Bi430/530
Download
1 / 78

Bi430/530 Theory of Recombinant DNA Techniques - PowerPoint PPT Presentation


  • 259 Views
  • Updated On :
  • Presentation posted in: General

Bi430/530 Theory of Recombinant DNA Techniques. First part of course : Technical aspects of molecular biology work--Molecular Cloning Second part of course : Applications of molecular biology techniques Emerging science Bi530 student presentations Prerequisite: Molecular Biology (Bi 338)

Related searches for Bi430/530 Theory of Recombinant DNA Techniques

loader
I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
capcha

Download Presentation

Bi430/530 Theory of Recombinant DNA Techniques

An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -

Presentation Transcript


Slide1 l.jpg

Bi430/530

Theory of Recombinant DNA Techniques

First part of course:

Technical aspects of molecular biology work--Molecular Cloning

Second part of course:

Applications of molecular biology techniques

Emerging science

Bi530 student presentations

Prerequisite: Molecular Biology (Bi 338)

FRIDAY February 8: Midterm exam

THURSDAY March 20: Final exam



Slide3 l.jpg

Syllabus--first half

The basics of DNA manipulation

(and the Molecular Cloning Manual)


Slide4 l.jpg

“Molecular Cloning” (2001), Sambrook and Russel (3rd ed.)

See also Course Reading #2 (detailed table of contents) in course packet


Slide5 l.jpg

Syllabus--second half ed.)

Using DNA manipulation techniques


Slide8 l.jpg

Recombinant ed.)

DNA


Slide9 l.jpg

Information ed.) flow in the cell

DNA

RNA

protein


Slide10 l.jpg

Evolution: a dialog between the genome and its environment ed.)

Replication/mutation

DNA

RNA

protein

Natural selection


Slide11 l.jpg

Organisms respond to their environment via information from ed.)sensory input and changes in gene expression

DNA

RNA

protein

environment

Dynamic, immediate, transient modification of DNA program


Slide12 l.jpg

Species respond to environment over long time frames via mutations in the DNA program

DNA

RNA

protein

evolution

environment

--Stable (“permanent”)

--reflects effect of environment over large time scales


Slide13 l.jpg

Human activity: transient modifications of environment, permanent modifications of DNA program

DNA

RNA

protein

Human intervention: genetics (indirect), rDNA (direct)

environment


2006 53 years of dna structure l.jpg
2006: 53 years of DNA structure permanent modifications of DNA program

Rosalind Franklin and Maurice Wilkins:

X-Ray fiber diffraction pattern of pure B-form DNA (1953)

James Watson and Francis Crick:

Proposed two antiparallel, helical strands forming a stable duplex with DNA bases on interior of the molecule, joined by hydrogen bonds (1953)

But DNA was not discovered in 1953--it had been known as the element of genetic transmission at least since 1947, when Avery showed that DNA could “transform” bacterial colony morphology

Why was the structure so important?


Structure of dna l.jpg
Structure of DNA permanent modifications of DNA program

To Watson and Crick, the structure suggested:

--Mechanism for replication

--Stability for information storage, yet accessing the information not difficult

The DNA structure provided a new template for hypotheses regarding biological phenomena (amenability to study)


Dna is easy to work with l.jpg
DNA is easy to work with… permanent modifications of DNA program

  • Readily isolated--plasmid isolation, PCR

  • Stable--not chemically reactive like RNA (even archaeologically stable!)

  • Easy to propagate and move from cell to cell

  • Easy to make specific constructs

  • Easy to make specific mutations

  • Very easy to sequence (record-keeping)

  • Predictable behavior

  • Sequence lends itself to analysis--genome projects


Slide17 l.jpg

DNA is very easy to sequence permanent modifications of DNA program

Etc….


Slide18 l.jpg

http://www.genomesonline.org/ permanent modifications of DNA program


Slide19 l.jpg

The behavior of DNA (genes) is predictable permanent modifications of DNA program

Gene sequence conservation often indicates

functional similarity

Non-protein coding information sequences

can often be detected by homology (promoters for transcription initiation, transcription terminators, ribosome binding sites, DNA binding protein binding sites)

the genetic code


Slide20 l.jpg

The genetic code and the roots of biotechnology permanent modifications of DNA program

1961

Marshall Nirenberg and Heinrich J. Matthaei:

polyU mRNA encodes poly-phenylalanine

1966

Nirenberg and colleagues had deciphered the 61 codons (and 3 nonsense codons) for all 20 amino acids

1968

Nobel prize for Nirenberg, Holley, and Khorana


Slide21 l.jpg

1966 permanent modifications of DNA program

George and Muriel Beadle write:

“The deciphering of the DNA code has revealed our possession of a language much older than hieroglyphics, a language as old as life itself, a language that is the most living language of all--even if its letters are invisible and its words are buried deep in the cells of our bodies.”


Slide22 l.jpg

The public reaction to the deciphering of the genetic code permanent modifications of DNA program

Wow

“…just as big a breakthrough in biology as [Newton's discovery of gravitation in the seventeenth century] was in physics.” --John Pfeiffer, journalist, 1961

Optimism

“No stronger proof of the universality of all life has been developed since Charles Darwin's 'The Origin of Species' demonstrated that all life is descended from one beginning. In the far future, the hope is that the hereditary lineup will be so well known that science may deal with the aberrations of DNA arrangements that produce cancer, aging, and other weaknesses of the flesh.” Chicago Sun-Times, 1962


Slide23 l.jpg

Caution permanent modifications of DNA program

…knowledge gained from the genetic code “might well lead in the foreseeable future to a means of directing mutations and changing genes at will.” 1961, A. G. Steinberg of Case Western Reserve University

…knowledge of the genetic code could “lead to methods of tampering with life, of creating new diseases, of controlling minds, of influencing heredity, even perhaps in certain desired directions.”1961, Arne Wilhelm Kaurin Tiselius, 1948 Nobel Laureate in Chemistry


Slide24 l.jpg

1967 permanent modifications of DNA program

“Will Society Be Prepared?” Marshall Nirenberg, editorial in Science (see WebCT)


Slide25 l.jpg

Nirenberg, 1967 permanent modifications of DNA program

"When man becomes capable of instructing his own cells, he must refrain from doing so until he has sufficient wisdom to use this knowledge for the benefit of mankind....

[D]ecisions concerning the application of this knowledge must ultimately be made by society, and only an informed society can make such decisions wisely."


Slide26 l.jpg

Response from Joshua Lederberg, 1967 (see letter on WebCT): permanent modifications of DNA program

(paraphrased)

-- We need to be particularly careful with manipulation of the germ cell lines (heritable changes).

-- Considerations governing control of our biology are equally important to considerations governing control of our cultural institutions (given that culture is mutable and heritable)


Slide27 l.jpg

1975: The Asilomar Conference on Recombinant DNA permanent modifications of DNA program

  • 1974: moratorium on recombinant DNA research

  • “…new technology created extraordinary novel avenues for genetics and could ultimately provide exceptional opportunities for medicine, agriculture and industry…. …concerns that unfettered pursuit of this research might engender unforeseen and damaging consequences for human health and the Earth's ecosystems”

http://nobelprize.org/nobel_prizes/chemistry/articles/berg/index.html


Slide28 l.jpg

1975: The Asilomar Conference on Recombinant DNA permanent modifications of DNA program

  • Conference included internationally prominent scientists, government officials, doctors, lawyers, members of the press

  • Conclusion: “…recombinant DNA research should proceed but under strict guidelines.”

  • The moratorium was lifted, and “… guidelines were subsequently promulgated by the National Institutes of Health and by comparable bodies in other countries.”

http://nobelprize.org/nobel_prizes/chemistry/articles/berg/index.html


Slide29 l.jpg

  • The Asilomar principles: permanent modifications of DNA program

  • containment should be made an essential consideration in the experimental design

  • the effectiveness of the containment should match the estimated risk as closely as possible.

    Additional suggestions:

    Use biological barriers to limit the spread of recombinant DNA

    • fastidious bacterial hosts that are unable to survive in natural environments

    • nontransmissible and equally fastidious vectors (plasmids, bacteriophages, or other viruses) that are able to grow in only specified hosts


Slide30 l.jpg

  • The Asilomar principles: permanent modifications of DNA program

    Safety factors

    • physical containment, exemplified by the use of hoods or where applicable, limited access or negative pressure laboratories

    • strict adherence to good microbiological practices, which would limit the escape of organisms from the experimental situation

    • education and training of all personnel involved in the experiments would be essential to effective containment measures.


Slide31 l.jpg

  • Regulation of biotechnology: US National Institutes of Health (NIH) Guidelines

    • stipulations of biosafety and containment measures for recombinant DNA research

    • delineations of critical ethical principles and safety reporting requirements for human gene transfer research

  • See http://www4.od.nih.gov/oba/Rdna.htm

  • (see also CR #3 in course packet)


Slide32 l.jpg

“Unnatural Selection” (first reading in the course packet)

By Allison Snow

Is the process for altering genes (evolution vs. human): irrelevant?

Product (transgenic organism): is the phenotype the only thing that is important?

Reverberations from introduction of modified organisms?

Spread of gene? Effects of spread?

Success of organism? Effects on other organisms?

“The technology’s main hazards are probably yet to manifest themselves”


Slide33 l.jpg

What can we do with recombinant DNA technology? packet)

  • begin to learn how cells, tissues, organisms, communities work, interact, respond to the environment (gain scientific knowledge)

  • improve human health

  • industrial production of useful enzymes, metabolic products

  • improve industrial process

  • raise agricultural productivity

  • investigate problems of geneology, paternity, anthropology, archaeology

  • investigate criminal cases

  • etc….


Slide34 l.jpg

How is recombinant DNA technology useful in medicine? packet)

  • Diagnosis of disease

  • Animal models for human diseases

  • Therapies

    • nucleic acids: gene therapy

    • pharmacologically active proteins

    • small molecule design and testing

  • Antimicrobials

    • Vaccines

    • Microbicides


Slide35 l.jpg

The biotechnology industry is very new packet)

Case in point: Genentech (S. San Francisco)

2006: Genentech to open production facility in Portland (2010)


Slide36 l.jpg

Day 1 summary: packet)

The simplicity of a DNA-based information system makes genetic manipulation possible

This represents an unprecedented level of interaction with living systems

Benefits and costs of technology require continuous assessment


Visualizing dna and rna protein non specific detection methods l.jpg
Visualizing DNA (and RNA, protein): non-specific detection methods

  • Quantitation of DNA (Course Reading 4)

  • Electrophoresis (Course Reading 5 )

  • Visualizing DNA (& protein) in gels (Course Reading 6)


Quantitation of dna by uv absorbance l.jpg
Quantitation of DNA by UV absorbance methods

  • Measure absorbance of UV light by sample (the aromatic bases have a characteristic absorbance maximum at around 260 nanometers)

  • 1.0 A260 (1 cm light path) = DNA concentration of 50 micrograms per ml (double stranded DNA) or 38 micrograms per ml (single-stranded DNA or RNA)

  • the effective range for accurate measurement is rather narrow: A260 from 0.05 to 2.0 (DNA concentrations from 2.5 to 100 micrograms/ml)

  • Sample must be very pure for accurate measurements (RNA, EDTA and phenol all absorb at 260 nm)


Slide39 l.jpg

How can concentration be determined by absorbance? methods

DNA has a characteristic “molar extinction coefficient” 

The Beer-Lambert law:

I = Io10- dc

I = intensity of transmitted light

Io = intensity of incident light

 = molar extinction coefficient

d = optical path length

c = concentration of absorbing material

How much light gets through a solution depends on what’s in it and how much of it there is


Slide40 l.jpg

  • The Beer-Lambert law: methods

  • I = Io10- dc

  • Absorbance A measured by a spec is log I/Io

  • When path length d = 1 cm, A is called the optical density OD

  • If you know the , the absorbance of a solution will tell you the concentration:

  • OD = c

  • for nucleic acids:

    dsDNA: 6.6

    ssDNA, RNA: 7.4

    (but these values change with pH and salt concentration!)


Slide41 l.jpg

A typical (good) “scan” (multiple wavelengths) of a DNA sample

A260/A280: 1.8 is good (lower values indicate significant protein contamination)

0.5

A260 = 0.327

Absorbance

(1 cm path length)

0

200

260

400

Wavelength (nm)


Slide42 l.jpg

How does A sample260 give you the quantity of DNA?

Example:

sample of 250 base pair fragment of DNA has an A260 = .327

What is its molar concentration?

Given: (1.0 A = 50 micrograms/ml DNA)

DNA conc. = .327 x 50 = 16.35 micrograms/ml

MW of an average bp. = 650 Daltons

Therefore 250 bp. Fragment has a MW of 1.6 x 10 5 Daltons

Solve for molarity: 1.02 x 10 -7 M, or 102 nanomolar (nM)

Important to know how to do this calculation


Slide43 l.jpg

What is the molarity of a 16.35 microgram/ml solution of a 250 base pair DNA fragment?

1 gram

1 mole

1000 ml

16.35 micrograms

1 ml

106 micrograms

1 L

1.6 x 105 grams

1.02 x 10 -7 molar

0.102 x 10-6 molar [0.1 micromolar (M)]

102 x 10-9 molar [102 nanomolar (nM)]


Slide44 l.jpg

  • Fluorometry: another method for quantitation of DNA 250 base pair DNA fragment?

    • Hoechst 33258 (a fluorescent dye)

    • Binds to DNA in the minor groove (without intercalation)

    • Fluorescence increases following binding

    • Good for quantitation of low concentrations of DNA (10-250 ng/ml)

    • rRNA and protein do not interfere

    • But you need a fluorometer


Slide45 l.jpg

  • Another method for quantitation of DNA: 250 base pair DNA fragment?

  • Ethidium bromide (fluorescent dye) binding

    • Compare sample DNA fluorescence to standards of known concentration (dilution series)

    • In solution *or* using gel electrophoresis

A commercially available quantitative DNA standard


Visualizing dna electrophoresis l.jpg
Visualizing DNA: Electrophoresis 250 base pair DNA fragment?

  • Allows separation of biomolecules (DNA, RNA, protein) on basis of size

  • A separation matrix, or gel (agarose or polyacrylamide), is saturated with an electrically conductive buffer

  • Samples are loaded, an electric field is applied, and negatively charged biomolecules in the sample travel toward the cathode

  • The larger the molecule, the slower the travel through the gel matrix

  • Dyes allow a visual estimate of the rate of travel through the gel

  • The choice of matrix depends mainly on the size of DNA being analyzed


Agarose gels l.jpg
Agarose gels 250 base pair DNA fragment?

Agarose: a polysaccharide polymer of alternating D- and L-galactose monomers, isolated from seaweed

  • Pore size is defined by the agarose concentration (higher concentration, slower DNA migration overall)

  • The conformation of the DNA (supercoiled, nicked circles, linear) affects the mobility of the DNA in gels

  • Rate of DNA migration is affected by voltage (5 to 8 Volts/cm is close to optimal)

  • Agarose comes in a myriad of types (variable melting temperatures, generated by differential hydroxyethylation of the agarose)


Agarose gels48 l.jpg
Agarose gels 250 base pair DNA fragment?

Standard gels can separate DNA fragments from 100 bp to about 20,000 bp

Pulsed-field gels separate very large DNA fragments (up to 10,000,000 bp, or 10 Mb)

This apparatus allows periodic shifts in the direction of DNA migration: 120° refers to the reorientation angle (difference between orientation of electric fields A and B


Slide49 l.jpg

Typical agarose gel 250 base pair DNA fragment?

Load samples in wells

xylene

cyanol

bromophenol

blue

-

+

(the DNA fragments are not visible without some sort of staining)

time of electrophoresis

(progress monitored by marker dyes)


Polyacrylamide gels l.jpg
Polyacrylamide gels 250 base pair DNA fragment?

  • Acrylamide monomers (toxic!) polymerized to form gel matrix

  • The gel structure is held together by the cross-linker-- usually N, N'-methylenebisacrylamide ("bis" for short)

  • Pore size defined by concentration of gel (total percentage) and concentration of the crosslinker (bis) relative to acrylamide monomer

  • Very high resolution (better than agarose)

  • Suitable for separation of nucleic acids from 6 to 1000 base pairs in length


Polyacrylamide gels52 l.jpg
Polyacrylamide gels 250 base pair DNA fragment?

  • Native gels (DNA stays double-stranded)

  • Denaturing gels--run in the presence of high concentrations of denaturant (usually urea) and at high temperature: DNA is single stranded (sequencing gels)

  • (also useful in separation of proteins, when proteins are treated with SDS, which denatures proteins and gives a uniformly negative surface charge)


Slide53 l.jpg

Recipe for a polyacrylamide gel: 250 base pair DNA fragment?

  • Acrylamide (anywhere from 4 to 20 %, depending size of nucleic acids or proteins in the gel)

  • Bis-acrylamide (the ratio of Bis to regular acrylamide is important)

  • Water

  • Buffer

  • To initiate polymerization, add

  • APS: Ammonium persulfate

  • -- generates free radicals needed for polymerization

  • TEMED: N,N,N’,N’ - tetramethylethylenediamine

  • -- accelerates free radical generation by APS


  • Slide54 l.jpg

    • More about gels 250 base pair DNA fragment?

    • There has to be a buffer (for carrying current)

      • TAE (Tris-acetate-EDTA): good resolution of DNA, but buffering capacity is quickly depleted

      • TBE (Tris-borate-EDTA): High buffering capacity, resolution is pretty good

    • Use gel loading “buffers” (relatively simple)

      • Dense material to carry sample to bottom of wells (sucrose, glycerol, or ficoll)

      • Dyes for tracking progress of electrophoresis

        • Bromophenol blue: fast migration

        • Xylene cyanol: slow migration

      • Occasionally denaturant is present (formamide) for denaturing gels (e.g. sequencing gels)


    Slide55 l.jpg

    • Protein electrophoresis 250 base pair DNA fragment?

    • Almost always polyacrylamide based

    • The anionic detergent SDS (sodium dodecyl sulfate) is used to denature the proteins, giving each protein a “uniform” negative charge

    • Protein separation occurs as a function of size

    • Discontinous Tris-Cl/glycine buffer system:

      • Stacking gel:pH 6.8, low polyacrylamide concentration, focuses proteins into thin layer (gives higher resolution upon separation)

      • Separating gel:pH 8.8, separates proteins on the basis of size


    Slide56 l.jpg

    Polyacrylamide gel set up (protein gels) 250 base pair DNA fragment?

    Stacking gel: at low pH, glycine is protonated (no neg. charge), Cl- ions at the leading edge, glycine trailing, steep voltage gradient in between, that’s where the proteins get “focused” into a thin band

    Separating gel: at higher pH, glycine deprotonates, runs with the Cl- at the leading edge, and the proteins separate based on size


    Staining nucleic acids l.jpg
    Staining nucleic acids 250 base pair DNA fragment?

    ethidium bromide, an anti-trypanosomal drug for cattle

    Stain works by intercalating in stacked base pairs, elongates DNA helix

    Fluorescence increases upon DNA binding

    Stained bands visualized by UV illumination (302 or 260 nm)

    G-C base pair

    Ethidium bromide


    Slide58 l.jpg

    Example of an agarose-DNA gel, 250 base pair DNA fragment?

    Stained with ethidium bromide

    Fragments of bacteriophage  genomic DNA (48 kb) cut with the restriction enzyme Hind III

    The fragments are equimolar--why is the band intensity different?

    Direction of

    electrophoresis


    Slide59 l.jpg

    Another ethidium bromide-stained agarose gel 250 base pair DNA fragment?

    samples

    M

    The marker lane (M) gives size standards for comparison with the sample lanes


    Slide60 l.jpg

    Other methods for staining DNA 250 base pair DNA fragment?

    • SYBR gold (Molecular Probes, Eugene, OR), more than 10-fold more sensitive than ethidium bromide for detecting DNA, but expensive!

    • methylene blue: not toxic, but the staining protocol is time consuming, and sensitivity somewhat lower than ethidium bromide

    • silver staining: high degree of sensitivity, but the protocols are time consuming, and proteins are also stained by silver


    Protein detection in gels l.jpg
    Protein detection in gels 250 base pair DNA fragment?

    • Coomassie Brilliant Blue R-250: dye from the textile industry that has a high affinity for proteins

      • Proteins in gels must be “fixed” (rendered insoluble) first with acetic acid/methanol

      • Dye probably interacts with NH3- groups of the proteins, also through van der Waals forces

    http://www.galab.de/laboratories/services/biopharma/img/sds.jpg


    Protein detection in gels62 l.jpg
    Protein detection in gels 250 base pair DNA fragment?

    • Silver staining:

      • 100 to 1000-fold more sensitive than Coomassie stain for detecting proteins (need far less sample to see it on a gel)

      • Process relies on differential reduction of silver ions bound to amino acid side chains (like the photographic process)

      • There is protein-to-protein variability of staining

    ugly (keratin)

    good

    bad (overstained)


    Protein detection in gels63 l.jpg
    Protein detection in gels 250 base pair DNA fragment?

    • Sypro Ruby (Molecular Probes inc, proprietary compound)

      • As sensitive as silver staining, less variability

      • Fast protocol

      • Expensive

    1 nanogram of protein

    Standard gel

    2-D gel


    Visualizing dna and rna protein non specific methods l.jpg
    Visualizing DNA (and RNA, protein): non-specific methods 250 base pair DNA fragment?

    • Quantitation of DNA (Course Reading 4)

    • Electrophoresis (Course Reading 5 )

    • Visualizing DNA (& protein) in gels (Course Reading 6)


    Slide65 l.jpg

    Methods for detecting 250 base pair DNA fragment?specific biomolecules

    • Southern blots (DNA-DNA hybridization)(Methods for labeling “probe” DNA) CR7, MC 6.33 - 6.38

      B. Northern blots (DNA-RNA hybridization) CR8,

      MC 7.21 - 7.26, MC 7.82 - 7.84

    • Western blots (detection of proteins with specific antibodies) CR9, MC A9.28, MC A8.52-A8.55


    Visualizing dna rna and protein detecting specific sequences or proteins l.jpg
    Visualizing DNA, RNA and Protein: detecting specific sequences or proteins

    • Techniques allow one to distinguish specific sequences or proteins in a large, mixed population, e.g. in cell extracts or genomic DNA preparations

    • For DNA and RNA, specific sequence detection is based on DNA and RNA complementarity and base-pairing

    • For proteins, the specific detection is based on antibodies that recognize the protein of interest (or based on a specific assay for activity of the protein)


    Detecting specific dna sequences the southern blot l.jpg
    Detecting specific DNA sequences: the sequences or proteinsSouthern blot


    Slide68 l.jpg

    Immobilization of nucleic acids sequences or proteins

    nitrocellulose

    or nylon membrane boundary:

    DNA binds to it

    Agarose or

    Polyacrylamide gel

    A typical capillary blotting apparatus. Electroblotting is also commonly used


    Slide69 l.jpg

    Southern blotting: sequences or proteins

    Immobilization of target DNA and detection

    • DNA is fixed to the nylon membrane by:

      • Baking, 80°C

      • UV crosslinking (links thymines in DNA to + charged amine groups in membrane), DNA only

    • Probe to detect sequence of interest by base-pairing (hybridization)

      • Obtain probe DNA: synthetic oligonucleotide or cloned gene (single stranded)

      • Label probe for later detection

        • Radioactivity

        • Non-radioactive label


    Slide70 l.jpg

    Radioactive probes: sequences or proteins32P labeling

    • Use T4 polynucleotide kinase

      --catalyzes the transfer of the gamma phosphate of 32P ATP to the 5’ end of DNA fragment to be used as a probe

    • 32P is a high energy beta particle emitter, and provides good sensitivity for detection of hybridization between the probe DNA and the target (blot) DNA

    • Detect radiolabel with

      --autoradiography (X ray film)

      --phosphorimager (phosphor coated plates store the energy of the radioactive particle, laser excitation releases photons of light that are collected and represented as a picture, greater dynamic range than film, and faster too


    Slide71 l.jpg

    Non-radioactive labels sequences or proteins

    …e.g. horseradish peroxidase

    oxidation


    Slide72 l.jpg

    Non-radioactive labels sequences or proteins

    …or digoxygenin/antibody-conjugated HRP

    oxidation

    can also use

    biotinylated

    DNA probe


    Slide73 l.jpg

    Hybridize probes to membranes sequences or proteins

    • blocking agents (e.g. milk, SDS) prevent non-specific interactions between probes and membrane

    • Volume exclusion agents (eg. dextran sulfate) increase rate and level of hybridization

    • Wash blot with increasing stringency…

      • Low stringency: high salt, low temperature, probe binds to sequences with mismatches

      • High stringency: low salt, higher temp., probe binds only to fully complementary sequences


    Slide74 l.jpg

    Southern Blot--one example sequences or proteins

    (or PCR fragment)

    (RFLPs)


    Slide75 l.jpg

    Northern blots: sequences or proteins

    Same basic technique as Southern blots, but RNA is run on the initial gel and is transferred to the membrane.

    Use this method to measure levels of gene transcription in vivo (detecting changes in the levels of RNA transcript under differing conditions)

    Microarrays for measuring mRNA abundance are based on this principle, but many probes are immobilized in a regular array -- reverse transcribed (and fluorescently labelled) RNA “lights up” the probes on the microarray


    Slide76 l.jpg

    Western blots: proteins sequences or proteins

    Proteins are transferred tomembranes using the same principle as Southern blots

    Specific proteins detected

    by probing blot with

    antibodies to protein of interest

    Antibody binding is detected by antibody to the original antibody that has enzyme (horseradish peroxidase, alkaline phosphatase) or radioactivity (125I) conjugated to it


    Slide77 l.jpg

    Methods for detecting sequences or proteinsspecific biomolecules

    • Separate DNA, RNA, or proteins on the basis of size (gel electrophoresis)

    • Immobilize the separated DNA, RNA, or protein

    • “Probe” the blot with something that will specifically interact with a target

      • DNA and RNA: complementary nucleic acid

      • Protein: antibody to that protein


    ad
  • Login