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Promoter region containing proximal and distal elements EXON and enhancers 5 DNA sense strand cap site
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INTRON EXON AG..TTT...
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INTRON GT
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EXON 3
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..ATG.. GT
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AG ..TAA.....AATAA splice junctions
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splice junctions translation initiation codon
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polyadenylation signal translation termination codon
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TRANSCRIPTION hnRNA ..AUG.. GU AG...UUU... GU AG ..UAA....AAUAA AAAAAAA
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PROCESSING mRNA 5' ..AUG... ..UUU....UAA...AAUAA AAAAAAAA 3'
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TRANSLATION Protein Amino terminus Met..........Phe.....Stop Carboxy terminus
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Figure 2.2 Transcription, mRNA processing, and translation. DNA sense strand is designated by bold lines, hnRNA and mRNA by thinner lines. Exons are shown as rectangles and introns as the intervening spaces between exons. (From An Introduction to Biochemical Toxicology, 3rd edition, E. Hodgson and R. C. Smart, eds., Wiley, 2001.)
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ability to develop knockout animals lacking a particular gene and transgenic animals with an additional transgene is also proving important in toxicological studies. Gene structure and any of the processes involved in DNA expression including transcription, mRNA processing and translation and protein synthesis (Figure 2.2) can all be examined by molecular techniques. In toxicology this may include toxic effects on these processes or the role of the processes in the mechanism of toxic action.
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2.3.1 Molecular Cloning
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The basic principle of molecular cloning is the insertion of a DNA segment into a suitable vector. The vector is an autonomously replicating DNA molecule and the inserted DNA segment may be as large as a gene or a small as a few nucleotides. The vector containing the DNA is inserted into a cell such as yeast, where it can be replicated many times, and either the DNA or the expressed protein subsequently isolated (Figure 2.3).
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2.3.2 cDNA and Genomic Libraries
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cDNA or genomic libraries are collections of DNA fragments incorporated into a recombinant vector and transformed into an appropriate host cell. In the case of cDNA libraries, the cDNAs complementary to all of the mRNAs in the tissue or cell sample are synthesized in a procedure using reverse transcriptase, before incorporation into the vector. With genomic DNA libraries the genomic DNA is digested, before cloning into the vector, with a restriction enzyme to produce an overlapping set of DNA fragments of some 12 to 20 kb.
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INTRODUCTION TO BIOCHEMICAL AND MOLECULAR METHODS IN TOXICOLOGY
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Eco-RI Eco-RI Amp R O-RI
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G CT
A TA
C TT G
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AATTC G
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Bacterial colonies containing plasmid DNA
Figure 2.3 Molecular cloning using a plasmid vector. (From An Introduction to Biochemical Toxicology, 3rd ed., E. Hodgson and R. C. Smart, eds., Wiley, 2001.)
These libraries are used in many screening procedures and many transgenic proteins now routinely available were obtained by their use. Although in some applications the use of cDNA and genomic libraries has been superceded by other methods, particularly those based on PCR, they are still used to advantage in many applications.
Northern and Southern Blot Analyses
Northern analysis is usually used to identify and quantitate speci c mRNAs in a sample. Southern analysis is used to determine whether or not a gene of interest is present as well as its copy number. Other uses for Southern analysis include identifying restriction fragment length polymorphisms and changes in heterozygosity. In both Southern and Northern analyses restriction-digested DNA fragments, mRNA, and polyA mRNA are separated by size when electrophoresed on agarose gel. The separated molecules are transferred, by electroblotting or capillary blotting, on to a nylon or nitrocellulose membrane. The immobilized RNA or DNA is reacted with a radiolabeled, chemiluminescent, or uorescent probe that is complementary to the DNA/RNA of interest, unbound probe is washed off, and the membrane exposed, in the case of radioactive probes, to radioautographic lm to visualize the sample of interest.
Polymerase Chain Reaction (PCR)
PCR is a powerful technique that can, starting with amounts of DNA as small as those found in single cells, amplify the DNA until large amounts are available for many
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different kinds of research. Twenty to 40 cycles of can provide up to 105 times the original DNA sample. It is necessary to know as much of the sequence of the DNA of interest as possible in order to construct appropriate primers. These primers are complementary to the sequence at each end of the DNA sequence to be ampli ed. The DNA is incubated in a thermal cycler with thermostable DNA polymerase, all four dNTP, and the primers. The incubation temperature is raised to separate the DNA strands, lowered to permit annealing of the primers to the complementary regions of the DNA and then raised to permit the polymerase to synthesize DNA. This cycle is then repeated up to 40 times. The PCR technique has been used for many types of toxicological investigation including; uncovering polymorphisms in xenobiotic-metabolizing enzymes, isolating genes from cDNA and genomic libraries and for mutational analysis, to name only a few.