Introduction • The use of biotechnology to produce lifesaving drugs, improved crop plants, and even land mine detecting plants has come from our knowledge of DNA transcription and translation. Cleaving and Rejoining DNA • Recombinant DNA technology is the manipulation and combination of DNA molecules from different sources. • Recombinant DNA technology uses the techniques of sequencing, rejoining, amplifying, and locating DNA fragments, making use of the complementary base pairing of A with T (or U) and of G with C. Restriction enzymes cleave DNA at specific sequences • Bacteria defend themselves against invasion by viruses (bacteriophage) by producing restriction enzymes (restriction endonucleases), which catalyze the cleavage of double-stranded DNA molecules into smaller, noninfectious fragments. (See Figure 16.1.) • The enzymes cut the bonds between the 3 hydroxyl of one nucleotide and the 5phosphate of the next one. • There are many such enzymes, each of which recognizes and cuts a specific DNA sequence of bases, called a recognition sequence or restriction site (which generally is four to six base pairs in length). • Host DNA is not damaged due to the addition of methyl groups to certain bases at the restriction sites; this methylation is performed by specific modifying enzymes, called methylases. • The enzyme EcoRI cuts double-stranded DNA with the following paired sequence:5... GAATTC ... 3; 3CTTAAG • Notice that the sequence is palindromic: It reads the same in the 5-to-3 direction on both strands. • The likelihood of randomly matching any given six-base sequence is 1 in 46 (1 in 4,098). • There are four possibilities for each base, so the total number of possible six-base sequences is 4 4 4 4 4 4. • Using this restriction enzyme on a long stretch of random DNA would create fragments with an average length of 4,098 bases. Note that this is the average length for random DNA. Actual lengths will vary widely. • Using EcoRI to cut up small viral genomes with only a few thousand base pairs may result in only a few fragments. • For a eukaryotic genome with tens of millions of base pairs, the number of fragments will be very large. • In nature, DNA is not random. A phage called T7, which has E. coli as a host, has no occurrences of the EcoRI recognition sequence in its 40,000-base-pair genome. • Hundreds of restriction enzymes have been purified from various organisms, and these enzymes serve as “knives” for genetic surgery. Gel electrophoresis identifies the sizes of DNA fragments • The fragments of DNA can be separated using gel electrophoresis. (See Figure 16.2.) • Because of its phosphate groups, DNA is negatively charged at neutral pH. • When DNA is placed in a semisolid gel and an electric field (with + and – ends) is applied, the DNA molecules migrate toward the positive pole because opposite charges attract. • The porous gel acts as a sieve, and smaller molecules can migrate more quickly than larger ones. • After a fixed time, the electric power is shut off. The separated molecules can then be stained with a fluorescent dye and examined under ultraviolet light. • Electrophoresis gives two types of information: • The size of the DNA fragments can be determined by comparison to DNA fragments of known molecular size added to the gel as a reference. • The presence of a specific DNA sequence can be confirmed by transferring the DNA to a nylon membrane, denaturing the DNA, and using a complementary labeled single-stranded DNA probe. (See Figure 16.3 and Animated Tutorial 16.1.) • If a specific fragment of DNA is desired, it can be cut out as a lump of gel and removed from the gel by diffusion into a small volume of water. Recombinant DNA can be made in the test tube • Some restriction enzymes cut DNA strands bluntly, exactly opposite one another, while others leave staggered ends of single-stranded DNA. • The enzyme EcoRI leaves staggered, or “sticky”, ends that attract complementary sequences. • If two different DNAs are cut so each has EcoRI staggered ends, different fragments with complementary sticky ends can be recombined (annealed) and sealed with the enzyme DNA ligase. (See Figure 16.4.) • DNA ligase can also connect blunt-ended DNA fragments, but it does so with reduced efficiency. • These simple techniques, which give scientists the power to manipulate genetic material, have revolutionized biological science in the past 30 years. Getting New Genes into Cells • The goal of recombinant DNA work is to produce many copies (clones) of a particular gene. • If the DNA is to be used to make its protein, it must be introduced, or transfected, into a host cell. • The host cells or organisms, referred to as transgenic, are transfected with DNA under special conditions. • The cells that get the DNA are distinguished from those that do not by means of genetic markers, called reporter genes. Genes can be inserted into prokaryotic or eukaryotic cells • Bacteria have been useful as hosts for recombinant DNA. • Bacteria are easy to manipulate, and they grow and divide quickly (20–60 minutes per division). • They have genetic markers that make it easy to screen for insertion. • They have been intensely studied and much of their molecular biology is known. • Bacteria have some disadvantages as well. • Bacteria lack splicing machinery to excise introns. • Protein modifications, such as glycosylation and phosphorylation, fail to occur as they would in an appropriate eukaryotic cell. • In some applications, the expression of the new gene in a eukaryote (the creation of a transgenic organism) is the desired outcome. • Saccharomyces, baker’s and brewer’s yeast, are commonly used eukaryotic hosts for recombinant DNA studies. • In comparison to many other eukaryotic cells, yeasts divide quickly, they are easy to grow, and have relatively small genomes (about 20 million base pairs). • Plants are also used as hosts if the goal is to make a transgenic plant. • It is relatively easy to regenerate an entire plant from differentiated plant cells because of plant cell totipotency. • The transgenic plant can then reproduce naturally in the field and will carry and express the gene on the recombinant DNA. Vectors can carry new DNA into host cells • New DNA can be introduced into the cell’s genome by its integration into a chromosome of the host cell. • If the new DNA is to be replicated, it must become part of a segment of DNA that contains an origin of replication called a replicon, or replication unit. • New DNA can be incorporated into the host cell by a carrier, or vector, which should possess the following characteristics: • The ability to replicate independently in the host cell. • A recognition sequence for a restriction enzyme, permitting it to form recombinant DNA. • A reporter gene that will reveal its presence in the host cell. • A small size in comparison to host chromosomes. • Plasmids as vectors: • A plasmid is a small (2,000–6,000 base pairs) circular DNA molecule, separate from the bacterial chromosome. Plasmids are ideal vectors for the introduction of recombinant DNA into bacteria. • Plasmids have their own origin of replication and can divide separately from the host bacterium’s chromosome. • They often have just one recognition site, if any, for a given restriction enzyme. (See Figure 16.5a.) • Cutting the plasmid at one site makes it a linear molecule with sticky ends. • If another DNA is cut with the same enzyme, leaving staggered “sticky” ends, it is possible to insert the DNA into the plasmid. (See Figure 16.4.) • Plasmids often contain antibiotic resistance genes, which serve as genetic markers for host cells carrying the recombinant plastid. (See Figure 16.5.) • Viruses as vectors: • Only about 10,000 base pairs can be inserted into plasmid DNA, so for most eukaryotic genes a vector that accommodates larger DNA inserts is needed. • For inserting larger DNA sequences, both prokaryotic and eukaryotic viruses are often used as vectors. • If the genes that cause death and lysis in E. coli are eliminated (about 200,000 base pairs), the bacteriophage can still infect the host and inject its DNA. • The deleted 20,000 base pairs can be replaced by DNA from another organism, creating recombinant viral DNA. • Artificial chromosomes as vectors: • Bacterial plasmids are not good vectors for yeast (eukaryotic) hosts because prokaryotic and eukaryotic DNA sequences use different origins of replication. • A yeast artificial chromosome, or YAC, has been made that has a yeast origin of replication, a centromere sequence, and telomeres, making it a true eukaryotic chromosome. • YACs have been engineered to include specialized single restriction sites and selectable markers. (See Figure 16.5b.) • YACs are 10,000 base pairs in size, but can accommodate up to 1.5 million base pairs of inserted DNA. • Human artificial chromosomes (HACs) constructed of a human centromere, telomeres, and origins of replication one day may be used as gene therapy vectors. • Plasmid vectors for plants: • Plasmid vectors for plants include a plasmid found in the bacterium Agrobacterium tumefaciens, which causes the tumor-producing disease, crown gall, in plants. (See Figure 16.5c.) • Part of the tumor-inducing (Ti) plasmid of A. tumefaciens is T DNA, a transposon, which inserts copies of itself into the host chromosomes. • If T DNA is replaced with the new DNA, the plasmid no longer produces tumors, but the transposon still can be inserted into the host cell’s chromosomes. • The plant cells containing the new DNA can be used to generate transgenic plants. Reporter genes identify host cells containing recombinant DNA • When a population of host cells is treated to introduce DNA, just a fraction actually incorporate and express it. • In addition, only a few vectors that move into cells actually contain the new DNA sequence. • Therefore, a method for selecting for transfected cells and screening for inserts is needed. • A classic example of how this was originally done is as follows: • The plasmid pBR322 carries within its sequences an origin of replication and two antibiotic resistance genes: ampr (ampicillin resistance) and tetr (tetracyclineresistance). • Within the antibiotic resistance genes are restriction enzyme recognition sites. • The tetr gene has a recognition site for the restriction enzyme BamHI; this is the only restriction site for this enzyme in the entire plasmid. • If both the foreign DNA and the plasmid are cut with BamHI, they can be recombined and sealed together with ligase. (See Figure 16.6.) • BamHI cuts the plasmid in the gene that codes for resistance to tetracycline, so the resistance to tetracycline is inactivated. • In practice, when plasmid and foreign DNA are placed together in the test tube, three outcomes are possible: • Some plasmids just reseal their own ends with no insert incorporated. • Some foreign DNA remains free in the solution, without becoming incorporated into plasmids. • Some foreign DNA is integrated into plasmids. This is the rarest result. • Bacteria treated with these plasmids might get just the foreign DNA or a plasmid either with or without the insert. (See Figure 16.6.) • Bacteria that take up unaltered plasmids are resistant to both antibiotics. • Bacteria that take up unincorporated foreign DNA (or no DNA at all) are sensitive to both antibiotics. • Bacteria that take up recombinant plasmids are resistant to ampicillin but sensitive to tetracycline. • If the resulting bacteria are grown on a medium that contains ampicillin, the survivors might have a plasmid that either contains or does not contain an insert. • To determine the presence of the insert, the colonies on the plate containing ampicillin are copied over to a plate with tetracycline. • Those that fail to grow are the ones likely to have the insert. This process of testing bacterial colonies for the target recombinant plasmids is called screening. • The colonies that failed to grow on the tetracycline plate are selected from the ampicillin plate. • Other methods have since been developed for screening. • The gene for luciferase, the enzyme that makes fireflies glow in the dark, has been used as a reporter gene. • Green fluorescent protein, which is the product of a jellyfish gene, glows without any required substrate. • Cells with this gene in the plasmid grow on ampicillin and glow when exposed to ultraviolet light. • Many vectors in common use have just a single antibiotic resistance gene outside of the sites for foreign DNA insertion. • (See Video 16.1.) Sources of Genes for Cloning • • DNA). DNA for insertion can be random fragments of the DNA from an organism (a DNA library). DNA can be generated by reverse transcription from mRNA. This DNA is called cDNA (complementary • Organic chemists can synthesize DNA in the laboratory. Gene libraries contain pieces of a genome • The 23 pairs of human chromosomes can be thought of as a library that contains the entire genome of our species. • The average size of each chromosome, or “volume,” is 80 million base pairs. Each chromosome encodes several thousand genes. • To study them, chromosomes are sorted and fragmented. (See Figure 16.7.) • Using plasmids for insertion of DNA, about one million separate fragments are required for the human genome library. • Phage , which carries four times as much DNA as a plasmid, can also be used to hold these random fragments. • It takes about 250,000 different phage to ensure a copy of every sequence. • This number seems large, but just one growth plate can hold as many as 80,000 phage colonies. A DNA copy of mRNA can be made by reverse transcriptase • A smaller DNA library (genes for a particular tissue) can be made from complementary DNA (cDNA). (See Figure 16.8.) • The poly A tail, found on many mRNA molecules from eukaryotes, makes this synthesis possible. • Oligo dT primer is added to mRNA tissue where it hybridizes with the poly A tail. • Reverse transcriptase, an enzyme that uses an RNA template to synthesize a DNA–RNA hybrid, is then added. • The resulting DNA is complementary to the RNA and is called cDNA. DNA polymerase can be used to synthesize a DNA strand that is complementary to the cDNA. • cDNAs from certain cell types have been useful in discovering the nature of differential gene expression. • Their use has shown that up to one-third of all genes of an animal are expressed only during prenatal development. • They are also useful for cloning genes expressed at low levels in only a few cell types. DNA can be synthesized chemically in the laboratory • If the amino acid sequence of a protein is known, it is possible, using organic chemistry, to synthesize a DNA that can code for the protein. • Using the knowledge of the genetic code and known amino acid sequences, the most likely base sequence for the gene may be found. • Often sequences are added to this sequence to promote expression of the protein. • These noncoding sequences must be the ones actually recognized by the host cell if the synthetic gene is to be transcribed. • Human insulin has been manufactured using this approach. DNA can be mutated in the laboratory • Recombinant DNA technology is an effective tool for studying mutations without having to look for them in nature. • With synthetic DNA, mutational effects can be studied by creating specific mutations. • Additions, deletions, and base-pair substitutions can be manipulated and tracked. • The functional importance of certain amino acid sequences can be studied. • The signals that mark proteins for passage through the ER membrane were discovered by site-directed mutagenesis. • When the signal sequences were removed, proteins weren’t transported across the ER membrane. • When the signal sequences were added to a protein that normally doesn’t get transported across the ER membrane, it was transported. Some Additional Tools for DNA Manipulation Genes can be inactivated by homologous recombination • Homologous recombination is used to study the role of a gene at the level of the organism. • In a knockout experiment, a gene inside a cell is replaced with an inactivated gene to see the inactivated gene’s effect on the organism. (See Figure 16.9.) • A gene of interest is cloned into a plasmid. • Additional DNA is added within the gene to disable it. • Mouse embryonic cells are transfected with the DNA. • Homologous recombination knocks out the normal functioning copy. • Transfected cells are identified by selecting or screening for a genetic marker included in the insert. • These transfected cells are inserted into an early mouse embryo. Some of the cells end up as germ cells, and mice homozygous for the knockout gene can be generated. • This technique is important to assess the roles of genes during development. DNA chips can reveal DNA mutations and RNA expression • The emerging science of genomics has to contend with two difficulties: the large number of genes in eukaryotic genomes, and the fact that the pattern of gene expression in different tissues at different times is distinctive. To find these patterns, DNA sequences have to be arranged in an array on some solid support. • DNA chip technology, which has merged DNA technology with the manufacturing technology of the semiconductor industry, provides these large arrays of sequences for hybridization. (See Figure 16.10 and Animated Tutorial 16.2.) • DNA sequences are attached in precise order onto a glass slide divided into 24 24 m squares, each containing about 10 million copies of a particular sequence, up to 20 nucleotides long. Up to 60,000 different sequences can be put on a single chip. • Analysis of cellular mRNA using DNA chips: • In a process called RT-PCR, cellular mRNA is isolated from cells and incubated with reverse transcriptase (RT) to make complementary DNA (cDNA). The cDNA is amplified by the polymerase chain reaction (PCR) prior to hybridization. • The amplified cDNA is coupled to a fluorescent dye and then hybridized to the chip. • A sensitive scanner detects glowing spots on the array. The combinations of these spots differ with different types of cells or different physiological states. • DNA chip technology can be used to detect genetic variants and to diagnose human genetic diseases. • Instead of sequencing the entire gene, it is possible to make a chip with 20-nucleotide fragments including every possible mutant sequence. • Hybridizing that sequence with a person’s DNA may reveal whether any of the DNA hybridized to a mutant sequence on the chip. Antisense RNA and RNA interference can prevent the expression of specific genes • Base-pairing rules can be used not only to make genes but also to stop mRNA translation. • Antisense RNA is complementary to a sequence of mRNA. (See Figure 16.11.) • The antisense RNA forms a double-stranded RNA hybrid with an mRNA molecule, preventing tRNA from binding to that mRNA. • These hybrids are broken down rapidly in the cytoplasm, so although the gene is transcribed, translation does not occur. • In the laboratory, either antisense RNA or DNA that codes for it is introduced into cells. • A tissue-specific promoter makes it possible to have mRNA inactivation occur only in a certain type of cell so that expression only occurs in targeted tissue. • Translation of mRNA occurs naturally in the inactivation of the X chromosome (see Figure 14.18.) • The presence of interference RNA (RNAi) is responsible for this inactivation. • In this type of inhibition, a short (about 20 nucleotides) double-stranded RNA is unwound to single strands by a protein complex that guides this RNA to a complementary region on mRNA. • Scientists have exploited this knowledge to produce small interfering RNA (siRNA) to inhibit the translation of any known gene. (See Figure 16.11.) • Double-stranded siRNAs are more stable than single-stranded antisense RNAs, making RNAi a much easier technique to use. The two-hybrid system shows which proteins interact in a cell • The two-hybrid system allows scientists to test for protein interactions within a living cell. • A two-hybrid system uses a transcription factor that activates the transcription of an easily detectable reporter gene. This transcription factor has two domains: one that binds to DNA at the promoter, and another that binds to the transcription complex to activate transcription. • In the yeast two-hybrid system, these two domains are separated in two different yeast plasmids. (See Figure 16.12.) • One plasmid contains the gene encoding the DNA binding domain fused to a gene that encodes the target protein (the “bait”). • The other plasmid contains the gene encoding the transcriptional activation domain fused to a gene that encodes the protein to be tested for binding to the target protein (the “prey”). • When these plasmids are introduced into host cells, the hybrid “bait” and “prey” proteins may bind, resulting in the transcription of the reporter gene. (See Figure 16.12.) • • If the proteins do not bind, no reporter protein is made. This method has revealed hundreds of protein–protein interactions. Biotechnology: Applications of DNA Manipulation • Biotechnology is the use of microbial, plant, and animal cells to produce materials—such as foods, medicines, and chemicals—that are useful to people. • The use of yeast to create beer and wine and of bacterial cultures to make yogurt and cheese are examples of centuries-old biotechnology. • Pasteur explained the use of microbes as biological converters to make certain products, and Fleming discovered the use of a mold to make the antibiotic penicillin. • Gene cloning techniques of modern molecular biology have vastly increased the number of these products beyond those that are naturally made by microbes. Expression vectors can turn cells into protein factories • Expression vectors are typical vectors, but they also have extra sequences needed for the foreign gene to be expressed in the host cell. • For a eukaryotic gene transfected into bacteria, this includes the promoter for RNA polymerase binding, the terminator for transcription, and the mRNA sequence for ribosome binding. (See Figure 16.13.) • For eukaryote hosts, the additional sequences include the poly A addition sequence, transcription factor binding sites, and enhancers. • An expression vector might have an inducible promoter, which can be stimulated into expression by responding to a specific signal such as a hormone. • A tissue-specific promoter is expressed only in a certain tissue at a certain time. • Targeting sequences are sometimes added to direct the protein product to an appropriate destination. Medically useful proteins can be made by DNA biotechnology • Many medical products have been made using recombinant DNA technology. Hundreds more are in various stages of development. (See Table 16.1.) • Tissue plasminogen activator (TPA), a drug that dissolves blood clots in patients suffering from heart attacks and strokes, is currently being produced in E. coli by recombinant DNA techniques. • TPA, which is produced by cells lining the blood vessels, is an enzyme that converts blood plasminogen into plasmin, a protein that dissolves clots. • The only drug available before TPA was streptokinase, a bacterial enzyme that can elicit an immune reaction (because the body sees it as a foreign body), and that can cause a hemophilia-like condition. • Recombinant DNA technology has made it possible to produce the naturally occurring protein in quantities large enough to be medically useful. DNA manipulation is changing agriculture • Selective breeding has been used for centuries to improve plant and animal species to meet human needs. • Molecular biology is accelerating progress in these applications. (See Table 16.2.) • There are three major advantages over traditional techniques: specific genes can be affected, genes can be introduced from other organisms, and whole plants can be regenerated much more quickly by cloning than by traditional breeding. • Plants that make their own insecticides: • Insecticides tend to be nonspecific, killing both pests and beneficial insects. In addition, they are usually applied to the surface of plants and tend to be blown or washed away, contaminating non-target sites. • Bacillus thuringiensis bacteria produce a protein toxin that kills insect larvae pests and is 80,000 times more toxic than the typical chemical insecticide. • Transgenic tomato, corn, potato, and cotton plants have been made that produce a toxin from B. thuringiensis. They show considerable resistance to insects that normally feed on them. • Transgenic animals express useful genes: • The process of producing pharmaceuticals using agriculture is nicknamed “pharming.” Goats, sheep, and cows are all being used for the production of medically useful products in their milk. • Transgenic sheep are being used to produce human -1-antitrypsin (-1-AT) in their milk; this protein inhibits the enzyme elastase, which breaks down connective tissue in the lungs. Treatment with -1-AT alleviates symptoms in people suffering from emphysema. • Other products of “pharming” include blood clotting factors and antibodies for treating colon cancer. • Crops that are resistant to herbicides: • Glyphosate (“Roundup”) is a broad-spectrum herbicide that inhibits an enzyme system in chloroplasts that is involved in the synthesis of amino acids. • A bacterial gene, which confers resistance to glyphosate, is inserted into useful food crops (corn, cotton, soybeans) to protect them from the herbicide, which otherwise would kill them along with the weeds. • Grains with improved nutritional characteristics: • Genes from bacteria and daffodil plants are transferred to rice using the vector Agrobacterium tumefaciens. • A genetically modified strain of rice produces -carotene, a molecule that is converted to vitamin A in animals. (See Figure 16.15.) • Crops that adapt to the environment: • A gene was recently discovered in the thale cress (Arabidopsis thaliana) that allows it to thrive in salty soils. • When this gene is added to tomato plants, they can grow in soils four times as salty as the normal lethal level. (See Figure 16.16.) • This finding raises the prospect of growing useful crops on unproductive soils with high salt concentration, such as the Fertile Crescent. • Biotechnology may allow us to adapt plants to different environments, thereby lessening some of the negative effects of agriculture, such as water pollution. There is public concern about biotechnology • Early concerns about biotechnology focused on the danger that genetically modified E. coli, the bacterium used most in biotechnology, might share their genes with the E. coli bacteria that live normally in the human intestines. • Researchers now take precautions against this. For example, the strains of E. coli used in the lab have a number of mutations that make their survival in the human intestine impossible. • By now, medical products made by DNA technology have become widely accepted. • There currently is, however, resistance to the introduction of genetically modified crops. There are concerns that genetic manipulation interferes with nature, that genetically altered foods are unsafe, and that genetically altered plants might allow transgenes to escape to other species and thus threaten the environment. • Advocates of biotechnology point out that traditional methods of genetic manipulation (hybridization and artificial selection) have already produced crops that are far removed from their natural ancestors. • Regarding safety for human consumption, advocates of genetic engineering note that typically only single genes specific for plant function are added. • As plant biotechnology moves from adding genes to improve plant growth to adding genes that affect human nutrition, such concerns will become more pressing. • The risks to the environment are more difficult to assess. • Transgenic plants undergo extensive field testing before they are approved for use, but the complexity of the biological world makes it impossible to predict all potential environmental effects of transgenic organisms. • Because of the potential benefits of agricultural biotechnology, most scientists believe we should proceed, but with caution. DNA fingerprinting is based on the polymerase chain reaction • With the exception of identical twins, each human being is genetically distinct from all other human beings. • To develop a test that can find distinctions, scientists look for DNA sequences that are highly polymorphic (genes having multiple alleles in the human population). • Sequences called VNTRs (variable number of tandem repeats) are easily detectable if they are between two restriction enzyme recognition sites. • Different individuals have different numbers of repeats. Each gets two sequences of repeats, one from the mother and one from the father. (See Figure 16.17.) • Using PCR and gel electrophoresis, patterns for each individual can be determined. • DNA from a single cell is sufficient to determine the DNA fingerprint because PCR can amplify a tiny amount of DNA in a few hours. • DNA fingerprints have been used in forensics (e.g., in cases of murder and rape) and in contested paternity. The technique is used to establish innocence more often than it is used to prove guilt because the same genome sample may turn up in people with the same patterns. • Russian Tsar family members have been studied to show that bodies recently discovered are probably related to several living descendants of the Tsar. (See Figure 16.18.) • Genetic testing has revealed a strong likelihood that Thomas Jefferson had an illegitimate child by a female slave, Sally Hemmings. • This was determined using chromosome markers from Hemmings’s descendants and Jefferson’s uncle. • California condors, which are extinct in the wild, are tested to reduce inbreeding and increase genetic variation in captive breeding populations. • PCR is used in diagnosing infections in which the infectious agent is present in small amounts. • Genetic diseases such as sickle-cell disease are now diagnosable before they manifest themselves. • New treatments are being developed based on genetic knowledge.