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This document provides information on plasmid extraction, transformation, and protein expression in E. coli. It discusses key steps in the process including plasmid extraction via alkaline lysis, transformation of E. coli via heat shock or electroporation, expression of recombinant proteins using vectors like pET and factors that influence transformation efficiency and protein yield. Common techniques used in molecular biology labs such as agarose gel electrophoresis, spectrophotometry, and SDS-PAGE are also summarized.
This document provides information on plasmid extraction, transformation, and protein expression in E. coli. It discusses key steps in the process including plasmid extraction via alkaline lysis, transformation of E. coli via heat shock or electroporation, expression of recombinant proteins using vectors like pET and factors that influence transformation efficiency and protein yield. Common techniques used in molecular biology labs such as agarose gel electrophoresis, spectrophotometry, and SDS-PAGE are also summarized.
This document provides information on plasmid extraction, transformation, and protein expression in E. coli. It discusses key steps in the process including plasmid extraction via alkaline lysis, transformation of E. coli via heat shock or electroporation, expression of recombinant proteins using vectors like pET and factors that influence transformation efficiency and protein yield. Common techniques used in molecular biology labs such as agarose gel electrophoresis, spectrophotometry, and SDS-PAGE are also summarized.
Methods and Processes o Plasmid extraction o Transformation o Protein expression o Purification o DNA and Protein quantification
Plasmid Extra-chromosomal, autonomously replicating DNA Covalently closed circular dsDNA Non essential but gives competitive advantage such as antibiotic resistance
Plasmid vectors Contain an antibiotic resistance marker so you can select your transformed bacteria Has a multiple cloning site TA cloning plasmid: creates overhang in gene insert. Most plasmid in nature have many RE sites where you can insert gene of interest
Molecular Biology applications Cloning different DNA fragments Protein production
Nucleic acid extraction 3 specific goals 1. Disruption of cell wall and membrane 2. Inactivation of nucleic acid degrading enzymes (i.e. DNases, RNases) 3. Separation of nucleic acids from other cellular components
Isolation of Plasmid DNA Harvest cells by centrifugation Discard supernatant & remove other media components that could interfere w/ extraction protocol or end product it self o Residual media may interfere w/ downstream steps Resuspend cells in solution o Tris-Cl: maintain pH of environment o EDTA: chelates divalent cations that activate DNases o RNase A: contamination may appear as giant bright smear
Alkaline Lysis method Lyse cells with Soln 2 (SDS/NaOH) o SDS denaturing anionic detergent o Dissolves membranes o Binds and denature proteins NaOH o Double stranded DNA is unwound, genomic DNA easier to unwind o Denatures both plasmid and chromosomal DNA o Plasmid DNA easily find other strand
Solution 3 Neutralize NaOH (KOAc solution) o Production of fluffy, white precipitate ! Precipitates SDS-protein complex o Renaturation of plasmid DNA o Separation of plasmid DNA from contaminants via centrifugation
Isolation of plasmid DNA Alcohol precipitation 70% ethanol wash o remove contaminants precipitated by absolute (e.g. salts) Dissolve with TE (or other aqueous soln) o Buffer solution with EDTA to prevent activity of DNases by chelating divalent cations
Nucleic acid yield and purity Agarose gel electrophoresis Absorbance Fluorescent dyes that intercalate with DNA Kits that allow you to add dyes to see amount of fluorescence to determine quantity and percent ot DNA added
Factors affecting Agarose Gel Electrophoresis Molecular size of DNA Concentration of DNA Concentration of agarose gel Conformation of DNA o Loose conformation is retarded o Presence of intercalating agents that may alter characteristics of DNA including shape o Voltage ! In relation to amount of ions in your gel. ! Higher voltage leads to higher mobility but causes more heating. ! If too slow, diffusion might occur and lead to bad bands o Type of agarose o Electrophoresis buffers
*There are specific concentrations of agarose that would yield best resolution. Typically, we use 1% agarose because it is in the range of 500-1000 bp *It is hard to resolve large and small DNAs on the same gel.
Separation by size PFGE (Pulse Field Gel Electrophoresis) o Zig-zag path to increase effective path Agarose Acrylamide o You cant view in UV if theres still a glass plate. Check in UV, if not enough, but back in glass plate
Conformation of DNA Brightest band is usually supercoiled DNA In order of increasing mobility: nicked, linear, covalently bonded, supercoiled Run in PCR to check size It is sufficient because it is a check if plasmid extraction is successful. If there is a band then plasmid extraction is a success.
DNA visualization Most common dye is Ethidium Bromide o It intercalates with DNA in the hydrophobic region and is therefore considered as a mutagen o Fluoresces when intercalated with DNA because it is in hydrophobic region and thus quenching is lessened Gel red has a similar mode of action Other dyes like acridine orange and SYBR green, Actinomycin D
Determining DNA concentration AGE run can be used to determine concentration of DNA per band using a special kind of marker Same number of moles per band because they are derived from one plasmid (lambda Hind III) Some machines like GNOC can quantify brightness o Select band and tell you size of band Higher mass = higher brightness because it has more DNA;calculation based on % of mass
DNA purity Nucleic acids, absorption peak at ~260 nm A260/A280 ~ 1.8 for dsDNA and ~2.0 for ssRNA o Ratios lower than 1.7 usually indicate significant protein contamination A260/A230 ratio of DNA and RNA should be roughly equal to its A260/A280 ratio (greater than or equal to 1.8) o Lower ratios may indicate contamination by organic compounds (e.g. phenol, alcohol, or carbohydrates) It measures light that is transmitted so you can backtrack what light was absorbed.
Transformati on Make your cell take up your plasmid Uptake of exogenous genetic material Methods: o Electroporation ! Electrical shock makes cell membranes permeable to DNA o CaCl/Heat shock ! Chemical-component cells uptake DNA
Competence Some bacteria are naturally competent, this is not the case for E. coli. Artificial o Chemical competence o Electrical competence Electroporation has a higher chance of killing Heat Shock transformation CaCl2 positive charges of Ca 2+ shields negative charges of DNA phosphates, no longer ionic 1. Incubate on ice Slows fluid cell membrane 2. Heat-shock Increases permeability of membranes 3. Nutrient broth incubation Allows beta-lactamase expression Even if a cell has antibiotic resistance gene, putting antibiotic right away would kill it. Wait for 1 hour to ensure production of antibiotic resistance gene
Selection and Screening Selection such as antibiotic resistance Screening: makes others grow but your desired cells can be selectively chosen
Assessment of transformation LB bacteria probably wont have fluorescence because transformed cells are out competing one another to even produce GFP Dont over incubate because beta-lactamase can seep out and enable growth of non- resistant bacteria forming satellite colonies Positive control tells you if cells are alive Negative control tells you if amp works
Transformation efficiency Expressed as number of CFU/ug of plasmid In E. coli, the theoretical limit = 1 x 10 11 cfu/ug Factors o Plasmid size (inversely proportional) o Conformation of DNA (supercoiled DNA with highest efficiency) o Amount of DNA o Purity of DNA o Source of DNA (Is it methylated) o Growth of genotype of cells (consider OD of cellsusually at 0.4) o Method of transformation
Fluorescent Proteins They are proteins based visual markers in the study of biological processes Localization and regulation of gene expressions Cell movement and cell fate during development Screenable marker to identify organisms
Heterologous protein expression Synthesis of foreign proteins in a host organism following transformation of that organism by a vector carrying genes from a different organism.
Expression systems Bacteria, esp. E. coli Yeast cells, insect cells, mammalian cells, cell free (wheat germ extract, E. coli extract) There are reasons why E. coli is preferred o Fast growth o Simple media o Highest yield *But proper folding is not attained for proteins derived from higher organisms (glycosylation)
Expression Vectors May differ depending on expression systems Usually inducible. IPTG induction-lac operon is inherent. Vectors that have a T7 promoter. T7 polymerase is inducible inside the cell Arabinose induction-ara operon His tag Enterokinase site can be used to cut His tag *yeast vectors require methanol
Ara operon Arabinose acts as an effector. Binding of arabinose cause downstream expression of genes. Essentially, you just change what genes are expressed
E. coli strains used for expression BL21-protease-deficient; inducible high level of expression uses T7 RNA polymerase BL21(DE3)-lacI repression of T7 RNA polymerase; tighter regulation o IPTG binds to repressor on the gene then now your polymerase
BL21(DE3) pLysS/pLysE-production of T7 lysozyme (inhibitor of T7 RNA pol transcription o You have an inhibitor that removes inherent T7 RNA pol transcription
Why use a starter culture? Starter culture to select for living cells and help even out inoculation. In theory, same time to grow.
Extraction Resuspend pellet o proteins expressed in media Sonicate 3x 30 sec/pulse o Heat generated may denature proteins 60 secs on ice between pulses Centrifuge to remove cell debris Transfer clarified supernatant *GFP makes it easy to check, look at fluorescence. Possible that there is high expression but GFP remains in the pellet.
Pol yacryl ami de Gel El ectrophoresi s
Acrylamide Polymerization APS is the source of free radical that starts the polymerization of acrylamide TEMED catalyzes formation of free radical from your APS %T: % concentration of bis + acrylamide %C: % of bisacrylamide or crosslinker o Max %C is 5% because after that the pore size becomes larger at higher %C o 19:1 " 5%C
Different PAGE systems Gradient PAGE o Usually from pre-cast, because you need a gradient mixer
Continuous vs. Discontinuous (Laemmli) PAGE Stacking gel o Zwitterionic glycine, less mobility o Sandwich effect of protein o pH 6.8 Resolving gel o Glycinate form, greater mobility o pH 8.8 SDS-PAGE o Includes DDT and Beta- Mecaptoethanol w/c are reducing o Pseudonative PAGE: SDS but no boiling and reducing agent. Run still based in structure (This is in your unboiled sample) ! Native PAGE is quite difficult because there are many other factors (+conformation, charge) at play to get discrete bands
Protein visualization Staining solution o Fixation: water: acetic acid: methanol o Coomassie Brilliant Blue R-250 ! Slightly reddish at acidic pH o Coomassie binds to proteins Destaining solution o I-same water:acetic acid: methoanol ratio as staining solution ! Methanol is a fixative that prevents dispersion o II-lower concentration of methanol ! You can keep it in destain II for a very long time. o If you want to check protein activity, do it before putting destaining solution due to presence of acid
Protein visualization Coomassie vs. Silver staining o Increase detection of bands but you actually need a lot of solutions o High background is likely
Molecular Weight markers Know what marker you used and buffer you used. Thus, different mobilities in different buffers Aprotinin and Insulin are below limit of resolution in our runs. Precision Plus standards (Bio-Rad)
Protein Purification Chromatography o Size exclusion chromatography o Ion exchange chromatography o Affinity chromatography o Hydrophobic interaction chrom Decreases amount of proteins you have to deal with because you elute out other proteins
Size exclusion chromatography Larger proteins do not enter gel matrix and they just flow out. Smaller molecules elute at a later time because they interact with matrix Some proteins may have the same size
Ion exchange chromatography Based on charge. Separate acidic/basic Elute with salt gradients.
Immobilized Metal Affinity Chromatography Co 2+ was used. Bound to linker, Sepharose Binding of Co 2+ is lower than Ni 2+ creates lower yield but higher purity Elute out with imidazole or pH
Fast Protein Liquid Chromatography Automated chromatography system System consists of high precision pumps, control unit, column, detection system, and fraction collector Vs. HPLC o FPLC can withstand up to 5MPa only
Purification Flowthrough o Proteins that dont bind to resin Wash o Excess or non-specific binding Elution o Protein w/ His tag Strip o Remove imidazole using MES buffer o Remove Co 2+ using EDTA o Replenish afterwards Why equilibrate resin before use o Maintain binding pH o Has a level of salt that prevent the non- specific binding, which could occur.
Purification of GFP Increases size from 25 kDa to 29 kDa due to His tag and plasmid components Unboiled samples, you generally wont get size that you are looking for because some structures are retained Fraction 1 may have equilibration buffer
Protein quantification Bradford assay o Colorimetric assay for measuring total protein concentration o It involves the binding of Coomassie Brilliant Blue G-250 1. Make solutions of a known proteins (Bovine Serum Albumin) 2. Mix from each solution with Bradford reagent (CBBG + Phosphoric acid + Ethanol) Binds to basic residues If higher basic, detect a lot more protein therefore overestimate 3. Measure absorbance at 600 nm Biuret assay o Relies on reduction of copper (II) ions to copper (I), the latter forma complex with the nitrogens of the peptide bond in an alkaline solution o Absorption at 540 nm is directly proportional to protein concentration o Bind to peptide bond Lowry Assay o Uses Folin Ciocalteu reagent (phosphomolybdic/phosphotungstic acid) o Cuprous ions (Cu + ) reduction of Folin Ciocalteu reagent produces blue color that can be read at 650-750 nm. More aromatic residues also detected BCA assays o React with reduced cuprous cation o Intense purple-colored reaction product reacts from the chelation of 2 molecules of BCA with one Cu + ions o BCA/copper complex is water-soluble and exhibits strong o Linear absorbance at 562 nm with increasing protein concentration o Better because more specific
(Fungal Biology) Monika Schmoll, Christoph Dattenböck (Eds.) - Gene Expression Systems in Fungi - Advancements and Applications (2016, Springer International Publishing)