Lee Yiu Fai. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2001. / Includes bibliographical references (leaves 178-183). / Abstracts in English and Chinese. / Acknowledgements --- p.ii / Abstract --- p.iii / Abstract (Chinese version) --- p.vi / Table of contents --- p.viii / List of Abbreviations --- p.xvi / List of Figures --- p.xviii / List of Tables --- p.xxiv / Chapter Chapter 1 --- INTRODUCTON / Chapter 1.1 --- Cytochrome P450 (P450) --- p.1 / Chapter 1.1.1 --- Cytochrome P450 family --- p.1 / Chapter 1.1.2 --- Role in metabolism --- p.4 / Chapter 1.1.3 --- P450 catalytic cycle --- p.6 / Chapter 1.2 --- NADPH-cytochrome P450 reductase (RED) --- p.6 / Chapter 1.2.1 --- Characterization and distribution --- p.6 / Chapter 1.2.2 --- Structural and functional domains --- p.8 / Chapter 1.2.3 --- Role in P450 catalytic cycle --- p.10 / Chapter 1.3 --- Drug metabolism --- p.10 / Chapter 1.3.1 --- Understanding of drug metabolism is important for drug development --- p.10 / Chapter 1.3.2 --- Role of P450 in drug metabolism --- p.12 / Chapter 1.4 --- Production of RED knockout in vivo mouse model for screening of P450-dependent new drugs --- p.13 / Chapter 1.4.1 --- Background --- p.13 / Chapter 1.4.2 --- Gene targeting --- p.13 / Chapter 1.4.3 --- Gene targeting vector --- p.15 / Chapter 1.4.3.1 --- Classical knockout --- p.15 / Chapter 1.4.3.2 --- Conditional knockout --- p.19 / Chapter 1.4.4 --- Gene knockout mice and its use --- p.21 / Chapter Chapter 2 --- OBJECTIVES --- p.22 / Chapter Chapter 3 --- MATERIALS AND METHODS --- p.24 / Chapter 3.1 --- Preparation of RED cDNA by RT-PCR --- p.24 / Chapter 3.1.1 --- Total RNA isolation --- p.24 / Chapter 3.1.1.1 --- Materials --- p.24 / Chapter 3.1.1.2 --- Methods --- p.24 / Chapter 3.1.2 --- Reverse transcription- polymerase chain reaction (RT-PCR) --- p.25 / Chapter 3.1.2.1 --- Materials --- p.25 / Chapter 3.1.2.2 --- Methods --- p.25 / Chapter 3.1.3 --- T/A cloning of RED cDNA --- p.28 / Chapter 3.1.3.1 --- Materials --- p.28 / Chapter 3.1.3.2 --- Methods --- p.28 / Chapter 3.1.4 --- Midi-preparation of RED cDNA clone --- p.32 / Chapter 3.1.4.1 --- Materials --- p.33 / Chapter 3.1.4.2 --- Methods --- p.33 / Chapter 3.1.5 --- Confirmation of RED cDNA clone --- p.34 / Chapter 3.1.5.1 --- Restriction enzyme mapping --- p.34 / Chapter 3.1.5.1.1 --- Materials --- p.34 / Chapter 3.1.5.1.2 --- Methods --- p.34 / Chapter 3.1.5.2 --- DNA sequencing of RED cDNA sequence --- p.35 / Chapter 3.1.5.2.1 --- Materials --- p.35 / Chapter 3.1.5.2.2 --- Methods --- p.35 / Chapter 3.1.6 --- Preparation and purification of RED cDNA for probe labeling --- p.38 / Chapter 3.1.6.1 --- Materials --- p.38 / Chapter 3.1.6.2 --- Methods --- p.38 / Chapter 3.1.7 --- Non-radioactive random-primed labeling of RED cDNA --- p.39 / Chapter 3.1.7.1 --- Materials --- p.39 / Chapter 3.1.7.2 --- Methods --- p.39 / Chapter 3.2 --- Isolation of RED gene by genomic library screening --- p.40 / Chapter 3.2.1 --- Titering of genomic library --- p.41 / Chapter 3.2.1.1 --- Materials --- p.41 / Chapter 3.2.1.2 --- Methods --- p.41 / Chapter 3.2.2 --- Primary screening of genomic library by RED cDNA probe --- p.42 / Chapter 3.2.2.1 --- Plaque lift --- p.42 / Chapter 3.2.2.1.1 --- Materials --- p.42 / Chapter 3.2.2.1.2 --- Methods --- p.42 / Chapter 3.2.2.2 --- Proteinase K treatment --- p.43 / Chapter 3.2.2.2.1 --- Materials --- p.43 / Chapter 3.2.2.2.2 --- Methods --- p.43 / Chapter 3.2.2.3 --- "Pre-hybridization, hybridization and detection" --- p.44 / Chapter 3.2.2.3.1 --- Materials --- p.44 / Chapter 3.2.2.3.2 --- Methods --- p.44 / Chapter 3.3 --- Isolation of RED by hybridization screening by Genome System Inc. --- p.45 / Chapter 3.4 --- Characterization of BAC clones containing RED genomic DNA fragments commercially obtained from Genome System Inc. --- p.45 / Chapter 3.4.1 --- Large scale preparation of BAC DNA --- p.45 / Chapter 3.4.1.1 --- Materials --- p.47 / Chapter 3.4.1.2 --- Methods --- p.47 / Chapter 3.4.2 --- Restriction enzyme mappings and Southern blotting analysis of BAC DNA fragments --- p.47 / Chapter 3.4.2.1 --- Materials --- p.48 / Chapter 3.4.2.2 --- Methods --- p.48 / Chapter 3.4.3 --- Shot-gun sub-cloning of RED genomic DNA fragments from BAC clone in pGEM®-3Z vector --- p.49 / Chapter 3.4.3.1 --- Preparation of cloning vector and DNA insert for ligation --- p.50 / Chapter 3.4.3.1.1 --- Materials --- p.50 / Chapter 3.4.3.1.2 --- Methods --- p.50 / Chapter 3.4.3.1.2.1 --- Cloning vectors --- p.50 / Chapter 3.4.3.1.2.2 --- DNA inserts --- p.52 / Chapter 3.4.3.2 --- Preparation of competent cells and transformation --- p.52 / Chapter 3.4.3.2.1 --- Materials --- p.52 / Chapter 3.4.3.2.2 --- Methods --- p.53 / Chapter 3.4.3.3 --- Screening for positive recombinant clones --- p.54 / Chapter 3.4.3.3.1 --- Picking of colonies randomly from the agar plates (method 1) --- p.54 / Chapter 3.4.3.3.1.1 --- Materials --- p.54 / Chapter 3.4.3.3.1.2 --- Methods --- p.54 / Chapter 3.4.3.3.2 --- Colony lifts and hybridization with RED cDNA probes (method 2) --- p.55 / Chapter 3.4.3.3.2.1 --- Materials --- p.55 / Chapter 3.4.3.3.2.2 --- Methods --- p.55 / Chapter 3.5 --- Restriction enzyme mappings and Southern blotting analysis of RED gene subcloned in pGEM®-3Z vector --- p.56 / Chapter 3.5.1 --- Materials --- p.56 / Chapter 3.5.2 --- Methods --- p.56 / Chapter 3.6 --- Exon mappings of the RED genomic DNA fragments by PCR --- p.57 / Chapter 3.6.1 --- Materials --- p.57 / Chapter 3.6.2 --- Methods --- p.57 / Chapter 3.7 --- Construction of gene targeting vector --- p.57 / Chapter 3.7.1 --- Gene targeting vectors la and lb derived from clone H (strategy 1) --- p.60 / Chapter 3.7.1.1 --- Sub-cloning 3.65 kb Hind Ill/Hind III RED gene fragment to pGEM®-3Z vector --- p.60 / Chapter 3.7.1.1.1 --- Materials --- p.62 / Chapter 3.7.1.1.2 --- Methods --- p.62 / Chapter 3.7.1.2 --- Deletion of exonic sequence of RED gene and modification of the digested restriction end to Xho I site --- p.62 / Chapter 3.7.1.2.1 --- Materials --- p.63 / Chapter 3.7.1.2.2 --- Methods --- p.63 / Chapter 3.7.1.3 --- Preparation of neo cassette --- p.63 / Chapter 3.7.1.3.1 --- Materials --- p.64 / Chapter 3.7.1.3.2 --- Methods --- p.64 / Chapter 3.7.1.4 --- Cloning of neo cassette --- p.66 / Chapter 3.7.1.4.1 --- Methods --- p.66 / Chapter 3.7.1.5 --- Sub-cloning the neo cassette containing RED genomic fragment to pMCI-Thymidine kinase (TK) Poly A vector --- p.67 / Chapter 3.7.1.5.1 --- Materials --- p.67 / Chapter 3.7.1.5.2 --- Methods --- p.67 / Chapter 3.7.2 --- "Gene targeting vectors 2a/2b, 3a/3b and 4a derived from clone X8 (strategy 2,3 and 4 respectively)" --- p.67 / Chapter 3.8 --- Preparation and testing the genomic probes for screening recombinant embryonic stem (ES) cells --- p.73 / Chapter 3.8.1 --- Cloning of genomic probes --- p.73 / Chapter 3.8.1.1 --- Materials --- p.73 / Chapter 3.8.1.2 --- Methods --- p.73 / Chapter 3.8.2 --- Purification of DNA for labeling --- p.78 / Chapter 3.8.2.1 --- Materials --- p.78 / Chapter 3.8.2.2 --- Methods --- p.78 / Chapter 3.8.3 --- ECF random prime labeling of genomic probes --- p.79 / Chapter 3.8.3.1 --- Materials --- p.79 / Chapter 3.8.3.2 --- Methods --- p.79 / Chapter 3.8.4 --- Restriction enzyme digestion of genomic DNA and Southern blotting --- p.80 / Chapter 3.8.4.1 --- Materials --- p.80 / Chapter 3.8.4.2 --- Methods --- p.80 / Chapter 3.8.5 --- Testing the specificity of genomic probes --- p.80 / Chapter 3.8.5.1 --- Materials --- p.80 / Chapter 3.8.5.2 --- Methods --- p.80 / Chapter Chapter 4 --- RESULTS --- p.86 / Chapter 4.1 --- Total RNA isolation and RT-PCR of RED cDNAs --- p.86 / Chapter 4.2 --- Confirmation of the RT-PCR RED cDNA clone --- p.86 / Chapter 4.2.1 --- Restriction enzyme mapping --- p.86 / Chapter 4.2.2 --- DNA sequencing --- p.86 / Chapter 4.3 --- Genomic library screening of RED gene --- p.90 / Chapter 4 4 --- Restriction enzyme mappings and Southern blotting analysis of RED Gene containing BAC clone from Genome System Inc. --- p.90 / Chapter 4.5 --- Shot-gun sub-cloning of RED gene containing genomic DNA fragments to pGEM®-3Z vectors --- p.93 / Chapter 4.5.1 --- Cloning of Hind III cut RED gene fragment --- p.93 / Chapter 4.5.2 --- Cloning of Xba I cut RED gene fragment --- p.93 / Chapter 4.5.3 --- Cloning of EcoR I cut RED gene fragment --- p.95 / Chapter 4.6 --- Identification of RED exons in the shot-gun sub-cloning clones by PCR --- p.95 / Chapter 4.7 --- Construction of restriction enzyme maps of the RED gene containing clones --- p.100 / Chapter 4.7.1 --- Clone H --- p.100 / Chapter 4.7.1.1 --- Single restriction enzyme digestions and Southern blotting --- p.100 / Chapter 4.7.1.2 --- Double restriction enzyme digestions and Southern blotting --- p.100 / Chapter 4.7.1.3 --- Restriction enzyme map --- p.101 / Chapter 4.7.2 --- Clone X8 --- p.101 / Chapter 4.7.2.1 --- Single restriction enzyme digestions and Southern blotting --- p.101 / Chapter 4.7.2.2 --- Double restriction enzyme digestion and Southern blotting --- p.104 / Chapter 4.7.2.3 --- Restriction enzyme map --- p.104 / Chapter 4.7.3 --- Clone El4 --- p.105 / Chapter 4.7.3.1 --- Single restriction enzyme digestions and Southern blotting --- p.105 / Chapter 4.7.3.2 --- Double restriction enzyme digestion and Southern blotting --- p.108 / Chapter 4.7.3.3 --- Restriction enzyme map --- p.108 / Chapter 4.8 --- Construction of gene targeting vector --- p.108 / Chapter 4.8.1 --- Gene targeting vector based on the clone H (strategy 1) with deletion of RED exon 16 --- p.113 / Chapter 4.8.1.1 --- Cloning a smaller RED genomic DNA into pGEM®-3Z vectors --- p.113 / Chapter 4.8.1.2 --- Replacement of exon of RED gene by neo cassette --- p.113 / Chapter 4.8.1.3 --- Cloning to TK vector --- p.113 / Chapter 4.8.2 --- Targeting vector based on the clone X8 --- p.124 / Chapter 4.8.2.1 --- Strategy 2 (deletion of RED exon 4) --- p.124 / Chapter 4.8.2.1.1 --- Cloning 3.9 kb Kpn I/Hinc II RED genomic DNA into pGEM®-3Z vectors --- p.124 / Chapter 4.8.2.1.2 --- Replacement of exon of RED gene by neo cassette --- p.124 / Chapter 4.8.2.1.3 --- Cloning to TK vector --- p.124 / Chapter 4.8.2.2 --- Strategy 3 (deletion of RED exon 5-8) --- p.136 / Chapter 4.8.2.2.1 --- Cloning the genomic DNA into pGEM®-3Z vectors --- p.136 / Chapter 4.8.2.2.2 --- Replacement of exon of RED gene by neo cassette --- p.136 / Chapter 4.8.2.2.3 --- Cloning to TK vector --- p.136 / Chapter 4.8.2.3 --- Strategy 4 (deletion of RED exon 7-10) --- p.136 / Chapter 4.8.2.3.1 --- Cloning the genomic DNA into pGEM®-3Z vectors --- p.136 / Chapter 4.8.2.3.2 --- Replacement of exon of RED gene by neo cassette --- p.152 / Chapter 4.8.2.3.3 --- Cloning to TK vector --- p.152 / Chapter 4.9 --- Testing for the specificity of genomic DNA probes --- p.152 / Chapter 4.9.1 --- Preparation of restriction enzyme digested genomic DNA --- p.152 / Chapter 4.9.2 --- Hybridization of the probes to genomic DNA --- p.163 / Chapter Chapter 5 --- DISCUSSION --- p.167 / Chapter 5.1 --- Proposed significant of RED knockout mice for new drug screening --- p.167 / Chapter 5.2 --- Experimental problems --- p.168 / Chapter 5.2.1 --- Genomic library screening --- p.168 / Chapter 5.2.2 --- Cloning --- p.168 / Chapter 5.3 --- RED gene targeting vector construction / Chapter 5.3.1 --- Isolation of RED gene for gene targeting vectors construction --- p.169 / Chapter 5.3.2 --- Deletion of different exons in different RED gene targeting vectors --- p.169 / Chapter 5.3.3 --- Components in the targeting vectors --- p.170 / Chapter 5.3.4 --- Enhancements of homologous recombination --- p.171 / Chapter Chapter 6 --- CONCLUSIONS --- p.173 / Chapter Chapter 7 --- FUTURE STUDIES --- p.175 / Chapter 7.1 --- Identification of the sizes of RED gene introns --- p.175 / Chapter 7.2 --- Production of RED knockout mice --- p.175 / Chapter 7.3 --- Characterization of RED knockout mice --- p.175 / Chapter 7.4 --- Conditional gene knockout for RED gene --- p.177 / REFERENCES --- p.178 / APPENDIX --- p.184

RNA interference (RNAi) is a conserved mechanism in a wide range of eukaryotes. Introduction of synthetic dsRNA could specifically target suppression of a gene or could result in off-target silencing of another gene due to sequence similarity. To verify if the observed phenotype in an RNAi transgenic line is due to silencing of a specific gene or if it is due to another nontarget gene, a synthetic gene complementation approach could be used. Synthetic gene complementation described in this method uses the technology of synthesizing a variant of a native gene (used in RNAi silencing) to maximize the difference in DNA sequences while coding for the exact same amino acids as the original native gene. This is achieved through the use of alternate codons. The new variant gene is expressed in the original RNAi transgenic lines and analyzed for complementation of the RNAi phenotype. Complementation of the RNAi-induced phenotype will indicate gene-specific silencing and not off-target silencing.