purification and detection of nucleic acids
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Purification and Detection of Nucleic Acids. Gel electrophoresis is a common technique used to separate nucleic acids. Based on motion of charged particles in an electric field. Purification and Detection (Cont’d). Radioactive labeling of sample used to detect products - PowerPoint PPT PresentationTRANSCRIPT
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Chapter 13Nucleic Acid Biotechnology Techniques
Mary K. CampbellShawn O. Farrellhttp://academic.cengage.com/chemistry/campbell
Paul D. Adams • University of Arkansas
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Purification and Detection of Nucleic Acids
• Gel electrophoresis is a common technique used to separate nucleic acids.
• Based on motion of charged particles in an electric field
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Purification and Detection (Cont’d)
• Radioactive labeling of sample used to detect products
• Label or tag allows visualization
• DNA undergo reaction that incorporate radioactive isotope into the DNA
• Autoradiography used to visualize image that has been exposed to oligonucleotides that have been radiolabeled
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Restriction Endonucleases
• Nucleases- catalyze the hydrolysis of the phosphodiester backbone of nucleic acids- Endonuclease: cleavage in the middle of the chain- Exonuclease: cleavage from the ends of the molecule
• Restriction Endonucleases- Have a crucial role in development of recombinant DNA technology
• Bacteriophages, viruses that infect bacteria, were being studied when restriction enzymes were discovered
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Methylation of DNA
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Restriction Endonucleases (Cont’d)
• Restriction endonuclease (RE) hydrolyzes only a specific bond of a specific sequence in DNA
• Sequences recognized by RE read the same from left to right as from right to left, known as palindrome
• Two As and 2 Ts between breaks in DNA strand which leave sticky ends
• Sticky ends are joined by by hydrogen bonding between complementary bases.
• Ligases reseal ends
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Restriction Endonucleases and Their Cleavage Sites
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Action of DNA Ligases
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Cloning
• Recombinant DNA- DNA molecules that contain covalently linked segments derived from 2 or more DNA sources
• Sticky Ends can be used to construct Recombinant DNA
• DNA Ligase- seals nicks in the covalent structure
• Plasmid- small circular DNA that is not part of the main circular DNA chromosome of the bacterium.
• Cloning- The process of making identical copies of DNA
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Production of Recombinant DNA
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The Cloning of a Virus
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Plamids
• How do we know which bacteria takes up the desired plasmid?
• Selection- Each plasmid chosen for cloning has a selectable marker that indicates that the growing bacteria colonies contain the plasmid of interest
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Plasmid pBR322
• One of the first plasmids used for cloning
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Plasmids (Cont’d)
• As the technology to design plasmids improved, regions were created that had many different restriction sites in a small place
• This region is known as a multiple cloning site (MCS), or polylinker
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Blue/White Screening
• Basis for selection
• pUC plasmids contain lacZ gene
• lacZ gene codes for the -subunit of -galactosidase, which cleaves disaccharides
• This procedure helps with selection
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Clone Selection with Blue/White Screening
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Cloning Summary
• Cloning refers to creating identical populations• DNA can be combined by using restriction enzymes • The target DNA sequence is carried in some type of
vector• The target DNA sequence is inserted into host
organism• Organisms that carry the target DNA are identified
through a process called selection
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Genetic Engineering
• When an organism is intentionally altered at the molecular level to exhibit different traits, it has been genetically engineered
• One focus of genetic engineering has been gene therapy, where cells of specific tissues in a living person are altered in a way that alleviates the affects of a disease
• DNA recombination can occur in nature• The reproductive power of bacteria can be used to
express large quantities of a mammalian protein of interest, however, process can be complicated
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Genetic Engineering (Cont’d)
• Human proteins can be made by bacteria, but process is not straight forward. e.g. human insulin
• An intron is a DNA sequence that codes for RNA that is eventually deleted in the processing of the mRNA that directs the synthesis of the protein
• Only the RNA transcribed from exons appear in the mature RNA
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Protein Expression Vectors
• Plasmid vectors pBR322 and pUC are cloning vectors
• Vectors are used to insert foreign DNA and amplify it
• If we want to produce produce protein from the foreign DNA, vectors are not good
• Instead, expression vectors are used
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What is an Expression Vector?
• Have many attributes as cloning vector:
• The origin of replication
• A multiple cloning site
• At least one selectable marker
• Must be able to be transcribed by the genetic machinery of the bacteria where it is transformed
• Must have a transcription termination sequence
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DNA Libraries
• Can we take all the DNA of an organism and clone it in chunks of reasonable size
• The result of this is a DNA library
• Several steps involved in construction of the library
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Finding an Individual Clone in a DNA Library• After the library has been
constructed, the next challenge is to find a single desired clone out of hundreds of thousands, or millions
• Technique used to select depends on separating and annealing complementary strands
• Known as Genomic Library Screening
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Finding an Individual Clone in a DNA Library (Cont’d)• RNA libraries not
constructed in the same way
• RNA of interest is used as template for the synthesis of complementary DNA (cDNA)
• Reaction catalyzed by reverse transcriptase
• cDNA is incorporated into vector, then process is identical to the production of genomic DNA library
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Summary
• A DNA library is a collection of clones of an entire genome
• The genome is digested with restriction enzymes and the pieces are cloned into vectors, and transformed into cell lines
• Specific radioactive probes to a sequence of interest are reacted to filters that have copies of the bacterial colonies in the library
• A cDNA library is constructed by using reverse transcriptase to make DNA from the mRNA in a cell. This cDNA is then used to construct a library similar to a genomic DNA library
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The Polymerase Chain Reaction
• It is possible to increase the amount of a given DNA many times over without cloning the DNA
• This method of amplification is known as the Polymerase Chain Reaction (PCR)
• Any chosen DNA can be amplified, and it does not need to be separated from the rest of the DNA in a sample before the procedure is applied
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The Polymerase Chain Reaction (Cont’d)
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DNA Fingerprinting
• DNA samples can be studied and compared by DNA fingerprinting
• DNA is digested with restriction enzymes and then run on an agarose gel
• When soaked in ethidium bromide, the DNA fragments can be seen directly under UV light
• If greater sensitivity needed or if number of fragments would be too great to distinguish the bands, technique can be modified to show only selected DNA sequences
• This begins with Southern blotting
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The Southern Blot
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Restriction-Fragment Length Polymorphisms• In organisms with two sets of chromosomes, a given gene on
one chromosome may differ slightly from the corresponding gene on the paired chromosome
• These are known as alleles• Organisms are homozygous when they have the same paired
chromosomes • Organisms are heterozygous when they have different paired
chromosomes
• Restriction fragments of different sizes are obtained by treatment with endonuclease. They are Restriction-Fragment Length Polymorphisms (RFLPs)
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The Basis for Restriction-Fragment Length Polymorphism
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Summary
• A DNA fingerprint is created by digesting DNA with restriction enzymes, separating the pieces on a gel, and visualizing some of the pieces by using labeled probes
• Differences in DNA patterns between different individuals are based on different base sequences of their DNA
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DNA Sequencing
• The nature and order of monomer units determine the properties of the whole molecule
• The method devised by Sanger and Coulson for determining the base sequences of nucleic acids depends on selective interruption of oligonucleotide synthesis
• A single-stranded DNA fragment whose sequence is to be determined is used as a template
• The synthesis is interrupted at every possible site in the population of molecules depending on the presence of ddNTPs
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DNA Sequencing (Cont’d)
• The incorporation of the ddNTP into the growing chain causes termination at the point of incorporation
• The DNA to be sequenced is mixed with a short oligonucleotide that serves as a primer for synthesis of the complementary strand
• Gel electrophoresis is performed on each reaction mixture, and a band corresponding to each position of the chain termination appears
• The sequence of the newly formed strand, complementary to the template DNA, can then be read from the sequencing gel
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The Sanger-Coulon Method for Sequencing DNA
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Summary
• DNA can be sequenced by using several techniques, the most common being the chain termination method
• Dideoxy nucleotides are used to terminate DNA synthesis. Multiple reactions are run with different dideoxy nucleotide in each reaction mix
• The reactions produce a series of DNA fragments of different length that can be run on a gel and the sequence determined by tracking the different length fragments in the lanes with the four different dideoxy nucleotides
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Genomics and Proteomics
• Knowing the full DNA sequence of the human genome allows for the investigation for the causes of disease in a way that has not been possible until now
• The proteome is a protein version of a genome
• Proteomics is the study of interactions among all the proteins in a cell
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Microarrays
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Summary
• As more DNA sequences become available, it becomes possible to compare these sequences
• Important medical applications are emerging, and new methods are making it possible to analyze large quantities of data
• The proteome is the protein version of the genome. It refers to all of the proteins being expressed in a cell
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Summary
• DNA or protein microchips is a powerful technique being used presently, as thousands of samples of DNA or proteins can be applied and then checked for binding of biological samples
• The binding can be visualized by using fluorescently labeled molecules and scanning the chip with a computer (Figure 13.30). The pattern of fluorescent labels then indicates which mRNA or proteins are being expressed in the samples