High-density gridding: Techniques and applications

Current Opinion in Biotechnology

Volumn 7, Issue 1, 1996, Pages 85-88

  Southern, Edwin M ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

LIGAND; OLIGONUCLEOTIDE; PEPTIDE;

ANALYTIC METHOD; BIOTECHNOLOGY; CHEMICAL STRUCTURE; GENE EXPRESSION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; REVIEW;

EID: 0030049164     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0958-1669(96)80100-5     Document Type: Article

References (21)

1. Grunstein M, Hogness DS: Colony hybridization: a method for the isolation of cloned DNAs that contain a specific gene. Proc Natl Acad Sci USA 1975, 72:3961-3965.
2. Cohen D, Chumakov I, Weissenbach J: A first-generation physical map of the human genome. Nature 1993, 366:698-701.
3. Copeland A, Lennon G: Rapid arrayed filter production using the 'ORCA' robot. Nature 1994, 369:421-422. A recent description of a versatile system for high-density gridding based on a commercially available robot.
4. Coulson A, Kozono Y, Lutterbach B, Shownkeen R, Sulston J, Waterston R: YACs and the C. elegans genome. Bioessays 1991, 13:413-417.
5. Hoheisel JD, Ross MT, Zehetner G, Lehrach H: Relational genome analysis using reference libraries and hybridisation fingerprinting. J Biotechnol 1994, 35:121-134. Describes an approach to genome analysis based on the shared use of gridded libraries. The idea is that each analysis of a library provides information that can be used to order the clones into sets, increasing the usefulness of the library; when a sufficient number of probes is used, the sets merge and become a physical map, indicating the positions of features such as genes and informative markers.
6. Hoheisel JD, Maier E, Mott R, McCarthy L, Grigoriev AV, Schalkwyk LC, Nizetic D, Francis F, Lehrach H: High resolution cosmid and P1 maps spanning the 14 Mb genome of the fission yeast S. pombe. Cell 1993, 73:109-120.
7. Weissenbach J, Gyapay G, Dib C, Vignal A, Morissette J, Millasseau P, Vaysseix G, Lathrop M: A second-generation linkage map of the human genome. Nature 1992, 359:794-801.
8. Lindsay S, Bird AP: Use of restriction enzymes to detect potential gene sequences in mammalian DNA. Nature 1987, 327:336-338.
9. Sulston J, Mallett F, Durbin R, Horsnell T: Image analysis of restriction enzyme fingerprint autoradiograms. Comput Appl Biosci 1989, 5:101-116.
10. Hastie ND, Bishop JO: The expression of three abundance classes of messenger RNA in mouse tissues. Cell 1976, 9:761-764.
11. Schena M, Shalon D, David RW, Brown PO: Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995, 270:467-470. A demonstration of how gridded cDNA sequences or ESTs can be used to study differential gene expression. These authors have developed a method of fixing cloned or amplified sequences in small spots on the surface of a microscope slide, using it to display differences in the pattern of gene expression during development in Arabidopsis.
12. Geysen HM, Rodda SJ, Mason TJ, Tribbick G, Schoofs PG: Strategies for epitope analysis using peptide synthesis. J Immunol Methods 1987, 102:259-274.
13. Fodor SP, Read JL, Pirrung MC, Stryer L, Lu AT, Solas D: Light-directed, spatially addressable parallel chemical synthesis. Science 1991, 251:767-773.
14. Holmes CP, Adams CL, Kochersperger LM, Mortensen RB, Aldwin LA: The use of light-directed combinatorial peptide synthesis in epitope mapping. Biopolymers 1995, 37:199-211.
15. Khrapko KR, Lysov YP, Khorlin AA, Ivanov IB, Yershov GM, Vasilenko SK, Florentiev VL, Mirzabekov AD: A method for DNA sequencing by hybridization with oligonucteotide matrix. DNA Seq 1991, 1:375-388.
16. Southern EM, Maskos U: Parallel synthesis and analysis of large numbers of related chemical compounds: applications to oligonucleotides. J Biotechnol 1994, 35:217-227. A review of potential applications of high-density arrays of ligands, with an emphasis on oligonucleotides.
17. Southern EM, Case-Green SC, Elder JK, Johnson M, Mir KU, Wang L, Williams JC: Arrays of complementary oligonucleotides for analysing the hybridisation behaviour of nucleic acids. Nucleic Acids Res 1994, 22:1368-1373. Describes a simple adaptation of a conventional oligonucleotide synthesizer in which the reaction column is replaced by a cell that is pressed against the surface of a glass or plastic sheet. Arrays of oligonucleotides complementary to a target of known sequence are created by coupling a base to the surface and then moving the cell along, before coupling the next base in the sequence.
18. Southern EM, Maskos U, Elder JK: Analysing and comparing nucleic acid sequences by hybridization to arrays of oligonucleotides: evaluation using experimental models. Genomics 1992, 13:1008-1017.
19. Bains W, Smith GC: Nucleic acid sequence determination. J Theor Biol 1988, 135:303-307.
20. Drmanac R, Labat I, Brukner I, Crkvenjakov R: Sequencing of megabase plus DNA by hybridization: theory of the method. Genomics 1989, 4:114-128.
21. Lipshutz RJ, Morris D, Chee M, Hubbell E, Kozal MJ, Shah N, Shen N, Yang R, Fodor SPA: Using oligonucleotide probe arrays to access genetic diversity. Biotechniques 1995, 19:442-447. Specialized arrays are made by the photolithographic technique for analysis of sequence differences. In this case, these authors use the method to analyze sequence variation in drug-resistant strains of HIV.