Target discrimination by surface-immobilized molecular beacons designed to detect Francisella tularensis

Biosensors and Bioelectronics

Volumn 19, Issue 7, 2004, Pages 727-736

  Ramachandran, Akhilesh ^a   Flinchbaugh, James ^a   Ayoubi, Patricia ^a   Olah, Glenn A ^a,b   Malayer, Jerry R ^a  

^a OKLAHOMA STATE UNIVERSITY   (United States)

^b OHIO STATE UNIVERSITY   (United States)

Author keywords

Francisella tularensis; Surface immobilized molecular beacons; Target discrimination

Indexed keywords

ALDEHYDES; CONFORMATIONS; HYDROGELS; RNA;

MOLECULAR BEACONS;

BIOSENSORS;

ALDEHYDE; ALKALI; GLASS; NUCLEOTIDE; RNA;

ACCURACY; AQUEOUS SOLUTION; ARTICLE; BACTERIUM DETECTION; BIOSENSOR; CONTROLLED STUDY; DNA MICROARRAY; DNA SEQUENCE; EXPERIMENTAL DESIGN; EXPOSURE; FLUORESCENCE; FRANCISELLA TULARENSIS; GENE LOCATION; GENE TARGETING; GENOME IMPRINTING; HYBRIDIZATION; HYDROGEL; IMMOBILIZATION; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; NONHUMAN; NUCLEIC ACID ANALYSIS; SURFACE PROPERTY;

BACTERIA (MICROORGANISMS); FRANCISELLA TULARENSIS;

EID: 0346725084     PISSN: 09565663     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bios.2003.08.004     Document Type: Article

References (31)

1. Afanassiev V., Hanemann V., Wolfl S. Preparation of DNA and protein micro arrays on glass slides coated with an agrarose film. Nucleic Acids Res. 28(12):2000;e66.
2. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 215:1990;403-410.
3. Beier M., Hoheisel J.D. Versatile derivatisation of solid support media for covalent bonding on DNA-microchips. Nucleic Acids Res. 27(9):1999;1970-1977.
4. Broude N.E. Stem-loop oligonucleotides: a robust tool for molecular biology and biotechnology. Trends Biotechnol. 20(6):2002;249-256.
5. Broude N.E., Woodward K., Cavallo R., Cantor C.R., Englert D. DNA microarrays with stem-loop DNA probes: preparation and applications. Nucleic Acids Res. 29(19):2001;e92.
6. Brown L.J., Cummins J., Hamilton A., Brown T. Molecular beacons attached to glass beads fluoresce upon hybridization to target DNA. Chem. Commun. 2000:2000;621-622.
7. Epstein C.B., Butow R.A. Microarray technology - enhanced versatility, persistent challenge. Curr. Opin. Biotechnol. 11:2000;36-41.
8. Fang X., Liu X., Schuster S., Tan W. Designing a novel molecular beacon for surface-immobilized DNA hybridization studies. J. Am. Chem. Soc. 121(12):1999;2921-2922.
9. 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.
10. Frutos A.G., Pal S., Quesada M., Lahiri J. Method for detection of single-base mismatches using bimolecular beacons. J. Am. Chem. Soc. 124(11):2002;2396-2397.
11. Kaboev O.K., Luchkina L.A., Tretiakov A.N., Bahrmand A.R. PCR hot start using primers with the structure of molecular beacons (hairpin-like structure). Nucleic Acids Res. 28:2000;e94.
12. Kato-Maeda M., Gao Q., Small P.M. Microarray analysis of pathogens and their interaction with hosts. Cell. Microbiol. 3:2001;713-719.
13. Leone G., van Schijndel H., van Gemen B., Kramer F.R., Schoen C.D. Molecular beacon probes combined with amplification by NASBA enable homogeneous, real-time detection of RNA. Nucleic Acids Res. 26:1998;2150-2155.
14. Li J.J., Geyer R., Tan W. Using molecular beacons as a sensitive fluorescence assay for enzymatic cleavage of single-stranded DNA. Nucleic Acids Res. 28:2000;e52.
15. Liu X., Tan W. A fiber-optic evanescent wave DNA biosensor based on novel molecular beacons. Anal. Chem. 71(22):1999;5054-5059.
16. Liu X., Farmerie W., Schuster S., Tan W. Molecular beacons for DNA biosensors with micrometer to submicrometer dimensions. Anal. Biochem. 283:2000;56-63.
17. Mathews D.H., Sabina J., Zuker M., Turner D.H. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288:1999;911-940.
18. Mhlanga M.M., Malmberg L. Using molecular beacons to detect single-nucleotide polymorphisms with real-time PCR. Methods. 25(4):2001;463-471.
19. Ramachandran A., Zhang M., Goad D., Olah G., Malayer J.R., El Rassi Z. Capillary electrophoresis and fluorescence studies on molecular beacon-based variable length oligonucleotide target discrimination. Electrophoresis. 24:2003;70-77.
20. Riccelli P.V., Merante F., Leung K.T., Bortolin S., Zastawny R.L., Janeczko R., Benight A.S. Hybridization of single-stranded DNA targets to immobilized complementary DNA probes: comparison of hairpin versus linear capture probes. Nucleic Acids Res. 29(4):2001;996-1004.
21. SantaLucia J. Jr. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl. Acad. Sci. U.S.A. 95:1998;1460-1465.
22. Scheller F.W., Wollenberger U., Warsinke A., Lisdat F. Research and development in biosensors. Curr. Opin. Biotechnol. 12:2001;35-40.
23. Sokol D.L., Zhang X., Lu P., Gewirtz A.M. Real-time detection of DNA-RNA hybridization in living cells. Proc. Natl. Acad. Sci. U.S.A. 95:1998;11538-11543.
24. Steemer F.J., Ferguson J.A., Walter D.R. Screening unlabeled DNA targets with randomly ordered fiber-optic gene arrays. Nat. Biotechnol. 18:2000;91-94.
25. Tsourkas A., Behlke M.A., Bao G. Structure-function relationships of shared-stem and conventional molecular beacons. Nucleic Acids Res. 30(19):2002;4208-4215.
26. Tyagi S., Kramer F.R. Molecular beacons: probes that fluoresce upon hybridization. Nat. Biotechnol. 14:1996;303-308.
27. Tyagi S., Bratu D.P., Kramer F.R. Multicolor molecular beacons for allele discrimination. Nat. Biotechnol. 16:1998;49-53.
28. Vasiliskov A.V., Timofeev E.N., Surzhikov S.A., Drobyshev A.L., Shick V.V., Mirzabekov A.D. Fabrication of microarray of gel-immobilized compounds on a chip by copolymerization. Biotechniques. 27(3):1999;596-598.
29. Vet J.A.M., Majithia A.R., Marras S.A.E., Tyagi S., Dube S., Poiesz B.J., Kramer F.R. Multiplex detection of four pathogenic retroviruses using molecular beacons. Proc. Natl. Acad. Sci. U.S.A. 96:1999;6394-6399.
30. Wang H., Li J., Liu H., Liu Q., Mei Q., Wang Y., Zhu J., He N., Lu Z. Label-free hybridization detection of a single nucleotide mismatch by immobilization of molecular beacons on an agarose film. Nucleic Acids Res. 30(12):2002;e61-e70.
31. Zuker, M., Mathews, D. H., Turner, D.H., 1999. Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide. In: RNA Biochemistry and Biotechnology. In: Barciszewski, J., Clark, B.F.C. (Eds.), NATO ASI Series. Kluwer Academic Publishers, Amsterdam, pp. 11-43.