excess (10-1000-fold) concentration.
33. Lee M., Walt D.R. A fiber-optic microarray biosensor using aptamers as receptors. Anal. Biochem. 282:2000;142-146.
34. Ferguson J.A., Boles T.C., Adams C.P., Walt D.R. A fiber-optic DNA biosensor microarray for the analysis of gene expression. Nat. Biotechnol. 14:1996;1681-1684.
35. Green L.S., Bell C., Janjic N. Aptamers as reagents for high-throughput screening. Biotechniques. 30:2001;1094-1110.
36. Wang H, Lu M, Weinfeld M, Le XC: Enhancement of immunocomplex detection and application to assays for DNA adduct of benzo[a]pyrene. Anal Chem: in press. Published on-line at: http://pubs.acs.org/journals/ancham/asap.cgi/ancham/asap/pdf/ac026204a.pdf.