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Chapter 14: Genetic engineering and biotechnology
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Cutting and joining DNA• Restriction endonucleases (aka. restriction
enzymes) cut double-stranded DNA at defined sequences
• Each restriction enzyme cuts a particular palindromic sequence
• The enzymes have been isolated from bacteria which use them to inactivate foreign DNA
• Identical DNA molecules will be cut into fragments of the same length based on the position of the endonuclease recognition sites on the molecule
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Fig. 14.1: Restriction endonucleases
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Restriction enzyme mapping• Cutting identical molecules with different enzymes
produces a different pattern of fragments• The patterns will overlap—cutting with two
enzymes together produces a greater number of smaller fragments which are equivalent in total length to either enzyme alone
• This allows the relative positions of the DNA recognition sequences to be mapped
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Restriction enzyme mapping (cont.)• Fragments are separated by size using gel
electrophoresis• The electric current causes fragment migration
through the gel, with small fragments moving faster than large fragments
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Fig. 14.2: Electrophoretic separation of fragments
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Recombinant DNA technology• Restriction enzymes cut at defined sites regardless
of the origin of the molecule • DNA from different sources can be joined to form a
recombinant molecule as long as the same restriction enzyme was used to cut each molecule
• Some enzymes produce staggered cuts in which short single-stranded regions protrude
• The molecules adhere at these sites and are ligated together by DNA ligase
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Fig. 14.4: Ligation of DNA fragments
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DNA vectors• Production of multiple copies of the DNA fragment
requires ligation into a self-replicating vector molecule– plasmids– bacteriophage– cosmids– YACs (yeast artificial chromosomes) and– BACs (bacterial artificial chromosomes)
• Replication of the recombinant vector occurs in the appropriate bacterial or yeast host
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Fig. 14.5: Cloning a gene (top)
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Fig. 14.5: Cloning a gene (bottom)
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DNA vectors (cont.)• Regardless of their size or origin, vector molecules
must have:– an origin of replication– at least one unique restriction site for insertion of DNA
fragment– a gene for an inducible character, such as antibiotic
resistance, to ensure efficient replication in the host organism
– a means of distinguishing between vector alone and recombinant vector molecules
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Fig. 14.6a: Plasmid DNA vector
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Fig. 14.6b: Selecting cells
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Fig. 14.6c: Plating transformed cells
Fig. 14.6d: Distinguishing cells
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Genomic DNA libraries• Entire genomes are fragmented and ligated into a
vector• Millions of resulting colonies or plaques are
produced, each one of which contains a piece of the genome
• If the library is large enough, each fragment of genome should be present at least once
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Fig. 14.7 (top): Constructing a genomic library
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Fig. 14.7 (bottom): Constructing a genomic library
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cDNA libraries• Genomic DNA libraries contain all DNA sequences• cDNA libraries contain only those coding
sequences present in transcribed genes• mRNA molecules are copied by reverse
transcriptase into complementary cDNA• cDNA molecules are ligated into vectors and a
library constructed• Each clone is derived from a gene being
expressed at the time of the mRNA isolation
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Fig. 14.8: Constructing a library of cDNA
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Identifying cloned sequences• Hybridisation
– colonies or plaques grown on plates– recombinant DNA in the colonies is denatured– a replica of the plate is made on a membrane filter and
the adherent cells lysed to reveal their DNA– a labelled, single-stranded probe to the gene of interest is
hybridised to complementary sequences on the membrane
– the original colony or plaque can be recovered from the plate and used in further analysis
Fig. 14.9: Colony hybridisation method
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Isolating genes by PCR amplification• Polymerase chain reaction (PCR) allows the
amplification of specific sequences without the need for cells– amplification is selective and repeated, using heat-stable
DNA polymerase and deoxynucleotide triphosphates– specificity is determined by the use of oligonucleotide
primers to known sequences flanking the fragment of interest
– each cycle of annealing and extension doubles the fragment copy number
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Fig. 14.10 (top): Polymerase chain reaction
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Fig. 14.10 (bottom): Polymerase chain reaction
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DNA (and RNA) blotting• Called Southern blotting after its inventor Edwin
Southern– DNA isolated and cut into different-sized fragments– fragments separated physically by size using gel
electrophoresis– separated fragments are denatured and transferred to a
membrane filter– radiolabelled single-strand probe is bound to the
fragment of interest, making it visible
• A similar technique is used to identify mRNA molecules
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Fig. 14.12: Southern (DNA) blotting
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Nucleotide sequence analysis• The base sequence of DNA can be determined in
vitro by DNA synthesis and electrophoresis– each synthesis reaction contains normal
deoxynucleoside triphosphates and a chain-terminating dideoxynucleoside triphosphate (ddNTP)
– four reactions are employed, each containing a different ddNTP to stop the reaction
– a series of fragments is generated with different lengths but each terminating in the same nucleotide (the ddNTP)
– each reaction is labelled with a different colour and the sequence read as a series of fluorescent bands
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Fig. 14.11: Automated enzymatic DNA sequencing
Question:
Now that you have a DNA sequence, what can you do with this information?
14-31Copyright 2010 McGraw-Hill Australia Pty Ltd PowerPoint slides to accompany Biology: An Australian focus 4e by Knox, Ladiges, Evans and SaintSlides prepared by Karen Burke da Silva, Flinders University
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Analysing genetic variation• Base changes in a gene result in restriction
fragment length polymorphisms (RFLPs)• The consistent presence of a particular RFLP in
people with the disease being investigated is strong evidence of the mutation causing the disease—also permits localisation of the gene in which the mutation has occurred
• RFLPs can be distinguished by Southern hybridisation or by PCR
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DNA technology in forensic science• Developed as a way of defining specific differences
in DNA sequences between people– differences must be extensive and detailed enough to
minimise risk of accidental identity– gene sequences are not used for this– microsatellites and minisatellites: regions of repeat-
sequence DNA, where short sequences (2–5 nucleotides) may be repeated many times
– VNTRs (variable number tandem repeats) are similar.They vary in number between individuals, so looking at several VNTRs at once provides a unique ‘fingerprint’ of sequence lengths for that person
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Fig. 14.18: Find the murderer!
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Mapping genes• Classical gene linkage analysis has limitations,
especially in mammals• DNA sequence polymorphisms can be used as
landmarks to detect recombination in offspring of heterozygous parents
• Association of linkage markers with disease alleles is important in the location and isolation of the disease gene
• The physical location on a chromosome of a gene can be found using a labelled probe from a cloned sequence
Fig. 14.19: Human X chromosome
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Biotechnology• Recombinant protein production
– gene products such as drugs, hormones and enzymes can be produced in large quantities in cell culture systems
• Modifying agricultural organisms– inserting genes for improved yield or pest resistance into
plants– cloning domestic animals chosen for their superior
qualities
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Fig. 14.22 (top): Animal cloning
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Fig. 14.22 (bottom): Animal cloning
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Biotechnology (cont.)• Gene therapy
– the introduction of a modified gene into the cells of a patient suffering a genetic disease to correct the abnormality
– still experimental– problems associated with directing the vector to the
target cells and maintaining expression
• Cell therapy– the use of stem cells, which can be induced to
differentiate in vitro– introduced into patient to replace absent or damaged
cells
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Cell therapy using embryonic stem cells
Summary• Recombinant DNA techniques isolate genes or
small segments of DNA from chromosomes• Specific cuts in DNA molecules can be made by
specialised enzymes• Fragments can be separated and sized by using
gel electrophoresis• DNA fragments can be joined (ligated) to form
recombinant DNA molecules• PCR technique offers a rapid means of obtaining
sizable quantities of genes and DNA fragments from small amounts of DNA
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Summary (cont.)• Cloned DNA molecules can be analysed by using
restriction enzymes and direct sequencing• DNA technology enables us to identify genetic
variation in terms of changes in base sequences• Recombinant DNA technology can be used to
change the genetic make-up of organisms by genetic modification
• Controlled growth and differentiation of stem cells may in the future offer therapy for disease or injury
14-43Copyright 2010 McGraw-Hill Australia Pty Ltd PowerPoint slides to accompany Biology: An Australian focus 4e by Knox, Ladiges, Evans and SaintSlides prepared by Karen Burke da Silva, Flinders University