Chemistry: molecular biology and microbiology – Measuring or testing process involving enzymes or... – Involving nucleic acid
Reexamination Certificate
2011-01-25
2011-01-25
Forman, BJ (Department: 1634)
Chemistry: molecular biology and microbiology
Measuring or testing process involving enzymes or...
Involving nucleic acid
C435S283100, C435S287200, C422S068100, C422S082010, C536S023100
Reexamination Certificate
active
07875426
ABSTRACT:
The subject invention concerns materials and methods for detecting nucleic acid sequences. One aspect of the invention concerns a silicon-based “biochip” comprising nucleic acid immobilized thereon. In one embodiment, the silicon comprises microcavities. The nucleic acid to be assayed for the presence of one or more target nucleic acid sequences is immobilized on the silicon. A nucleic acid, such as an oligonucleotide probe, having a sequence substantially complementary to the target nucleic acid sequence can be used to detect the immobilized nucleic acid on the silicon. If the nucleic acid used for detection hybridizes with a target nucleic acid sequence, the hybridized sequences can be detected directly or indirectly. In an exemplified embodiment, the oligonucleotide probe can be labeled with a detectable label, for example, a fluorescent molecule. The subject invention also concerns methods for detecting a target nucleic acid using a silicon-based biochip of the invention.
REFERENCES:
patent: 5206149 (1993-04-01), Oyama et al.
patent: 5223254 (1993-06-01), Paradiso et al.
patent: 5688642 (1997-11-01), Chrisey et al.
patent: 6017696 (2000-01-01), Heller
patent: 6066448 (2000-05-01), Wohlstadter et al.
patent: 6117643 (2000-09-01), Simpson et al.
patent: 6303290 (2001-10-01), Liu et al.
patent: 6495352 (2002-12-01), Brinker et al.
patent: 6730212 (2004-05-01), Yamagishi et al.
patent: 2003/0148291 (2003-08-01), Robotti
patent: 2006/0068407 (2006-03-01), Rupcich et al.
patent: WO 01/01139 (2001-01-01), None
Li et al “Optical DNA biosensor based on molecular beacon immobilized on Sol-Gel membrane” Proceedings of SPIE, 2001, vol. 4414: 27-30.
Anselmetti, D. et al. “Single Molecule DNA Biophysics with Atomic Force Microscopy,”Single Mol., (2000), pp. 53-58, vol. 1, No. 1.
Brinker, C.J. et al. “Sol→Gel→Glass :I. Gelation and Gel Structure,”J. Non-Crystalline Solids, (1985), pp. 301-322, vol. 70.
Broude, N. E. “Stem loop oligonucleotides:a robust tool for molecular biology and biotechnology,”TRENDS in Biotechnology, (2002), pp. 249-256, vol. 20, No. 6.
Canham, L.T. “Silicon quantum wire array fabrication by electrochemical and chemical dissolution of wafers,”Appl. Phy Lett., (Sep. 3, 1990), pp. 1046-1048, vol. 57, No. 10.
Chan, S. et al. “Porous Silicon Microcavities for Biosensing Applications,”Phys. Stat. Sol. A, (2000), pp. 541-546, vol. 182.
Cluzel, P. et al. “DNA: An Extensible Molecule,”Science, (Feb. 9, 1996), pp. 792-794, vol. 271.
Drobyshev, A. et al. “Sequence analysis by hybridization with oligonucleotide microchip: identification of β-thalassemia mutations,”Gene, (1997), pp. 45-52, vol. 188.
Fink, H.W. et al. “Electrical conduction through DNA molecules,”Science, (Apr. 1, 1999), pp. 407-410, vol. 398.
Garcia-Parajó, M.F. et al. “Optical Probing of Single Fluorescent Molecules and Proteins,”Chem Phys Chem, (2001), pp. 347-360, vol. 2, No. 6.
Goryachev, D. N. et al. “Electrolytic Fabrication of Porous Silicon with the Use of Internal Current Source,”Semiconductors, (2003), pp. 477-481, vol. 37, No. 4.
Guckenberger, R. et al. “Scanning Tunneling Microscopy of Insulators and Biological Specimens Based on Lateral Conductivity of Ultrathin Water Films,”Science, (Dec. 2, 1994), pp. 1538-1540, vol. 266.
Hansma, H.G. et al. “Atomic force microscopy of single- and double-stranded DNA,”Nucleic Acids Res., (1992), pp. 3585-3590, vol. 20, No. 14.
Hench, L.L. et al. “The Sol-Gel Process,”Chem. Rev., (1990), pp. 33-72, vol. 90.
Isola, N.R. et al. “Surface-Enhanced Raman Gene Probe for HIV Detection,”Anal. Chem., (1998), pp. 1352-1356, vol. 70.
Lauerhaas, J.M. et al. “Chemical Modification of the Photoluminescence Quenching of Porous Silicon,”Science, (Sep. 17, 1993), pp. 1567-1568, vol. 261.
Janshoff, A. et al. “Macroporous p-Type Silicon Fabry-Perot Layers. Fabrication, Characterization, and Application in Biosensing,”J. Amer. Chem. Soc., (1998), pp. 12108-12116, vol. 120.
Kumar, A. et al. “Co-immobilization of cholesterol oxidase and horseradish peroxidase in a sol-gel film,”Analytica Chimica Acta, (2000), pp. 43-50, vol. 414, Nos. (1-2).
Meurman, O. et al. “Diagnosis of Respiratory Syncytial Virus Infection in Children: Comparison of Viral Antigen Detection and Serology,”J. Med. Virol., (1984a), pp. 61-65, vol. 14.
Meurman, O. et al. “Immunoglobulin Class-Specific Antibody Response in Respiratory Syncytial Virus Infectioin Measured by Enzyme Immunoassay,”J Med. Virol., (1984b), pp. 67-72, vol. 14.
Mirzabekov, A.D. “DNA sequencing by hybridization a mega sequencing method and a diagnostic tool”TIBTECH, (Jan. 1994), pp. 27-32, vol. 12.
Richardson, L.S. et al. “Enzyme-Linked Immunosorbent Assay for Measurement of Serological Response to Respiratory Syncytial Virus Infection,”Infect. Immun., (1978), pp. 660-664, vol. 20, No. 3.
Selvin, P.R. “The renaissance of fluorescence resonance energy transfer,”Nat. Struct. Biol., (Sep. 2000), pp. 730-734, vol. 7, No. 9.
Singh, Y. et al. “Fluorescence Resonance Energy Transfer: A Diagnostic Tool in Oligonucleotide Therapy,”Curr. Sci., (2000), pp. 487-492, vol. 78.
Smith, S.B. et al. “Direct Mechanical Measurements of the Elasticity of Single DNA Molecules by Using Magnetic Beads,”Science, (Nov. 13, 1992), pp. 1122-1126, vol. 258.
Smith, R.L. et al. “Porous silicon formation mechanisms,”J. Appl. Phy., (Apr. 15, 1992), pp. 1-22, vol. 71, No. 8.
Smith, S.B. et al. “Overstretching B-DNA: The Elastic Response of Individual Double-Stranded and Single-Stranded DNA Molecules,”Science, (Feb. 9, 1996), pp. 795-799, vol. 271.
Speel, E.J.M. et al. Amplification Methods to Increase the Sensitivity of In Situ Hybridization: Play CARD(S),The Journal of Histochemistry&Cytochemistry, (1999), pp. 281-288, vol. 47, No. 3.
Strick, T.R. et al., “The Elasticity of a Single Supercoiled DNA Molecule,”Science, (Mar. 29, 1996), pp. 1835-1837, vol. 271.
Uhlir, A. “Electrolytic Shaping of Germanium and Silicon,”Bell Syst. Tech. J., (Mar. 1956), pp. 333-347, vol. 35.
Welliver, R.C. et al. “The anitbody response to primary and secondary infection with respiratory syncytial virus: Kinetics of class-specific responses,”J. Pediatr., (May 1980), pp. 808-813, vol. 96.
Wang, M.D. et al. “Stretching DNA with Optical Tweezers,”Biophys.J., (Mar. 1997), pp. 1335-1346, vol. 72.
Wennmalm, S. et al. “Conformational fluctuations in single DNA molecules,”Proc. Natl. Acad. Sci., (Sep. 1997), pp. 10641-10646, vol. 94.
Wittwer, C.T. et al. “Continuous Fluorescence Monitoring of Rapid Cycle DNA Amplification,”Biotechniques, (1997), pp. 130-138, vol. 22, No. 1.
Yanagida, M. et al.Cold Spring Harbor Symp. Quant .Biol., (1983), p. 177, vol. 47.
Yang, T. T. et al. “Optimized Codon Usage and Chromophore Mutations Provide Enhanced Sensitivity with the Green Fluorescent Protein,”Nucleic Acid Research, (1996), pp. 4592-4593, vol. 24, No. 22.
Genbank accession No. NC 001781.
Kumar A. et al. “Nanoscale Silicon Microcavity DNA Biosensor”Poster Presentation at 1stInternational Conference of Nanotechnology(Nanotech), Jul. 2004.
Karron, R.A., et al. “Respiratory syncytial virus (RSV) SH and G proteins are not essential for viral replication in vitro: Clinical evaluation and molecular characterization of a cold-passaged, attenuated RSV subgroup B mutant”Proc. Natl. Acad. Sci. U.S.A., (1997), pp. 13961-13966, vol. 94, No. 25.
Kumar Arun
Kumar Ashok
Singh Shree R.
Zekri Souheil
Alabama State University
Forman BJ
Saliwanchik Lloyd & Saliwanchik
University of South Florida
LandOfFree
DNA biochip and methods of use does not yet have a rating. At this time, there are no reviews or comments for this patent.
If you have personal experience with DNA biochip and methods of use, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and DNA biochip and methods of use will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-2664572