DNA Technology and Genomics
Dec 24, 2015
Recombinant DNA
Definition: DNA in which genes from 2 different sources are linked
Genetic engineering: direct manipulation of genes for practical purposes
Biotechnology: manipulation of organisms or their components to perform practical tasks or provide useful products
Bacterial genetics Nucleoid:
– region in bacterium densely packed with DNA (no membrane)
Plasmids: – small circles of DNA
Reproduction by binary fission (asexual)
Bacterial DNA-transfer processes
Transformation– genotype alteration by the uptake of
naked, foreign DNA from the environment (Griffith expt.)
Transduction– phages that carry bacterial genes from
1 host cell to another – generalized~ random transfer of host
cell chromosome – specialized~ incorporation of prophage
DNA into host chromosome Conjugation
– direct transfer of genetic material; cytoplasmic bridges
– pili; sexual
Bacterial Plasmids Small, circular, self-replicating DNA separate from
the bacterial chromosome F (fertility) Plasmid: codes for the production of
sex pili (F+ or F-) R (resistance) Plasmid: codes for antibiotic drug
resistance
Bacterial plasmids in gene cloning
Clone genes for insertion into organisms
Clone proteins for medical/ pharmaceutical purposes
DNA Cloning
Restriction enzymes (endonucleases)– in nature, these enzymes protect bacteria from
intruding DNA– they cut up the DNA (restriction)– very specific
Restriction site – recognition sequence for a particular restriction
enzyme Restriction fragments
– segments of DNA cut by restriction enzymes in a reproducable way
Sticky end– short extensions of restriction fragments
DNA ligase– enzyme that can join the sticky ends of DNA
fragments Cloning vector
– DNA molecule that can carry foreign DNA into a cell and replicate there (usually bacterial plasmids)
Eukaryotic Gene Cloning Isolation of cloning vector
(bacterial plasmid) & gene-source DNA (gene of interest)
Insertion of gene-source DNA into the cloning vector using the same restriction enzyme; bind fragmented DNA w/ DNA ligase
Introduction of cloning vector into cells (transformation by bacterial cells)
Cloning of cells (and foreign genes)
Identification of cell clones carrying the gene of interest
Genomic Libraries
Cloned genes from a genome are stored in a “genomic library”
Recombinant fragments in bacteria or phages
Complimentary DNA (cDNA) Library – mRNA extracted– Reverse
transcriptase makes a complimentary strand of gene
DNA Analysis
PCR (polymerase chain reaction)
Gel electrophoresis Restriction fragment
analysis (RFLPs) Southern blotting DNA sequencing
Practical DNA Technology Uses
Diagnosis of disease Human gene therapy Pharmaceutical products
– Vaccines– Hormones
Forensics– Crime scene analysis of DNA
Animal husbandry (transgenic organisms)– “Pharm” animals
Genetic engineering in plants– Disease/ pest resistance
Polymerase chain reaction (PCR)
Amplification of any piece of DNA without cells (in vitro)
Materials: heat, DNA polymerase, nucleotides, single-stranded DNA primers
Applications: fossils, forensics, prenatal diagnosis, etc.
DNA Analysis
Gel electrophoresis:– separates nucleic
acids or proteins on the basis of size or electrical charge creating DNA bands of the same length
Restriction fragment analysis Restriction fragment length
polymorphisms (RFLPs)– Differences in restriction
fragment patterns on homologous chromosomes
– Occur in noncoding DNA sequences
– Serve as inheritable genetic markers
Southern blotting: process that reveals sequences and the RFLPs in a DNA sequence
DNA Fingerprinting
DNA Sequencing
Determination of nucleotide sequences – Dideoxy Chain-Termination
Method (Sanger Method)– Whole-genome approach
(Venter and Celera Genomics)
Genomics: the study of genomes based on DNA sequences
Human Genome Project– Begun in 1990; largely
completed by 2003
Genomics
The National Center for Biotechnology Information (NCBI) – Created a database of gene
sequences created by the Human Genome Project and other sequencing endeavors
– Genbank– BLAST software allows for
comparison of sequences
Analyzing Gene Expression Northern Blotting
– Gel electrophoresis done with labeling probes to determine function
RT-PCR– Uses reverse
transcriptase and PCR– Compares gene
expression between different samples
Studying Gene Interaction
DNA Microassay– Many DNA
fragments on a glass slide or chip
– Can be tested for interaction with other genes marked with fluorescent markers
Determining Gene Function
In vitro mugagenasis– Disable certain genes and
observe consequences– Mutations “knock out” certain
genes RNA interference (RNAi)
– RNA used to block translation of certain genes
Transposons transposable genetic
element; piece of DNA that can move from location to another in a cell’s genome– chromosome to
plasmid, plasmid to plasmid, etc.)
– “jumping genes”
Eukaryotic Genes
98.5% of all DNA does not code for proteins, rRNA, or tRNA
Most is repetitive DNA 44% is made of
transposable elements
Transposable Elements
Transposons– Move w/in a genome by
DNA intermediate Barbara McClintock
(1940’s and 50’s)– “Jumping genes”– Researched the location of
colored kernels in maize Retrotransposons
– Move by means of a RNA intermediate
Multigene Families In the human genome, ½ of coding DNA is in multigene
families– Collections of identical or very similar genes– Identical- ribosomal RNA molecules– Similar- α-globin and β-globin
Pseudogenes- nonfunctional nucleotide sequences (very similar to functional genes)