John Wiley & Sons - 2004 - Analysis of Genes and Genomes

428 REFERENCES

Garcia-Saez,´ I., Parraga,´ A., Phillips, M.F., Mantle, T.J. and Coll, M. (1994) Molecular

˚

structure at 1.8 A of mouse liver class pi glutathione S-transferase complexed with S-(p-nitrobenzyl)glutathione and other inhibitors. J. Mol. Biol., 237, 298 – 314.

Garrick, D., Fiering, S., Martin, D.I. and Whitelaw, E. (1998) Repeat-induced gene silencing in mammals. Nat. Genet., 18, 56 – 59.

Gatignol, A., Durand, H. and Tiraby, G. (1988) Bleomycin resistance conferred by a drug-binding protein. FEBS Lett., 230, 171 – 175.

Gavin, A.C. et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature, 415, 141 – 147.

Genilloud, O., Garrido, M.C. and Moreno, F. (1984) The transposon Tn5 carries a bleomycin-resistance determinant. Gene, 32, 225 – 233.

Georgiadis, M.M., Jessen, S.M., Ogata, C.M., Telesnitsky, A., Goff, S.P. and Hendrickson, W.A. (1995) Mechanistic implications from the structure of a catalytic fragment of Moloney murine leukemia virus reverse transcriptase. Structure, 3, 879 – 892.

Giaever, G. et al. (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature, 418, 387 – 391.

Giga-Hama, Y. and Kumagai, H. (1999) Expression system for foreign genes using the fission yeast Schizosaccharomyces pombe. Biotechnol. Appl. Biochem., 30, 235 – 244.

Giniger, E., Varnum, S.M. and Ptashne, M. (1985) Specific DNA binding of GAL4, a positive regulatory protein of yeast. Cell, 40, 767 – 774.

Glazer, A.N. and Mathies, R.A. (1997) Energy-transfer fluorescent reagents for DNA analyses. Curr. Opin. Biotechnol., 8, 94 – 102.

Gnatt, A.L., Cramer, P., Fu, J., Bushnell, D.A. and Kornberg, R.D. (2001) Structural

˚

basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution. Science, 292, 1876 – 1882.

Goff, S.A. et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science, 296, 92 – 100.

Goffeau, A. et al. (1997) The yeast genome directory. Nature, 387 supp, 5 – 6. Goldfarb, D.S., Gariepy, J., Schoolnik, G. and Kornberg, R.D. (1986) Synthetic pep-

tides as nuclear localization signals. Nature, 322, 641 – 644. Goldschmidt-Clermont, M. (1991) Transgenic expression of aminoglycoside adenine

transferase in the chloroplast: a selectable marker of site-directed transformation of

Chlamydomonas. Nucleic Acids Res., 19, 4083 – 4089.

Gonczy,¨ P. et al. (2000) Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III. Nature, 408, 331 – 336.

Gorman, C.M., Merlino, G.T., Willingham, M.C., Pastan, I. and Howard, B.H. (1982) The Rous sarcoma virus long terminal repeat is a strong promoter when introduced into a variety of eukaryotic cells by DNA-mediated transfection. Proc. Natl. Acad. Sci. USA, 79, 6777 – 6781.

Gorman, C.M., Moffat, L.F. and Howard, B.H. (1982) Recombinant genomes which express chloramphenicol acetyltransferase in mammalian cells. Mol. Cell. Biol., 2, 1044 – 1051.

REFERENCES 429

Gorziglia, M.I., Kadan, M.J., Yei, S., Lim, J., Lee, G.M., Luthra, R. and Trapnell, B.C. (1996) Elimination of both E1 and E2 from adenovirus vectors further improves prospects for in vivo human gene therapy. J. Virol., 70, 4173 – 4178.

Gossen, M. and Bujard, H. (1992) Tight control of gene expression in mammalian cells by tetracycline-responsive promoters. Proc. Natl. Acad. Sci. USA, 89, 5547 – 5551.

Gossen, M. and Bujard, H. (2002) Studying gene function in eukaryotes by conditional gene inactivation. Annu. Rev. Genet., 36, 153 – 173.

Gossen, M., Freundlieb, S., Bender, G., Muller, G., Hillen, W. and Bujard, H. (1995) Transcriptional activation by tetracyclines in mammalian cells. Science, 268, 1766 – 1769.

Gottesman, S. (1996) Proteases and their targets in Escherichia coli. Annu. Rev. Genet., 30, 465 – 506.

Gottschalk, A., Bartels, C., Neubauer, G., Luhrmann,¨ R. and Fabrizio, P. (2001) A novel yeast U2 snRNP protein, Snu17p, is required for the first catalytic step of splicing and for progression of spliceosome assembly. Mol. Cell. Biol., 21, 3037 – 3046.

Gottschalk, S., Sparrow, J.T., Hauer, J., Mims, M.P., Leland, F.E., Woo, S.L. and Smith, L.C. (1996) A novel DNA-peptide complex for efficient gene transfer and expression in mammalian cells. Gene Ther., 3, 48 – 57.

Graham, F.L., Smiley, J., Russell, W.C. and Nairn, R. (1977) Characteristics of a human cell line transformed by DNA from human adenovirus type 5. J. Gen. Virol., 36, 59 – 74.

Graham, F.L. and van der Eb, A.J. (1973) A new technique for the assay of infectivity of human adenovirus 5 DNA. Virology, 52, 456 – 467.

Green, E.D., Riethman, H.C., Dutchik, J.E. and Olson, M.V. (1991) Detection and characterization of chimeric yeast artificial-chromosome clones. Genomics, 11, 658 – 669.

Green, N.M. (1963) Avidin. 1. The use of [14C] biotin for kinetic studies and for assay.

Biochem. J., 89, 585 – 591.

Green, P.J., Pines, O. and Inouye, M. (1986) The role of antisense RNA in gene regulation. Annu. Rev. Biochem., 55, 569 – 597.

Gressel, J. (2000) Molecular biology of weed control. Transgenic Res., 9, 355 – 382. Griffin, H.G. and Griffin, A.M. (1993) Dideoxy sequencing reactions using Sequenase

version 2.0. Methods Mol. Biol., 23, 103 – 108.

Griffith, F. (1928) The significance of pneumococcal types. J. Hyg., 27, 113 – 159. Griggs, D. and Johnston, M. (1991) Regulated expression of the GAL4 activator gene

in yeast provides a sensitive genetic switch for glucose repression. Proc. Natl. Acad. Sci. USA, 88, 8597 – 8601.

Gronenborn, B. (1976) Overproduction of phage lambda repressor under control of the lac promotor of Escherichia coli. Mol. Gen. Genet., 148, 243 – 250.

Gross, C., Kelleher, M., Iyer, V.R., Brown, P.O. and Winge, D.R. (2000) Identification of the copper regulon in Saccharomyces cerevisiae by DNA microarrays. J. Biol. Chem., 275, 32 310 – 32 316.

430 REFERENCES

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.

Grunstein, M. and Wallis, J. (1979) Colony hybridization. Methods Enzymol., 68, 379 – 389.

Gruss, P. and Walther, C. (1992) Pax in development. Cell, 69, 719 – 722.

Gu, H., Marth, J.D., Orban, P.C., Mossmann, H. and Rajewsky, K. (1994) Deletion of a DNA polymerase β-gene segment in T cells using cell type-specific gene targeting. Science, 265, 103 – 106.

Gubler, U. and Hoffman, B.J. (1983) A simple and very efficient method for generating cDNA libraries. Gene, 25, 263 – 269.

Gurdon, J.B., Laskey, R.A. and Reeves, O.R. (1975) The developmental capacity of nuclei transplanted from keratinized skin cells of adult frogs. J. Embryol. Exp. Morphol., 34, 93 – 112.

Hamer, D.H. and Leder, P. (1979) Expression of the chromosomal mouse β-maj-globin gene cloned in SV40. Nature, 281, 35 – 40.

Hammond, S.M., Bernstein, E., Beach, D. and Hannon, G.J. (2000) An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature, 404, 293 – 296.

Hampsey, M. (1998) Molecular genetics of the RNA polymerase II general transcriptional machinery. Microbiol. Mol. Biol. Rev., 62, 465 – 503.

Hanahan, D. (1983) Studies on transformation of Escherichia coli with plasmids. J. Mol. Biol., 166, 557 – 580.

Hanahan, D. and Meselson, M. (1980) Plasmid screening at high colony density. Gene, 10, 63 – 67.

Handler, M. and Iozzo, R.V. (2001) Constitutive and inducible antisense expression.

Methods Mol. Biol., 171, 251 – 259.

Hansen, G. and Wright, M.S. (1999) Recent advances in the transformation of plants.

Trends Plant. Sci., 4, 226 – 231.

Harbottle, R.P., Cooper, R.G., Hart, S.L., Ladhoff, A., McKay, T., Knight, A.M., Wagner, E., Miller, A.D. and Coutelle, C. (1998) An RGD-oligolysine peptide: a prototype construct for integrin-mediated gene delivery. Hum. Gene Ther., 9, 1037 – 1047.

Hardy, E., Martinez, E., Diago, D., Diaz, R., Gonzalez, D. and Herrera, L. (2000) Large-scale production of recombinant hepatitis B surface antigen from Pichia pastoris. J. Biotechnol., 77, 157 – 167.

Hargreaves, D., Rice, D.W., Sedelnikova, S.E., Artymiuk, P.J., Lloyd, R.G. and Rafferty, J.B. (1998) Crystal structure of E. coli RuvA with bound DNA Holliday

˚

junction at 6A resolution. Nat. Struct. Biol., 5, 441 – 446.

Harlow, E. and Lane, D. (1999) Using Antibodies: a Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.

Harrington, J.J., Van Bokkelen, G., Mays, R.W., Gustashaw, K. and Willard, H.F. (1997) Formation of de novo centromeres and construction of first-generation human artificial microchromosomes. Nat. Genet., 15, 345 – 355.

REFERENCES 431

Harris, L.J., Larson, S.B., Hasel, K.W., Day, J., Greenwood, A. and McPherson, A. (1992) The three-dimensional structure of an intact monoclonal antibody for canine lymphoma. Nature, 360, 369 – 372.

Haughn, G.W., Smith, J., Mazur, B. and Somerville, C. (1988) Transformation with a mutant Arabidopsis acetolactate synthase gene renders tobacco resistant to sulfonylurea herbicides. Mol. Gen. Genet., 211, 266 – 271.

Hayashi, M.N. and Hayashi, M. (1985) Cloned DNA sequences that determine mRNA stability of bacteriophage φX174 in vivo are functional. Nucleic Acids Res., 13, 5937 – 5948.

Hecht, A. and Grunstein, M. (1999) Mapping DNA interaction sites of chromosomal proteins using immunoprecipitation and polymerase chain reaction. Methods Enzymol., 304, 399 – 414.

Hedgpeth, J., Goodman, H.M. and Boyer, H.W. (1972) DNA nucleotide sequence restricted by the RI endonuclease. Proc. Natl. Acad. Sci. USA, 69, 3448 – 3452.

Helmer-Citterich, M., Anceschi, M.M., Banner, D.W. and Cesareni, G. (1988) Control of ColE1 replication: low affinity specific binding of Rop (Rom) to RNAI and RNAII. EMBO J., 7, 557 – 566.

Hendrix, R.W. (1983) Lambda II. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.

Henning, K.A., Novotny, E.A., Compton, S.T., Guan, X.Y., Liu, P.P. and Ashlock, M.A. (1999) Human artificial chromosomes generated by modification of a yeast artificial chromosome containing both human alpha satellite and single-copy DNA sequences. Proc. Natl. Acad. Sci. USA, 96, 592 – 597.

Herr, W., Sturm, R.A., Clerc, R.G., Corcoran, L.M., Baltimore, D., Sharp, P.A., Ingraham, H.A., Rosenfeld, M.G., Finney, M., Ruvkun, G. and Horvitz, H.R. (1988) The POU domain: a large conserved region in the mammalian pit-1, oct-1, oct-2, and Caenorhabditis elegans unc-86 gene products. Genes Dev., 2, 1513 – 1516.

Herrera, P.L. (2000) Adult insulinand glucagon-producing cells differentiate from two independent cell lineages. Development, 127, 2317 – 2322.

Hershey, A.D. (1947) Spontaneous mutations in bacterial viruses. Cold Spring Harbor Symp. Quant. Biol., 11, 67 – 77.

Hershey, A.D. and Chase, M. (1952) Independent functions of viral protein and nucleic acid in growth of bacteriophage. J. Gen. Physiol., 36, 39 – 56.

Hexham, J.M. (1998) Production of human Fab antibody fragments from phage display libraries. Methods Mol. Biol., 80, 461 – 474.

Hiei, Y., Ohta, S., Komari, T. and Kumashiro, T. (1994) Efficient transformation of rice (Oryza sativa L.) mediated by Agrobacterium and sequence analysis of the boundaries of the T-DNA. Plant J., 6, 271 – 282.

High, K.A. (2001) AAV-mediated gene transfer for hemophilia. Ann. NY Acad. Sci., 953, 64 – 74.

Higuchi, R., Krummel, B. and Saiki, R. (1988) A general method of in vitro preparation and specific mutagenesis of DNA fragments: study of protein and DNA interactions.

Nucleic Acids Res., 16, 7351 – 7367.

432 REFERENCES

Hinnebusch, A.G. (1997) Translational regulation of yeast GCN4. A window on factors that control initiator – tRNA binding to the ribosome. J. Biol. Chem., 272, 21 661 – 21 664.

Hirose, Y. and Manley, J.L. (1998) RNA polymerase II is an essential mRNA polyadenylation factor. Nature, 395, 93 – 96.

Hirt, R.P., Poulain-Godefroy, O., Billotte, J., Kraehenbuhl, J.P. and Fasel, N. (1992) Highly inducible synthesis of heterologous proteins in epithelial cells carrying a glucocorticoid-responsive vector. Gene, 111, 199 – 206.

Ho, S.Y. and Mittal, G.S. (1996) Electroporation of cell membranes: a review. Crit. Rev. Biotechnol., 16, 349 – 362.

Hoffman, A. and Roeder, R.G. (1991) Purification of his-tagged proteins in nondenaturing conditions suggests a convenient method for protein interaction studies.

Nucleic Acids Res., 19, 6337 – 6338.

Holland, P.M., Abramson, R.D., Watson, R. and Gelfand, D.H. (1991) Detection of specific polymerase chain reaction product by utilizing the 5 – 3 exonuclease activity of Thermus aquaticus DNA polymerase. Proc. Natl. Acad. Sci. USA, 88, 7276 – 7280.

Holley, R.W. (1966) The nucleotide sequence of a nucleic acid. Sci. Am., 214, 30 – 39. Holliday, R. (1964) A mechanism for gene conversion in fungi. Genet. Res., 5,

282 – 304.

Holt, R.A. et al. (2002) The genome sequence of the malaria mosquito Anopheles gambiae. Science, 298, 129 – 149.

Hooykaas, P.J. (1989) Transformation of plant cells via Agrobacterium. Plant Mol. Biol., 13, 327 – 336.

Hope, I.A. (2001) RNAi surges on: application to cultured mammalian cells. Trends Genet., 17, 440.

Horsch, R.B., Fry, J.E., Hoffmann, N.L., Eichholtz, D., Rogers, S.G. and Fraley, R.T. (1985) A simple and general method for transferring genes into plants. Science, 227, 1229 – 1231.

Hosoda, F., Arai, Y., Kitamura, E., Inazawa, J., Fukushima, M., Tokino, T., Nakamura, Y., Jones, C., Kakazu, N., Abe, T. and Ohki, M. (1997) A complete NotI restriction map covering the entire long arm of human chromosome 11. Genes Cells, 2, 345 – 357.

Hu, J.C., Kornacker, M.G. and Hochschild, A. (2000) Escherichia coli oneand twohybrid systems for the analysis and identification of protein – protein interactions. Methods, 20, 80 – 94.

Huang, J. and Schreiber, S.L. (1997) A yeast genetic system for selecting small molecule inhibitors of protein – protein interactions in nanodroplets. Proc. Natl. Acad. Sci. USA, 94, 13 396 – 13 401.

Hudson, J.R., Jr., Dawson, E.P., Rushing, K.L., Jackson, C.H., Lockshon, D., Conover, D., Lanciault, C., Harris, J.R., Simmons, S.J., Rothstein, R. and Fields, S. (1997) The complete set of predicted genes from Saccharomyces cerevisiae in a readily usable form. Genome Res., 7, 1169 – 1173.

Hudson, T.J. et al. (1995) An STS-based map of the human genome. Science, 270, 1945 – 1954.

REFERENCES 433

Hug, H., Costas, M., Staeheli, P., Aebi, M. and Weissmann, C. (1988) Organization of the murine Mx gene and characterization of its interferonand virus-inducible promoter. Mol. Cell. Biol., 8, 3065 – 3079.

Hull, R., Covey, S.N. and Maule, A.J. (1987) Structure and replication of caulimovirus genomes. J. Cell. Sci. Suppl., 7, 213 – 229.

Hull, R. and Shepherd, R.J. (1977) The structure of cauliflower mosaic virus genome. Virology, 79, 216 – 230.

Hutvagner,´ G., McLachlan, J., Pasquinelli, A.E., Balint,´ E., Tuschl, T. and Zamore, P.D. (2001) A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science, 293, 834 – 838.

Hutvagner,´ G. and Zamore, P.D. (2002) RNAi: nature abhors a double-strand. Curr. Opin. Genet. Dev., 12, 225 – 232.

Iamtham, S. and Day, A. (2000) Removal of antibiotic resistance genes from transgenic tobacco plastids. Nat. Biotechnol., 18, 1172 – 1176.

Ichikawa, H., Hosoda, F., Arai, Y., Shimizu, K., Ohira, M. and Ohki, M. (1993) A NotI restriction map of the entire long arm of human chromosome 21. Nat. Genet., 4, 361 – 366.

Innis, M.A., Gelfand, D.H. and Sninsky, J.J. (eds.). (1999) PCR Applications: Protocols for Functional Genomics. Academic, San Diego, CA.

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.

Ish-Horowicz, D. and Burke, J.F. (1981) Rapid and efficient cosmid cloning. Nucleic Acids Res., 9, 2989 – 2998.

Isono, K., McIninch, J.D. and Borodovsky, M. (1994) Characteristic features of the nucleotide sequences of yeast mitochondrial ribosomal protein genes as analyzed by computer program GeneMark. DNA Res., 1, 263 – 269.

Ivanova, N.B., Dimos, J.T., Schaniel, C., Hackney, J.A., Moore, K.A. and Lemischka, I.R. (2002) A stem cell molecular signature. Science, 298, 601 – 604.

Jackson, D.A., Symons, R.H. and Berg, P. (1972) Biochemical method for inserting new genetic information into DNA of Simian Virus 40: circular SV40 DNA molecules containing lambda phage genes and the galactose operon of Escherichia coli. Proc. Natl. Acad. Sci. USA, 69, 2904 – 2909.

Jacob, F. and Monod, J. (1961) Genetic regulatory mechanisms in the synthesis of proteins. J. Mol. Biol., 3, 318 – 356.

James, P., Halladay, J. and Craig, E.A. (1996) Genomic libraries and a host strain designed for highly efficient two-hybrid selection in yeast. Genetics, 144, 1425 – 1436.

Janknecht, R., de Martynoff, G., Lou, J., Hipskind, R.A., Nordheim, A. and Stunnenberg, H.G. (1991) Rapid and efficient purification of native histidine-tagged protein expressed by recombinant vaccinia virus. Proc. Natl. Acad. Sci. USA, 88, 8972 – 8976.

Jefferson, R.A., Burgess, S.M. and Hirsh, D. (1986) β-Glucuronidase from Escherichia coli as a gene-fusion marker. Proc. Natl. Acad. Sci. USA, 83, 8447 – 8451.

Jen-Jacobson,L., Engler, L.E., Lesser, D.R., Kurpiewski, M.R., Yee, C. and McVerry, B. (1996) Structural adaptations in the interaction of EcoRI endonuclease with methylated GAATTC sites. EMBO J., 15, 2870 – 2882.

434 REFERENCES

Johnsson, N. and Varshavsky, A. (1994) Split ubiquitin as a sensor of protein interactions in vivo. Proc. Natl. Acad. Sci. USA, 91, 10 340 – 10 344.

Johnston, S.A., Salmeron, J.M. and Dincher, S.S. (1987) Interaction of positive and negative regulatory proteins in the galactose regulon of yeast. Cell, 50, 143 – 146.

Johnston, S.A. and Tang, D.C. (1994) Gene gun transfection of animal cells and genetic immunization. Methods Cell. Biol., 43 Pt A, 353 – 365.

Joshi, L., Davis, T.R., Mattu, T.S., Rudd, P.M., Dwek, R.A., Shuler, M.L. and Wood, H.A. (2000) Influence of baculovirus-host cell interactions on complex N-linked glycosylation of a recombinant human protein. Biotechnol. Prog., 16, 650 – 656.

Juers, D.H., Jacobson, R.H., Wigley, D., Zhang, X.J., Huber, R.E., Tronrud, D.E. and Matthews, B.W. (2000) High resolution refinement of β-galactosidase in a new crystal form reveals multiple metal-binding sites and provides a structural basis for α-complementation. Protein Sci., 9, 1685 – 1699.

Kamada, K., Horiuchi, T., Ohsumi, K., Shimamoto, N. and Morikawa, K. (1996) Structure of a replication-terminator protein complexed with DNA. Nature, 383, 598 – 603.

Kamath, R.S., Fraser, A.G., Dong, Y., Poulin, G., Durbin, R., Gotta, M., Kanapin, A., Le Bot, N., Moreno, S., Sohrmann, M., Welchman, D.P., Zipperlen, P. and Ahringer, J. (2003) Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature, 421, 231 – 237.

Karger, A.E., Harris, J.M. and Gesteland, R.F. (1991) Multiwavelength fluorescence detection for DNA sequencing using capillary electrophoresis. Nucleic Acids Res., 19, 4955 – 4962.

Karimi, M., Inze, D. and Depicker, A. (2002) GATEWAY vectors for Agrobacterium- mediated plant transformation. Trends Plant. Sci., 7, 193 – 195.

Katz, R.A. and Skalka, A.M. (1994) The retroviral enzymes. Annu. Rev. Biochem., 63, 133 – 173.

Keller, G.M. (1995) In vitro differentiation of embryonic stem cells. Curr. Opin. Cell. Biol., 7, 862 – 869.

Kellermann, O.K. and Ferenci, T. (1982) Maltose-binding protein from Escherichia coli. Methods Enzymol., 90, 459 – 463.

Kellogg, D.E., Rybalkin, I., Chen, S., Mukhamedova, N., Vlasik, T., Siebert, P.D. and Chenchik, A. (1994) TaqStart Antibody: ‘hot start’ PCR facilitated by a neutralizing monoclonal antibody directed against Taq DNA polymerase. Biotechniques, 16, 1134 – 1137.

Kennedy, M., Firpo, M., Choi, K., Wall, C., Robertson, S., Kabrun, N. and Keller, G. (1997) A common precursor for primitive erythropoiesis and definitive haematopoiesis. Nature, 386, 488 – 493.

Keohavong, P., Ling, L., Dias, C. and Thilly, W.G. (1993) Predominant mutations induced by the Thermococcus litoralis, vent DNA polymerase during DNA amplification in vitro. PCR Methods Appl., 2, 288 – 292.

Keohavong, P. and Thilly, W.G. (1989) Fidelity of DNA polymerases in DNA amplification. Proc. Natl. Acad. Sci. USA, 86, 9253 – 9257.

Kilby, N.J., Snaith, M.R. and Murray, J.A. (1993) Site-specific recombinases: tools for genome engineering. Trends Genet., 9, 413 – 421.

REFERENCES 435

Kim, K.K., Chamberlin, H.M., Morgan, D.O. and Kim, S.H. (1996a) Three-dimen- sional structure of human cyclin H, a positive regulator of the CDK-activating kinase. Nat. Struct. Biol., 3, 849 – 855.

Kim, S., Lin, H., Barr, E., Chu, L., Leiden, J.M. and Parmacek, M.S. (1997) Transcriptional targeting of replication-defective adenovirus transgene expression to smooth muscle cells in vivo. J. Clin. Invest., 100, 1006 – 1014.

Kim, U.J., Birren, B.W., Slepak, T., Mancino, V., Boysen, C., Kang, H.L., Simon, M.I. and Shizuya, H. (1996b) Construction and characterization of a human bacterial artificial chromosome library. Genomics, 34, 213 – 218.

Knapp, J.E., Carroll, D., Lawson, J.E., Ernst, S.R., Reed, L.J. and Hackert, M.L. (2000) Expression, purification, and structural analysis of the trimeric form of the catalytic domain of the Escherichia coli dihydrolipoamide succinyltransferase. Protein Sci., 9, 37 – 48.

Knittel, T. and Picard, D. (1993) PCR with degenerate primers containing deoxyinosine fails with Pfu DNA polymerase. PCR Methods Appl., 2, 346 – 347.

Kodadek, T. (2002) Development of protein-detecting microarrays and related devices.

Trends Biochem. Sci., 27, 295 – 300.

Koleske, A. and Young, R.A. (1994) An RNA polymerase II holoenzyme responsive to activators. Nature, 368, 466 – 469.

Konisky, J. and Tokuda, H. (1979) Mode of action of colicins Ia, E1 and K. Zentralbl. Bakteriol. [Orig. A], 244, 105 – 120.

Kornberg, A. and Baker, T.A. (1992) DNA Replication. Freeman, New York.

Kotin, R.M., Siniscalco, M., Samulski, R.J., Zhu, X.D., Hunter, L., Laughlin, C.A., McLaughlin, S., Muzyczka, N., Rocchi, M. and Berns, K.I. (1990) Site-specific integration by adeno-associated virus. Proc. Natl. Acad. Sci. USA, 87, 2211 – 2215.

Koutz, P., Davis, G.R., Stillman, C., Barringer, K., Cregg, J. and Thill, G. (1989) Structural comparison of the Pichia pastoris alcohol oxidase genes. Yeast, 5, 167 – 177.

Kovall, R.A. and Matthews, B.W. (1999) Type II restriction endonucleases: structural, functional and evolutionary relationships. Curr. Opin. Chem. Biol., 3, 578 – 583.

Kozak, M. (1986) Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes. Cell, 44, 283 – 292.

Kramer, B., Kramer, W. and Fritz, H.J. (1984) Different base/base mismatches are corrected with different efficiencies by the methyl-directed DNA mismatch-repair system of E. coli. Cell, 38, 879 – 887.

Kuhn,¨ R., Schwenk, F., Aguet, M. and Rajewsky, K. (1995) Inducible gene targeting in mice. Science, 269, 1427 – 1429.

Kumar, S. and Fladung, M. (2001) Controlling transgene integration in plants. Trends Plant Sci., 6, 155 – 159.

Kunkel, T.A. (1985) Rapid and efficient site-specific mutagenesis without phenotypic selection. Proc. Natl. Acad. Sci. USA, 82, 488 – 492.

Kunst, F. et al. (1997) The complete genome sequence of the gram-positive bacterium

Bacillus subtilis. Nature, 390, 249 – 256.

Samuel, M., Bonk, A., Rieke, A., Day, B.N., Murphy, C.N., Carter, D.B., Hawley, R.J. and Prather, R.S. (2002) Production of α-1,3-galactosyltransferase knockout pigs by nuclear transfer cloning. Science, 295, 1089 – 1092.

Lakso, M., Sauer, B., Mosinger, B., Jr., Lee, E.J., Manning, R.W., Yu, S.H., Mulder, K.L. and Westphal, H. (1992) Targeted oncogene activation by site-specific recombination in transgenic mice. Proc. Natl. Acad. Sci. USA, 89, 6232 – 6236.

Lama, J. and Carrasco, L. (1992) Inducible expression of a toxic poliovirus membrane protein in Escherichia coli: comparative studies using different expression systems based on T7 promoters. Biochem. Biophys. Res. Commun., 188, 972 – 981.

Lander, E.S. et al. (2001) Initial sequencing and analysis of the human genome. Nature, 409, 860 – 921.

Larschan, E. and Winston, F. (2001) The S. cerevisiae SAGA complex functions in vivo as a coactivator for transcriptional activation by Gal4. Genes Dev., 15, 1946 – 1956.

LaVallie, E.R., DiBlasio, E.A., Kovacic, S., Grant, K.L., Schendel, P.F. and McCoy, J.M. (1993a) A thioredoxin gene fusion expression system that circumvents inclusion body formation in the E. coli cytoplasm. Bio/technology, 11, 187 – 193.

LaVallie, E.R., Rehemtulla, A., Racie, L.A., DiBlasio, E.A., Ferenz, C., Grant, K.L., Light, A. and McCoy, J.M. (1993b) Cloning and functional expression of a cDNA encoding the catalytic subunit of bovine enterokinase. J. Biol. Chem., 268, 23 311 – 23 317.

Lawlor, D.A., Dickel, C.D., Hauswirth, W.W. and Parham, P. (1991) Ancient HLA genes from 7,500-year-old archaeological remains. Nature, 349, 785 – 788.

Lawyer, F.C., Stoffel, S., Saiki, R.K., Myambo, K., Drummond, R. and Gelfand, D.H. (1989) Isolation, characterization, and expression in Escherichia coli of the DNA polymerase gene from Thermus aquaticus. J. Biol. Chem., 264, 6427 – 6437.

Lazzari, G., Wrenzycki, C., Herrmann, D., Duchi, R., Kruip, T., Niemann, H. and Galli, C. (2002) Cellular and molecular deviations in bovine in vitro-produced embryos are related to the large offspring syndrome. Biol. Reprod., 67, 767 – 775.

Leanna, C.A. and Hannink, M. (1996) The reverse two-hybrid system: a genetic scheme for selection against specific protein/protein interactions. Nucleic Acids Res., 24, 3341 – 3347.

Lederberg, J. and Tatum, E.L. (1946) Gene recombination in Escherichia coli. Nature, 158, 558.

Lee, J. and Goldfarb, A. (1991) lac repressor acts by modifying the initial transcribing complex so that it cannot leave the promoter. Cell, 66, 793 – 798.

Lee, P., Morley, G., Huang, Q., Fischer, A., Seiler, S., Horner, J.W., Factor, S., Vaidya, D., Jalife, J. and Fishman, G.I. (1998) Conditional lineage ablation to model human diseases. Proc. Natl. Acad. Sci. USA, 95, 11 371 – 11 376.

Lee, T.I. et al. (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science, 298, 799 – 804.

Lee, T.I. and Young, R.A. (2000) Transcription of eukaryotic protein-coding genes.

Annu. Rev. Genet., 34, 77 – 137.

Legrain, P. and Selig, L. (2000) Genome-wide protein interaction maps using twohybrid systems. FEBS Lett., 480, 32 – 36.

Lesley, S.A. et al. (2002) Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline. Proc. Natl. Acad. Sci. USA, 99, 11 664 – 11 669.

Lester, S.C., LeVan, S.K., Steglich, C. and DeMars, R. (1980) Expression of human genes for adenine phosphoribosyltransferase and hypoxanthine – guanine phosphoribosyltransferase after genetic transformation of mouse cells with purified human DNA. Somatic Cell Genet., 6, 241 – 259.

Levene, P.A. and Simms, H.S. (1926) Nucleic acid structure as determined by electrometric titration data. J. Biol. Chem., 70, 327 – 341.

Lewandoski, M. (2001) Conditional control of gene expression in the mouse. Nat. Rev. Genet., 2, 743 – 755.

Li, H.H., Gyllensten, U.B., Cui, X.F., Saiki, R.K., Erlich, H.A. and Arnheim, N. (1988) Amplification and analysis of DNA sequences in single human sperm and diploid cells. Nature, 335, 414 – 417.

Li, J.D., Carroll, J. and Ellar, D.J. (1991) Crystal structure of insecticidal δ-endotoxin

˚

from Bacillus thuringiensis at 2.5 A resolution. Nature, 353, 815 – 821.

Li, J.J. and Herskowitz, I. (1993) Isolation of ORC6, a component of the yeast origin recognition complex by a one-hybrid system. Science, 262, 1870 – 1874.

Li, Q.B. and Guy, C.L. (1996) Prolonged final extension time increases cloning efficiency of PCR products. Biotechniques, 21, 192 – 196.

Li, S., Crenshaw, E.B., III, Rawson, E.J., Simmons, D.M., Swanson, L.W. and Rosenfeld, M.G. (1990) Dwarf locus mutants lacking three pituitary cell types result from mutations in the POU-domain gene pit-1. Nature, 347, 528 – 533.

Liang, P., Averboukh, L., Keyomarsi, K., Sager, R. and Pardee, A.B. (1992) Differential display and cloning of messenger RNAs from human breast cancer versus mammary epithelial cells. Cancer Res., 52, 6966 – 6968.

Liang, P. and Pardee, A.B. (1992) Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction. Science, 257, 967 – 971.

Licitra, E.J. and Liu, J.O. (1996) A three-hybrid system for detecting small ligand – protein receptor interactions. Proc. Natl. Acad. Sci. USA, 93, 12 817 – 12 821.

Lillycrop, K.A., Budrahan, V.S., Lakin, N.D., Terrenghi, G., Wood, J.N., Polak, J.M. and Latchman, D.S. (1992) A novel POU family transcription factor is closely related to Brn-3 but has a distinct expression pattern in neuronal cells. Nucleic Acids Res., 20, 5093 – 5096.

Lin, H.J. and Chargaff, E. (1966) On the denaturation of deoxyribonucleic acid.

Biochim. Biophys. Acta, 123, 65 – 75.

Lin-Goerke, J.L., Robbins, D.J. and Burczak, J.D. (1997) PCR-based random mutagenesis using manganese and reduced dNTP concentration. Biotechniques, 23, 409 – 412.

Lipardi, C., Wei, Q. and Paterson, B.M. (2001) RNAi as random degradative PCR: siRNA primers convert mRNA into dsRNAs that are degraded to generate new siRNAs. Cell, 107, 297 – 307.

Lisser, S. and Margalit, H. (1993) Compilation of E. coli mRNA promoter sequences.

Nucleic Acids Res., 21, 1507 – 1516.

Liu, H.Y. and Rashidbaigi, A. (1990) Comparison of various competent cell preparation methods for high efficiency DNA transformation. Biotechniques, 8, 21 – 25.