Ordering of cosmid clones covering the herpes simplex virus type I (HSV-I) genome: a test case for fingerprinting by hybridisation (original) (raw)

Abstract

To allow the efficient construction of ordered clone libraries, we have been investigating the use of 'oligonucleotide fingerprinting' as an approach to identify overlapping clones, and ultimately restore the linear order of the clone set. To test the effectiveness of the procedure, we have constructed a cosmid library from the genome of the human DNA virus HSV-I and used hybridisation to multiple oligonucleotides selected from the nucleotide sequence to reconstruct the order of clones and oligonucleotides on the genome.

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Selected References

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  1. Carrano A. V., Lamerdin J., Ashworth L. K., Watkins B., Branscomb E., Slezak T., Raff M., de Jong P. J., Keith D., McBride L. A high-resolution, fluorescence-based, semiautomated method for DNA fingerprinting. Genomics. 1989 Feb;4(2):129–136. doi: 10.1016/0888-7543(89)90291-7. [DOI] [PubMed] [Google Scholar]
  2. Church G. M., Kieffer-Higgins S. Multiplex DNA sequencing. Science. 1988 Apr 8;240(4849):185–188. doi: 10.1126/science.3353714. [DOI] [PubMed] [Google Scholar]
  3. Coulson A., Sulston J., Brenner S., Karn J. Toward a physical map of the genome of the nematode Caenorhabditis elegans. Proc Natl Acad Sci U S A. 1986 Oct;83(20):7821–7825. doi: 10.1073/pnas.83.20.7821. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Cross S. H., Little P. F. A cosmid vector for systematic chromosome walking. Gene. 1986;49(1):9–22. doi: 10.1016/0378-1119(86)90381-1. [DOI] [PubMed] [Google Scholar]
  5. Delius H., Clements J. B. A partial denaturation map of herpes simplex virus type 1 DNA: evidence for inversions of the unique DNA regions. J Gen Virol. 1976 Oct;33(1):125–133. doi: 10.1099/0022-1317-33-1-125. [DOI] [PubMed] [Google Scholar]
  6. Drmanac R., Labat I., Brukner I., Crkvenjakov R. Sequencing of megabase plus DNA by hybridization: theory of the method. Genomics. 1989 Feb;4(2):114–128. doi: 10.1016/0888-7543(89)90290-5. [DOI] [PubMed] [Google Scholar]
  7. Evans G. A., Lewis K. A. Physical mapping of complex genomes by cosmid multiplex analysis. Proc Natl Acad Sci U S A. 1989 Jul;86(13):5030–5034. doi: 10.1073/pnas.86.13.5030. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Herrmann B. G., Barlow D. P., Lehrach H. A large inverted duplication allows homologous recombination between chromosomes heterozygous for the proximal t complex inversion. Cell. 1987 Mar 13;48(5):813–825. doi: 10.1016/0092-8674(87)90078-x. [DOI] [PubMed] [Google Scholar]
  9. Hoheisel J. D., Nizetic D., Lehrach H. Control of partial digestion combining the enzymes dam methylase and MboI. Nucleic Acids Res. 1989 Dec 11;17(23):9571–9582. doi: 10.1093/nar/17.23.9571. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Kohara Y., Akiyama K., Isono K. The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell. 1987 Jul 31;50(3):495–508. doi: 10.1016/0092-8674(87)90503-4. [DOI] [PubMed] [Google Scholar]
  11. Maas R., Silva R. M., Gomes T. A., Trabulsi L. R., Maas W. K. Detection of genes for heat-stable enterotoxin I in Escherichia coli strains isolated in Brazil. Infect Immun. 1985 Jul;49(1):46–51. doi: 10.1128/iai.49.1.46-51.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. McGeoch D. J., Dalrymple M. A., Davison A. J., Dolan A., Frame M. C., McNab D., Perry L. J., Scott J. E., Taylor P. The complete DNA sequence of the long unique region in the genome of herpes simplex virus type 1. J Gen Virol. 1988 Jul;69(Pt 7):1531–1574. doi: 10.1099/0022-1317-69-7-1531. [DOI] [PubMed] [Google Scholar]
  13. Michiels F., Craig A. G., Zehetner G., Smith G. P., Lehrach H. Molecular approaches to genome analysis: a strategy for the construction of ordered overlapping clone libraries. Comput Appl Biosci. 1987 Sep;3(3):203–210. doi: 10.1093/bioinformatics/3.3.203. [DOI] [PubMed] [Google Scholar]
  14. Murray N. E., Brammar W. J., Murray K. Lambdoid phages that simplify the recovery of in vitro recombinants. Mol Gen Genet. 1977 Jan 7;150(1):53–61. doi: 10.1007/BF02425325. [DOI] [PubMed] [Google Scholar]
  15. Olson M. V., Dutchik J. E., Graham M. Y., Brodeur G. M., Helms C., Frank M., MacCollin M., Scheinman R., Frank T. Random-clone strategy for genomic restriction mapping in yeast. Proc Natl Acad Sci U S A. 1986 Oct;83(20):7826–7830. doi: 10.1073/pnas.83.20.7826. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Olson M., Hood L., Cantor C., Botstein D. A common language for physical mapping of the human genome. Science. 1989 Sep 29;245(4925):1434–1435. doi: 10.1126/science.2781285. [DOI] [PubMed] [Google Scholar]
  17. Poustka A., Pohl T., Barlow D. P., Zehetner G., Craig A., Michiels F., Ehrich E., Frischauf A. M., Lehrach H. Molecular approaches to mammalian genetics. Cold Spring Harb Symp Quant Biol. 1986;51(Pt 1):131–139. doi: 10.1101/sqb.1986.051.01.016. [DOI] [PubMed] [Google Scholar]
  18. Poustka A., Pohl T., Barlow D. P., Zehetner G., Craig A., Michiels F., Ehrich E., Frischauf A. M., Lehrach H. Molecular approaches to mammalian genetics. Cold Spring Harb Symp Quant Biol. 1986;51(Pt 1):131–139. doi: 10.1101/sqb.1986.051.01.016. [DOI] [PubMed] [Google Scholar]
  19. Wood W. I., Gitschier J., Lasky L. A., Lawn R. M. Base composition-independent hybridization in tetramethylammonium chloride: a method for oligonucleotide screening of highly complex gene libraries. Proc Natl Acad Sci U S A. 1985 Mar;82(6):1585–1588. doi: 10.1073/pnas.82.6.1585. [DOI] [PMC free article] [PubMed] [Google Scholar]