Microarray-based method for combinatorial library sequence mapping and characterization

BioTechniques

Volumn 34, Issue 6, 2003, Pages 1272-1279

  Abecassis V ^a   Jaffrelo, L ^a   Rickman, D ^a   Aggerbeck, L ^a   Herbert, C ^a   Truan, G ^a   Pompon, Dennis ^a,b  

^a CENTRE DE GÉNÉTIQUE MOLÉCULAIRE   (France)

^b CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DIGITAL LIBRARIES; DNA SEQUENCES; ENZYME KINETICS; FLUORESCENCE; GENES;

MICROARRAYS; POLYMERASE CHAIN REACTIONS (PCR);

GENETIC ENGINEERING;

ARTICLE; COMBINATORIAL LIBRARY; CONCENTRATION RESPONSE; DIRECTED MOLECULAR EVOLUTION; DNA HYBRIDIZATION; DNA MICROARRAY; GENE MAPPING; GENE SEQUENCE; MULTIGENE FAMILY; OLIGONUCLEOTIDE PROBE; POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; TECHNIQUE; TEMPERATURE DEPENDENCE;

EID: 17144437543     PISSN: 07366205     EISSN: None     Source Type: Journal    
DOI: 10.2144/03346mt03     Document Type: Article

References (34)

1. Strezoska, Z., T. Paunesku, D. Radosavljevic, I. Labat, R. Drmanac, and R. Crkvenjakov. 1991. DNA sequencing by hybridization: 100 bases read by a non-gel-based method. Proc. Natl. Acad. Sci. USA 88:10089-10093.
2. Drmanac, R., S. Drmanac, Z. Strezoska, T. Paunesku, I. Labat, M. Zeremski, J. Snoddy, W.K. Funkhouser, et al. 1993. DNA sequence determination by hybridization: a strategy for efficient large-scale sequencing. Science 260:1649-1652.
3. Bains, W. 1993. Mixed hybridization and conventional strategies for DNA sequencing. Genet. Anal. Tech. Appl. 10:84-94.
4. Craig, A.G., D. Nizetic, J.D. Hoheisel, G. Zehetner, and H. Lehrach. 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.
5. Bains, W. 1993. Characterizing and sequencing cDNAs using oligonucleotide hybridization. DNA Seq. 4:143-150.
6. Drmanac, S. and R. Drmanac. 1994. Processing of cDNA and genomic kilobase-size clones for massive screening, mapping and sequencing by hybridization. BioTechniques 17:328-336.
7. Meier-Ewert, S., J. Lange, H. Gerst, R. Herwig, A. Schmitt, J. Freund, T. Elge, R. Mott, et al. 1998. Comparative gene expression profiling by oligonucleotide fingerprinting. Nucleic Acids Res. 26:2216-2223.
8. Drmanac, S., D. Kita, I. Labat, B. Hauser, C. Schmidt, J.D. Burczak, and R. Drmanac. 1998. Accurate sequencing by hybridization for DNA diagnostics and individual genomics. Nat. Biotechnol. 16:54-58.
9. Hacia, J.G., L.C. Brody, M.S. Chee, S.P. Fodor, and F.S. Collins. 1996. Detection of heterozygous mutations in BRCA1 using high density oligonucleotide arrays and two-colour fluorescence analysis. Nat. Genet. 14:441-447.
10. Wikman, F.P., M.L. Lu, T. Thykjaer, S.H. Olesen, L.D. Andersen, C. Cordon-Cardo, and T.F. Orntoft. 2000. Evaluation of the performance of a p53 sequencing microarray chip using 140 previously sequenced bladder tumor samples. Clin. Chem. 46:1555-1561.
11. Chetverin, A.B. and F.R. Kramer. 1993. Sequencing of pools of nucleic acids on oligonucleotide arrays. Biosystems 30:215-231.
12. Lipshutz, R.J., S.P. Fodor, T.R. Gingeras, and D.J. Lockhart. 1999. High density synthetic oligonucleotide arrays. Nat. Genet. 21:20-24.
13. Klasen, E.C., M.H. Hofker, H.M. van Paassen, M. Verlaan-de Vries, J.L. Bos, and R.R. Frants. 1987. Detection of alpha-1-antitrypsin deficiency variants by synthetic oligonucleotide hybridization. Clin. Chim. Acta 170:201-207.
14. Kurtzman, A.L., S. Govindarajan, K. Vahle, J.T. Jones, V. Heinrichs, and P.A. Patten. 2001. Advances in directed protein evolution by recursive genetic recombination: applications to therapeutic proteins. Curr. Opin. Biotechnol. 12:361-370.
15. Arnold, F.H. and A.A. Volkov. 1999. Directed evolution of biocatalysts. Curr. Opin. Chem. Biol. 3:54-59.
16. Cohen, N., S. Abramov, Y. Dror, and A. Freeman. 2001. In vitro enzyme evolution: the screening challenge of isolating the one in a million. Trends Biotechnol. 19:507-510.
17. Stemmer, W.P. 1994. DNA shuffling by random fragmentation and reassembly: in vitro recombination for molecular evolution. Proc. Natl. Acad. Sci. USA 91:10747-10751.
18. Crameri, A., S.A. Raillard, E. Bermudez, and W.P. Stemmer. 1998. DNA shuffling of a family of genes from diverse species accelerates directed evolution. Nature 391:288-291.
19. Joern, J.M., P. Meinhold, and F.H. Arnold. 2002. Analysis of shuffled gene libraries. J. Mol. Biol. 316:643-656.
20. Abécassis, V., D. Pompon, and G. Truan. 2000. High efficiency family shuffling based on multi-step PCR and in vivo DNA recombination in yeast: statistical and functional analysis of a combinatorial library between human cytochrome P450 1A1 and 1A2. Nucleic Acids Res. 28:E88.
21. Gibbs, M.D., K.M. Nevalainen, and P.L. Bergquist. 2001. Degenerate oligonucleotide gene shuffling (DOGS): a method for enhancing the frequency of recombination with family shuffling. Gene 271:13-20.
22. Kikuchi, M., K. Ohnishi, and S. Harayama. 2000. An effective family shuffling method using single-stranded DNA. Gene 243:133-137.
23. Eickhoff, H., J. Schuchhardt, I. Ivanov, S. Meier-Ewert, J. O'Brien, A. Malik, N. Tandon, E.W. Wolski, et al. 2000. Tissue gene expression analysis using arrayed normalized cDNA libraries. Genome Res. 10:1230-1240.
24. Radelof, U., S. Hennig, P. Seranski, M. Steinfath, J. Ramser, R. Reinhardt, A. Poustka, F. Francis, and H. Lehrach. 1998. Preselection of shotgun clones by oligonucleotide fingerprinting: an efficient and high throughput strategy to reduce redundancy in largescale sequencing projects. Nucleic Acids Res. 26:5358-5364.
25. Southern, E., K. Mir, and M. Shchepinov. 1999. Molecular interactions on microarrays. Nat. Genet. 21:5-9.
26. Cheung, V.G., M. Morley, F. Aguilar, A. Massimi, R. Kucherlapati, and G. Childs. 1999. Making and reading microarrays. Nat. Genet. 21:15-19.
27. Duggan, D.J., M. Bittner, Y. Chen, P. Meltzer, and J.M. Trent. 1999. Expression profiling using cDNA microarrays. Nat. Genet. 21:10-14.
28. Lander, E.S. 1999. Array of hope. Nat. Genet. 21:3-4.
29. Lazowski, K.W. and L. Kaczmarek. 2000. Highly sensitive detection of hybridization of oligonucleotides to specific sequences of nucleic acids by application of fluorescence resonance energy transfer. Antisense Nucleic Acid Drug Dev. 10:97-103.
30. Zhong, G.Y., J. Riov, R. Goren, and D. Holland. 2000. Competitive hybridization: theory and application in isolation and quantification of differentially regulated genes. Anal. Biochem. 282:129-135.
31. Urban, P., C. Cullin, and D. Pompon. 1990. Maximizing the expression of mammalian cytochrome P-450 monooxygenase activities in yeast cells. Biochimie 72:463-472.
32. Gautier, J.C., P. Urban, P. Beaune, and D. Pompon. 1993. Engineered yeast cells as model to study coupling between human xenobiotic metabolizing enzymes. Simulation of the two first steps of benzo[a]pyrene activation. Eur. J. Biochem. 211:63-72.
33. Diehl, F., S. Grahlmann, M. Beier, and J.D. Hoheisel. 2001. Manufacturing DNA microarrays of high spot homogeneity and reduced background signal. Nucleic Acids Res. 29:E38.
34. Maniatis, T., E.F. Fritsch, and J. Sambrook. 1989. Molecular Cloning: A Laboratory Manual. CSH Laboratory Press, Cold Spring Harbor, NY.