Organic compounds -- part of the class 532-570 series – Organic compounds – Carbohydrates or derivatives
Patent
1997-07-29
2000-01-25
Zitomer, Stephanie W.
Organic compounds -- part of the class 532-570 series
Organic compounds
Carbohydrates or derivatives
435 6, 935 77, 935 78, C07H 2102, C07H 2104, C12Q 168
Patent
active
060180412
ABSTRACT:
The conditions under which oligonucleotides hybridize only with entirely homologous sequences are recognized. The sequence of a given DNA fragment is read by the hybridization and assembly of positively hybridizing probes through overlapping portions. By simultaneous hybridization of DNA molecules applied as dots and bound onto a filter, representing single-stranded phage vector with the cloned insert, with about 50,000 to 100,000 groups of probes, the main type of which is (A,T,C,G)(A,T,C,G)N8(A,T,C,G), information for computer determination of a sequence of DNA having the complexity of a mammalian genome are obtained in one step. To obtain a maximally completed sequence, three libraries are cloned into the phage vector, M13, bacteriophage are used: with the 0.5 kb and 7 kbp insert consisting of two sequences, with the average distance in genomic DNA of 100 kbp. For a million bp of genomic DNA, 25,000 subclones of the 0.5 kbp are required as well as 700 subclones 7 kb long and 170 jumping subclones. Subclones of 0.5 kb are applied on a filter in groups of 20 each, so that the total number of samples is 2,120 per million bp. The process can be easily and entirely robotized for factory reading of complex genomic fragments or DNA molecules.
REFERENCES:
patent: 4562159 (1985-12-01), Shafritz
patent: 4613566 (1986-09-01), Potter
patent: 4677054 (1987-06-01), White et al.
patent: 4731325 (1988-03-01), Palva et al.
patent: 4766062 (1988-08-01), Diamond et al.
patent: 4883750 (1989-11-01), Whiteley
patent: 4981783 (1991-01-01), Augenlicht
patent: 5002867 (1991-03-01), Macevicz
patent: 5310893 (1994-05-01), Erlich et al.
patent: 5348855 (1994-09-01), Dattagupta et al.
patent: 5436327 (1995-07-01), Southern et al.
Saiki, R.K., Walsh, P.S., Levenson, C.H., Erlich, H.A., (1989), "Genetic Analysis of Amplified DNA with Immobilized Sequence-Specific Oligonucleotide Probes," Proc. Natl. Acad. Sci. USA, 86, 6230-6234.
Drmanac, R., Labat, I., Strezoska, Z., Paunesku, T., Radosavljevic, D., Drmanac, S., and Crkvenjakov, R., (1990), "Sequencing by Oligonucleotide Hybridization: A Promising Framework in Decoding of The Genome Program?," Research Article, p. 47-59.
Besmer, P., Miller Jr. , R.C. , Caruthers, M.H., Kumar, A., Minamoto, K., Van De Sande, J.H., Sidarova, N., and Khorana, H.G., (1972), "Hybridizatiion of Polydeoxynucleotides with Tyrosine Transfer RNA Sequences to the r-Strand of .phi.80psu.sub.III.sup.+ DNA," J. Mol. Biol., 72, 503-522.
Breslauer, K.J., Frank, R., Blocker, H., and Marky, L.A., (1986), "Predicting DNA Duplex Stability from the Base Sequence," Proc. Natl. Acad. Sci., 83, 3746-3750.
Craig, M.E., Crothers, D.M., and Doty, P., (1971), "Relaxation Kinetics of Dimer Formation by Self Complementary Oligonucleotides," J. Mol. Biol., 62, 383-401.
Craig, A.G., Nizetic, D., Hoheisel, J.D., Zehetner, G., and Lehrach, H., (1990), "Ordering of Cosmid Clones Covering the Herpes Simplex Virus Type I (HSV-I) Genome: A Test Case for Fingerprinting by Hybridisation," Nucleic Acids Research, 18(9), 2653-2660.
Drmanac, R., Lennon, G., Drmanac, S., Labat, I., Crkvenjakov, R., and Lehrach, H., (1990), "Partial Sequencing by Oligo-Hybridization: Concept and Applications in Genome Analysis," The First International Conference on Electrophoresis, Supercomputing and the Human Genome, pp. 66-70.
Gillam, S., Waterman, K., and Smith, M., (1975), "The Base-Pairing Specificity of Cellulose-pdT.sub.9," Nucleic Acids Research, 2(5), 625-634.
Ikuta, S., Takagi, K., Wallace, R.B., and Itakura, K., (1987), "Dissociation Kinetics of 19 Base Paired Oligonucleotide-DNA Duplexes Containing Different Single Mismatched Base Pairs," Nucleic Acids Research, 15(2) 797-811.
Khrapko, K.R., Lysov, Y.P., Khorlyn, A.A., Shick, V.V., Florentiev, V.L., and Mirzabekov, A.D., (1989), "An Oligonucleotide Hybridization Approach to DNA Sequencing," Febs Letters, 256(1,2) 118-122.
Gillam, S., Waterman, K., and Smith, M. (1975). "The Base-Pairing Specificity of Cellulose-pdT9." Nucleic Acids Res, 2(5), 625-34.
Kohara, Y., Akiyama, K., and Isono, K., (1987), "The Physical Map of the Whole E. coli Chromosome: Application of a New Strategy for Rapid Analysis and Sorting of a Large Genomic Library," 50, 495-508.
Lewin, R., (1986), "Proposal to Sequence the Human Genome Stirs Debate," Research News, Molecular Biology of Homo Sapians, 232, 1598-1600.
Craig, A., Michiels, F., Zehetner, G., Sproat, B., Burmeister, M., Bucan, M., Poustka, A., Pohl, T., Frischauf, A.M., Lehrach, H., (1987), "Molecular Techniques in Mammalian Genetics: A New Era in Genetic Analysis," Human Genetics, pp. 126-132.
Wallace, R.B., Shaffer, J., Murphy, R.F., Bonner, J., Hirose, T., and Itakura, K., (1979), "Hybridization of Synthetic Oligodeoxyribonucleotides to .phi..sub.x 174 DNA: The Effect of Single Base Pair Mismatch," Nucleic Acids Research, 6(11) 3543-3557.
Wallace, R.B., Johnson, M.J., Hirose, T., Miyake, T., Kawashima, E.H., and Itakura, K., (1981), "The Use of Synthetic Oligonucleotides as Hybridization Probes, II. Hybridization of Oligonucleotides of Mixed Sequence to Rabbit .beta. -Globin DNA," Nucleic Acids Research, 9(4) 879-894.
Wetmur, J.G., Davidson, N., (1968), "Kinetics of Renaturation of DNA," J. Mol. Biol., 31, 349-370.
Wetmur, J.G., (1976), "Hybridization and Renaturation Kinetics of Nucleic Acids," Annual Review of Biophysics and Bioengineering, 5, 337-361.
Wood, W.I., Gitschier, J., Lasky, L.A., and Lawn, R.M., (1985), "Base Composition-Independent Hybridization in Tetramethylammonium Chloride: A Method for Oligonucleotide Screening of Highly Complex Gene Libraries," Proc. Natl. Acad. Sci. USA, 82, 1585-1588.
Angelini, G., De Preval, C., Gorski, J., and Mach, B., (1986), "High-Resolution Analysis of the Human HLA-DR Polymorphism by Hybridization with Sequence-Specific Oligonucleotide Probes," Proc. Natl. Acad. Sci. USA, 83, 4489-4493.
Berdoz, J., Gorski, Jack, Termijtelen, A.M., Dayer, J.M., Irle, C., Schendel, D., Mach, B., (1987), "Constitutive and Induced Expression of the Individual HLA-DR .beta. and .alpha. Chain Loci in Different Cell Types," The Journal of Immunology, 139(4), 1336-1341.
Bugawan, T.L., Horn, G.T., Long, C.M., Mickelson, E., Hansen, J.A., Ferrara, G.B., Angeline, G., and Erlich, H.A., (1988), "Analysis of HLA-DP Allelic Sequence Polymorphism Using the in Vitro Enzymatic NDA Amplification of DP-.alpha. and DP-.beta. Loci," Journal of Immunology, 141(2), 4024-4030.
Church, G.M., and Gilbert, W., (1983), "Genomic Sequencing", Proc. Natl. Acad. Sci., 81, 1991-1995.
Crkvenjakov, R., Bucan, M., Konstantinovic, M., Fogel, M., Savic, A., and Glisin, V., (1984), "Characterization of Two Rat Globin cDNA Clones," Hemoglobin, 8(6), 597-611.
Crkvenjakov, R., Drmanac, R., Bucan, M., Konstantinovic, M., Fogel, M., Maksimovic, V., Petrovic, N., Savic, A., and Glisin, V., (1984), "Cloning of Eucaryotic Gene Sequences: Studies on Human Fibroblast Interferon and Rat Globin Genes," Periodicum Biologorum, 86(2) 115-124.
Gorski, J., Tilanus, M., Giphart, M., and Mach, B., (1987), "Oligonucleotide Genotyping Shows that Alleles at the HLA-DR III Locus of the Drw52 Supertypic Group Segregate Independently of Known DR or Dw Specificities," Immunogenetics, 25, 79-83.
Irle, C., Jaques, D., Tiercy, J.M., Fuggle, S.V., Gorski, J., Termijtelen, A., Jeannet, M., and Mach, B., (1988), "Functional Polymorphism of Each of the Two HLA-DR .beta. Chain Loci Demonstrated with Antigen-Specific DR3- and DRw52-Restricted T Cell Clones," J. Exp. Med., 167, 853-872.
Landry, M.D., M.L., Fong, Ph.D., C.K.Y., (1985), "Nucleic Acid Hybridization in the Diagnosis of Viral Infections," Clinics in Laboratory Medicine, 5(3), 513-529.
Lehrach, H., Zehetner, G., Nicetic, D., Craig, A., Michiels, F., (1988), "Oligonucleotide Fingerprinting, A Parallell Approach to Establish Ordered Clone Libraries," Abstracts and Papers presented at the 1988 meeting on Genome Mapping and Sequencing, p. 11.
Lehrach, H., Drmanac, R., Hoheisel, J., Larin, Z., Lennon, G., Monaco, A.P., Nizetic, D., Zehetner, G., and Poustka, A., (1990), "Hybridization Fingerprinting in Genome Mapping an
Crkvenjakov Radomir B.
Drmanac Radoje T.
Hyseq Inc.
Zitomer Stephanie W.
LandOfFree
Method of sequencing genomes by hybridization of oligonucleotide does not yet have a rating. At this time, there are no reviews or comments for this patent.
If you have personal experience with Method of sequencing genomes by hybridization of oligonucleotide, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Method of sequencing genomes by hybridization of oligonucleotide will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-2316781