Approaches to library screening

Journal of Molecular Microbiology and Biotechnology

Volumn 4, Issue 6, 2002, Pages 551-554

  Campbell, Tessa N ^a   Choy, Francis Y M ^a  

^a UNIVERSITY OF VICTORIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOMATION; BACTERIUM; COST EFFECTIVENESS ANALYSIS; DNA FINGERPRINTING; DNA SEQUENCE; GENE LIBRARY; GENETIC SCREENING; HYBRIDIZATION; MEDICAL GENETICS; NONHUMAN; POLYMERASE CHAIN REACTION; REVIEW; YEAST;

CHROMOSOMES, ARTIFICIAL, BACTERIAL; CHROMOSOMES, ARTIFICIAL, YEAST; DNA; DNA FINGERPRINTING; GENOMIC LIBRARY; NUCLEIC ACID HYBRIDIZATION; POLYMERASE CHAIN REACTION;

BACTERIA (MICROORGANISMS);

EID: 0036842674     PISSN: 14641801     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (60)

1. Alphey, L. 1997. PCR-based method for isolation of full-length clones and splice variants from cDNA libraries. BioTechniques. 22: 481-486.
2. Amemiya, CT., Alegria-Hartman, M.J., Aslanidis, C., Chen, C., Nikolic, J., Gingrich, J.C., and de Jong, P.J. 1992. A two-dimensional YAC pooling strategy for library screening via STS and Alu-PCR methods. Nucleic Acids Res. 20: 2559-2563.
3. Anand, R., Riley, J.H., Butler, R., Smith, J.C., and Markham, A.F. A 3.5 genome equivalent multi access YAC library: construction, characterisation, screening and storage. Nucleic Acids Res. 18: 1951-1956.
4. Asakawa, S., Abe, I., Kudoh, Y., Kishi, N., Wang, Y., Kubota, R., Kudoh, J., Kawasaki, K., Mioshima, S., and Shimizu, N. 1997. Human BAC library: construction and rapid screening. Gene. 191: 69-79.
5. Asakawa, S., and Shimizu, N. 1998. High-fidelity digital hybridization screening. Genomics. 49: 209-217.
6. Benton, W.D., and Davis, R.W. 1977. Screening λgt recombinant clones by hybridization to single plaques in situ. Science. 196: 180-182.
7. Bloem, L.J. and Yu, L. 1990. A time-saving method for screening cDNA or genomic libraries. Nucleic Acids Res. 18: 2830.
8. Bonnema, G., Hontelez, J., Verkerk, R., Zhang, Y.Q., van Daelen, R., van Kammen, A., and Zabel, P. 1996. An improved method of partially digesting plant megabase DNA suitable for YAC cloning: application to the construction of a 5.5 genome equivalent YAC library of tomato. Plant J. 9: 125-133.
9. Brodyanskii, V.M., Sulimova, G.E., Udina, I.G., Aitova, S.S., Shaikhaev, G.O., Sharikova, O.A., Zakhar'ev, V.M., Fedorova, L.I., Zelenin, A.V., Eikhorn, S., Baush, C., Laland, M., Ross, M., and Yankovskii, N.K., 1995. Screening of YAC clones and building a map of the chromosome 13 region often deleted during chronic B-cell lymphocytic leucosis. Mol. Biol. 29: 665-672.
10. Bruno, W.J., Knill, E., Balding, D.J., Bruce, D.C., Doggett, N.A., Sawhill, W.W., Stallings, R.L., Whittaker, C.C., and Torney, D.C. 1995. Efficient pooling designs for library screening. Genomics. 26: 21-30.
11. Campbell, T.N. and Choy, F.Y.M. 2001. Large-scale colony screening and insert orientation determination using PCR. BioTechniques. 30: 32-34.
12. Cao, Y., Kang, H.L., Xu, X., Wang, M., Dho, S.H., Huh, J.R., Lee, B-J., Kalush, F., Bocskai, D., Ding, Y., Tesmer, J.G., Lee, J., Moon, E., Jurecic, V., Baldini, A., Weier, H-U., Doggett, N.A., Simon, M.I., Adams, M.D., and Kim, U-J. 1999. A 12-Mb complete coverage BAC contig map in human chromosome 16p13.1-p11.2. Genome Res. 9: 763-774.
13. Chumakov, I., Rigault, P., Guillou, S., Ougen, P., Billaut, A., Guasconi, G., Gervy, P., LeGall, I., Soularue, P., Grinas, L., Bougueleret, L., Bellanne-Chantelot, C., Lacroix, B., Barillot, E., Gesnouin, P., Pook, S., Vaysseix, G., Frelat, G., Schmitz, A., Sambucy, J-L., Bosch, A., Estivill, X., Weissenbach, J., Vignal, A., Reithman, H., Cox, D., Patterson, D., Gardiner, K., Hattori, M., Sakaki, Y., Ichikawa, H., Ohki, M., Le Paslier, D., Heilig, R., Antonarakis, S., and Cohen, D. 1992. Continuum of overlapping clones spanning the entire human chromosome 21q. Nature. 359: 380-387.
14. Coulson, A., Waterston, R., Kiff, J., Sulston, J., and Kohara, Y. 1988. Genome linking with yeast artificial chromosomes. Nature. 335: 184-186.
15. 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 Res. 18: 2653-2660.
16. Crooijmans, R.P.M.A., Vrebalov, J., Dijkhof, R.J.M., van der Poel, J.J., and Groenen, M.A.M. 2000. Two-dimensional screening of the Wageningen chicken BAC library. Mammal. Genome. 11: 360-363.
17. Edwards, K.J., Thompson, H., Edwards, D., de Saizieu, A., Sparks, C., Thompson, J.A., Greenland, A.J., Eyers, M., and Schuch, W. 1992. Construction and characterisation of a yeast artificial chromosome library containing three haploid maize genome equivalents. Plant Mol. Biol. 19: 299-308.
18. Evans, G.A., and Lewis, K.A. 1989. Physical mapping of complex genomes by cosmid multiplex analysis. Proc. Natl. Acad. Sci. USA. 86: 5030-5034.
19. Gingrich, J.C., Boehrer, D.M., Garnes, J.A., Johnson, W., Wong, B.S., Bergmann, A., Eveleth, G.G., Langlois, R.G., and Carrano, A.V. Construction and characterization of human chromosome 2-specific cosmid, fosmid, and PAC clone libraries. Genomics. 32: 65-74.
20. Gosele, C., Hong, L., Kreitler, T., Rossmann, M., Hieke, B., Gross, U., Kramer, M., Himmelbauer, H., Bihoreau, M-T., Kwitek-Black, A.E., Twigger, S., Tonellato, P.J., Jacob, H.J., Schalkwyk, L.C., Lindpaintner, K., Ganten, D., Lehrach, H., and Knoblauch, M. 2000. High-throughput scanning of the rat genome using interspersed repetitive sequence-PCR markers. Genomics. 69: 287-294.
21. Green, E.D. and Olson, M.V. 1990a. Chromosomal region of the cystic fibrosis gene in yeast artificial chromosomes: a model for human genome mapping. Science. 250: 94-98.
22. Green, E.D. and Olson, M.V. 1990b. Systematic screening of yeast artificial-chromosome libraries by use of the polymerase chain reaction. Proc. Natl. Acad. Sci. USA. 87: 1213-1217.
23. Grunstein, M. and Hogness, D.S. 1975. Colony hybridization: a method for the isolation of cloned DNAs that contain a specific gene. Proc. Natl. Acad. Sci. USA. 72: 3961-3965.
24. Gussow, D. and Clackson, T. 1989. Direct clone characterization from plaques and colonies by the polymerase chain reaction. Nucleic Acids Res. 17:4000.
25. Han, C.S., Sutherland, R.D., Jewett, P.B., Campbell, M.L., Meincke, L.J., Tesmer, J.G., Mundt, M.O., Fawcett, J.J., Kim, U-J., Deaven, L.L., and Doggett, N.A. 2000. Construction of a BAC contig map of chromosome 16q by two-dimensional overgo hybridization. Genome Res. 10: 714-721.
26. Hunt, D.M., Sahota, V.K., Taylor, K., Simrak, D., Hornigold, N., Arnemann, J., Wolfe, J., and Buxton, R.S. 1999. Clustered cadherin genes: a sequence-ready contig for the desmosomal cadherin locus on human chromosome 18. Genomics. 62: 445-455.
27. Ioannou, P.A., Amemiya, C.T., Garnes, J., Kroisel, P.M., Shizuya, H., Chen, C., Batzer, M.A., and de Jong, P.J. 1994. A new bacteriophage P1-derived vector for the propagation of large human DNA fragments. Nat. Genet. 6:84-89.
28. Isola, N.R., Harn, H.J., and Cooper, D.L. 1991. Screening recombinant libraries: a rapid and efficient method for isolating cDNA clones utilizing the PCR. BioTechniques. 11: 580-582.
29. Israel, D.I. 1993. A PCR-based method for high stringency screening of DNA libraries. Nucleic Acids Res. 21: 2627-2631.
30. Kim, U-J., Birren, B.W., Slepak, T., Mancino, V., Boysen, C., Kang, H-L., Simon, M.I., and Shizuya, H. 1996. Construction and characterization of a human bacterial artificial chromosome library. Genomics. 34: 213-218.
31. Klein, P.E., Kelin, R.R., Cartinhour, S.W., Ulanch, P.E., Obert, J.A., Morishige, D.T., Schlueter, S.D., Childs, K.L., Ale, M., and Mullet, J.E. 2000. A high-throughput AFLP-based method for constructing integrated genetic and physical maps: progress toward a sorghum genome map. Genome Res. 10: 789-807.
32. Kwiatkowski, T.J., Zoghbi, H.Y., Ledbetter, S.A., Ellison, K.A., and Chinault, A.C. 1990. Rapid identification of yeast artificial chromosome clones by matrix pooling and crude lysate PCR. Nucleic Acids Res. 18: 7191.
33. Libert, F., Lefort, A., Okimoto, R., Womack, J., and Georges, M. 1993. Construction of a bovine genomic library of large yeast artificial chromosome clones. Genomics. 18: 270-276.
34. Liu, J., Stanton, V.P., Fujiwara, T.M., Wang, J-X., Rezonzew, R., Crumley, M.J., Morgan, K., Gros, P., Housman, D., and Schurr, E. 1995. Large-scale cloning of human chromosome 2-specific yeast artificial chromosomes (YACs) using an interspersed repetitive sequences (IRS)-PCR approach. Genomics. 26: 178-191.
35. Marra, M.A., Kucaba, T.A., Dietrich, N.L., Green, E.D., Brownstein, B., Wilson, R.K., McDonald, K.M., Hillier, L.W., McPherson, J.D., and Waterston, R.H. 1997. High throughput fingerprint analysis of large-insert clones. Genome Res. 7: 1072-1084.
36. McAlinden, T.P. and Krawetz, S.A. 1994. A practical method to screen libraries of cloned DNA. Anal. Biochem. 218: 237-238.
37. McCormick, M.K., Campbell, E., Deaven, L., and Moyzis, R. 1993. Low-frequency chimeric yeast artificial chromosome libraries from flow-sorted human chromosomes 16 and 21. Proc. Natl. Acad. Sci. USA. 90: 1063-1067.
38. Meldrum, D. 2000. Automation for genomics, part one: preparation for sequencing. Genome Res. 10: 1081-1092.
39. Mendez, M.J., Klapholz, S., Brownstein, B.H., Gemmill, R.M. 1991. Rapid screening of a YAC library by pulsed-field gel southern blot analysis of pooled YAC clones. Genomics. 10: 661-665.
40. Michalek, W., Kleine, M., Dargatz, H., Wenzel, G., and Jahoor, A. 1997. Stability of Hor1-specific YAC-clones and physical mapping of Hor1-loci in barley. Theor. Appl. Genet. 95: 369-374.
41. Nelson, D.L., Ballabio, A., Victoria, M.F., Pieretti, M., Bies, R.D., Gibbs, R.A., Maley, J.A., Chinault, A.C., Webster, T.D., and Caskey, C.T. 1991. Alu-primed polymerase chain reaction for regional assignment of 110 yeast artificial chromosome clones from the human X chromosome: identification of clones associated with a disease locus. Proc. Natl. Acad. Sci. USA. 88: 6157-6161.
42. Nelson, D.L., Ledbetter, S.A., Corbo, L., Victoria, M.F., Ramirez-Solis, R., Webster, T.D., Ledbetter, D.H., and Caskey, C.T. 1989. Alu-polymerase chain reaction: a method for rapid isolation of human-specific sequences from complex DNA sources. Proc. Natl. Acad. Sci. USA. 86: 6686-6690.
43. Nilsen, H., Otterlei, M., Haug, T., Solum, K., Nagelhus, T.A., Skorpen, F., and Krokan, H.E. 1997. Nuclear and mitochondrial uracil-DNA glycosylases are generated by alternative splicing and transcription from different positions in the UNG gene. Nucleic Acids Res. 750-755.
44. Nizetic, D., Zehetner, G., Monaco, A.P., Gellen, L., Young, B.D., and Lehrach, H. 1991. Construction, arraying, and high-density screening of large insert libraries of human chromosomes X and 21: their potential use as reference libraries. Proc. Natl. Acad. Sci. USA. 3233-3237.
45. Olsen, A. S., Coombs, J., Garcia, E., Elliott, J., Amemiya, C., de Jong, P., and Threadgill, G. 1993. Automated production of high density cosmid and YAC colony filters using a robotic workstation. BioTechniques. 14: 116-123.
46. Panussis, D.A., Stuebe, E.T., Weinstock, L.A., Wilson, R.K., and Mardis, E.R. Automated plaque picking and arraying on a robotic system equipped with a CCD camera and a sampling device using intramedic tubing. Lab. Robot. Autom. 8: 195-203.
47. Riley, J., Butler, R., Ogilvie, D., Finniear, R., Jenner, D., Powell, S., Anand, R., Smith, J.C., and Markham, A.F. 1990. A novel, rapid method for the isolation of terminal sequences from yeast artificial chromosome (YAC) clones. Nucleic Acids. Res. 18: 2887-2890.
48. Sambrook, J. and Russell, D.W. 2001. Molecular Cloning: A Laboratory Manual. 3rd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
49. Shizuya, H., Birren, B., Kim, U-J., Mancino, V., Slepak, T., Tachiri, Y., and Simon, M. 1992. Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. Proc. Natl. Acad. Sci. USA. 89: 8794-8797.
50. Silverman, G.A., Ye, R.D., Pollock, K.M., Sadler, J.E., and Korsmeyer, S.J. 1989. Use of yeast artificial chromosome clones for mapping and walking within human chromosome segment 18q21.3. Proc. Natl. Acad. Sci. USA. 86: 7485-7489.
51. Strauss, W.M., Jaenisch, E., and Jaenisch, R. 1992. A strategy for rapid production and screening of yeast artificial chromosome libraries. Mammal. Genome. 2: 150-157.
52. Traver, C.N., Klapholz, S., Hyman, R.W., and Davis, R.W. 1989. Rapid screening of a human genomic library in yeast artificial chromosomes for single-copy sequences. Proc. Natl. Acad. Sci. USA. 86: 5898-5902.
53. Uber, D.C., Jaklevic, J.M., Theil, E.H., Lishanskaya, A., and McNeely, M.R. 1991. Application of robotics and image processing to automated colony picking and arraying. BioTechniques. 11: 642-647.
54. Umehara, Y., Tanoue, H., Kurata, N., Ashikawa, I., Minobe, Y., and Sasaki, T. 1996. An ordered yeast artificial chromosome library covering over half of rice chromosome 6. Genome Res. 11: 935-942.
55. Valdes, J.M., Tagle, D.A., and Collins, F.S. 1994. Island rescue PCR: a rapid and efficient method for isolating transcribed sequences from yeast artificial chromosomes and cosmids. Proc. Natl. Acad. Sci. USA. 91: 5377-5381.
56. Vollrath, D. and Jaramillo-Babb, V.L. 1995. A sequence-ready BAC clone contig of a 2.2-Mb segment of human chromosome 1q24. Genome Res. 23: 4407-4414.
57. Vos, P., Hogers, R., Bleeker, M., Reijans, M., Van de lee, T., Hornes, M., Frijters, A., Pot, J., Peleman, J., Kuiper, M., and Zabeau, M. 1995. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 23: 4407-4414.
58. Yu, L. and Bloem, L.J. 1996. Use of the polymerase chain reaction to screen phage libraries. Methods Mol. Biol. 58: 335-339.
59. Zhu, H., Blackmon, B.P., Sasinowski, M., Dean, R.A. 1999. Physical map and organization of chromosome 7 in the rice blast fungus, Magnaporthe grisea. Genome Res. 9: 739-750.
60. Zon, L.I., Dorfman, D.M., and Orkin, S.H. 1989. The polymerase chain reaction colony miniprep. BioTechniques. 7: 696-698.