Direct detection of genomic DNA with fluidic force discrimination assays

Analytical Biochemistry

Volumn 392, Issue 2, 2009, Pages 139-144

  Mulvaney, S P ^a   Ibe, C N ^a   Tamanaha, C R ^a   Whitman, L J ^a  

^a NAVAL RESEARCH LABORATORY   (United States)

Author keywords

Bacillus anthracis; Bacillus thuringiensis; Biosensor; Fluidic force discrimination (FFD); Fragmentation by sonication; Genomic DNA; Magnetic bead

Indexed keywords

BACTERIOLOGY; BIOSENSORS; DNA; DNA SEQUENCES; GENES;

BACILLUS ANTHRACIS; BACILLUS THURINGIENSIS; DIRECT DETECTION; GENOMIC DNA; MAGNETIC BEADS; RESTRICTION ENZYMES; SPECIES IDENTIFICATION;

POLYMERASE CHAIN REACTION;

BACTERIAL DNA; GENOMIC DNA;

ARTICLE; ASSAY; BACILLUS; BACTERIAL STRAIN; CONTROLLED STUDY; DNA DETERMINATION; DNA EXTRACTION; DNA SEQUENCE; FLUIDIC FORCE DISCRIMINATION ASSAY; GENE AMPLIFICATION; NONHUMAN; PRIORITY JOURNAL; RESTRICTION MAPPING; ULTRASOUND;

BACILLUS (BACTERIUM); BACILLUS ANTHRACIS; BACILLUS THURINGIENSIS; BACTERIA (MICROORGANISMS);

EID: 67650472031     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2009.05.042     Document Type: Article

References (36)

1. Goel G., Kumar A., Puniya A.K., Chen W., and Singh K. Molecular beacon: a multitask probe. J. Appl. Microbiol. 99 (2005) 435-442
2. Li Y.S., Zhou X.Y., and Ye D.Y. Molecular beacons: an optimal multifunctional biological probe. Biochem. Biophys. Res. Commun. 373 (2008) 457-461
3. Hill H.D., Vega R.A., and Mirkin C.A. Nonenzymatic detection of bacterial genomic DNA using the bio bar code assay. Anal. Chem. 79 (2007) 9218-9223
4. Nam J.-M., Stoeva S.I., and Mirkin C.A. Bio-bar-code-based DNA detection with PCR-like sensitivity. J. Am. Chem. Soc. 126 (2004) 5932-5933
5. Stoeva S.I., Lee J.S., Smith J.E., Rosen S.T., and Mirkin C.A. Multiplexed detection of protein cancer markers with biobarcoded nanoparticle probes. J. Am. Chem. Soc. 128 (2006) 8378-8379
6. Goodrich T.T., Lee H.J., and Corn R.M. Direct detection of genomic DNA by enzymatically amplified SPR imaging measurements of RNA microarrays. J. Am. Chem. Soc. 126 (2004) 4086-4087
7. Minunni M., Tombelli S., and Mascini M. A biosensor approach for DNA sequences detection in non-amplified genomic DNA. Anal. Lett. 40 (2007) 1360-1370
8. Towery R.B., Fawcett N.C., Zhang P., and Evans J.A. Genomic DNA hybridizes with the same rate constant on the QCM biosensor as in homogeneous solution. Biosens. Bioelectron. 16 (2001) 1-8
9. Yao C.Y., Zhu T.Y., Tang J., Wu R., Chen Q.H., Chen M., Zhang B., Huang J.F., and Fu W.L. Hybridization assay of hepatitis B virus by QCM peptide nucleic acid biosensor. Biosens. Bioelectron. 23 (2008) 879-885
10. Minunni M., Tombelli S., Fonti J., Spiriti M.M., Mascini M., Bogani P., and Buiatti M. Detection of fragmented genomic DNA by PCR-free piezoelectric sensing using a denaturation approach. J. Am. Chem. Soc. 127 (2005) 7966-7967
11. Patolsky F., Lichtenstein A., and Willner I. Detection of single-base DNA mutations by enzyme-amplified electronic transduction. Nat. Biotechnol. 19 (2001) 253-257
12. Beuselinck K., van Ranst M., and van Eldere J. Automated extraction of viral-pathogen RNA and DNA for high-throughput quantitative real-time PCR. J. Clin. Microbiol. 43 (2005) 5541-5546
13. Bhattacharyya A., and Klapperich C.A. Microfluidics-based extraction of viral RNA from infected mammalian cells for disposable molecular diagnostics. Sens. Actuat. B 129 (2008) 693-698
14. Bhattacharyya A., and Klapperich C.M. Thermoplastic microfluidic device for on-chip purification of nucleic acids for disposable diagnostics. Anal. Chem. 78 (2006) 788-792
15. Breadmore M.C., Wolfe K.A., Arcibal I.G., Leung W.K., Dickson D., Giordano B.C., Power M.E., Ferrance J.P., Feldman S.H., Norris P.M., and Landers J.P. Microchip-based purification of DNA from biological samples. Anal. Chem. 75 (2003) 1880-1886
16. Belgrader P., Okuzumi M., Pourahmadi F., Borkholder D.A., and Northrup M.A. A microfluidic cartridge to prepare spores for PCR analysis. Biosens. Bioelectron. 14 (2000) 849-852
17. Taylor M.T., Belgrader P., Furman B.J., Pourahmadi F., Kovacs G.T.A., and Northrup M.A. Lysing bacterial spores by sonication through a flexible interface in a microfluidic system. Anal. Chem. 73 (2001) 492-496
18. Hwang K.-Y., Lim H.-K., Jung S.-Y., Namkoong K., Kim J.-H., Huh N., Ko C., and Park J.-C. Bacterial DNA sample preparation from whole blood using surface-modified Si pillar arrays. Anal. Chem. 80 (2008) 7786-7791
19. Casabianca A., Gori C., Chiara O.A., Forbici F., Perno C.F., and Maanani M. Fast and sensitive quantitative detection of HIV DNA in whole blood leucocytes by SYBR green I real-time PCR assay. Mol. Cell. Probes 21 (2007) 368-378
20. Chen W.J., He B., Li C.G., Zhang X.W., Wu W.L., Yin X.Y., Fan B.X., Fan X.L., and Wang J. Real-time rt-PCR for H5N1 avian influenza a virus detection. J. Med. Microbiol. 56 (2007) 603-607
21. Giulietti A., Overbergh L., Valckx D., Decallonne B., Bouillon R., and Mathieu C. An overview of real-time quantitative PCR: applications to quantify cytokine gene expression. Methods 25 (2001) 386-401
22. Mulvaney S.P., Cole C.L., Kniller M.D., Malito M., Tamanaha C.R., Rife J.C., Stanton M.W., and Whitman L.J. Rapid, femtomolar bioassays in complex matrices combining microfluidics and magnetoelectronics. Biosens. Bioelectron. 23 (2007) 191-200
23. Mulvaney S.P., Myers K.M., Sheehan P.E., and Whitman L.J. Attomolar protein detection in complex sample matrices with semi-homogeneous fluidic force discrimination assays. Biosens. Bioelectron. 24 (2009) 1109-1115
24. Baselt D.R., Lee G.U., Natesan M., Metzger S.W., Sheehan P.E., and Colton R.J. A biosensor based on magnetoresistance technology. Biosens. Bioelectron. 13 (1998) 731-739
25. Edelstein R.L., Tamanaha C.R., Sheehan P.E., Miller M.M., Baselt D.R., Whitman L.J., and Colton R.J. The BARC biosensor applied to the detection of biological warfare agents. Biosens. Bioelectron. 14 (2000) 805-813
26. Rife J.C., Miller M.M., Sheehan P.E., Tamanaha C.R., Tondra M., and Whitman L.J. Design and performance of GMR sensors for the detection of magnetic microbeads in biosensors. Sens. Actuat. A 107 (2003) 209-218
27. Lee J.-L., and Levin R.E. Use of ethidium bromide monoazide for quantification of viable and dead mixed bacterial flora from fish fillets by polymerase chain reaction. J. Microbiol. Methods 67 (2006) 456-462
28. Stine R., Cole C.L., Ainslie K.M., Mulvaney S.P., and Whitman L.J. Formation of primary amines on silicon nitride surfaces: a direct, plasma-based pathway to functionalization. Langmuir 23 (2007) 4400-4404
29. Sheehan P.E., Edelstein R.L., Tamanaha C.R., and Whitman L.J. A simple pen-spotting method for arraying biomolecules on solid substrates. Biosens. Bioelectron. 18 (2003) 1455-1459
30. Tamanaha C.R., Malito M., Mulvaney S.P., and Whitman L.J. Reusable, compression-sealed fluid cells for surface mounting to planar substrates. Lab Chip 9 (2009) 1468-1471
31. Wang R.H., Minunni M., Tombelli S., and Mascini M. A new approach for the detection of DNA sequences in amplified nucleic acids by a surface plasmon resonance biosensor. Biosens. Bioelectron. 20 (2004) 598-605
32. Lucarelli F., Tombelli S., Minunni M., Marrazza G., and Mascini M. Electrochemical and piezoelectric DNA biosensors for hybridisation detection. Anal. Chim. Acta 609 (2008) 139-159
33. Mann T.L., and Krull U.J. The application of ultrasound as a rapid method to provide DNA fragments suitable for detection by DNA biosensors. Biosens. Bioelectron. 20 (2004) 945-955
34. Borthwick K.A.J., Coakley W.T., McDonnell M.B., Nowotny H., Benes E., and Groschl M. Development of a novel compact sonicator for cell disruption. J. Microbiol. Methods 60 (2005) 207-216
35. Marentis T.C., Kusler B., Yaralioglu G.G., Liu S.J., Haeggstrom E.O., and Khuri-Yakub B.T. Microfluidic sonicator for real-time disruption of eukaryotic cells and bacterial spores for DNA analysis. Ultrasound Med. Biol. 31 (2005) 1265-1277
36. Tamanaha C.R., Mulvaney S.P., Rife J.C., and Whitman L.J. Magnetic labeling, detection, and system integration. Biosens. Bioelectron. 24 (2008) 1-13