20.109(S13):Prepare expression system (Day4)

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#The vector [http://tools.invitrogen.com/content/sfs/manuals/prset_man.pdf pRSET] has several properties that make it useful for protein expression and production in bacteria. Some of these were described in today’s Introduction, namely the T7 promoter and an ampicillin resistance gene. Name 1 other feature contained in the pRSET vector and tell what purpose it serves. (Use your own words to describe the purpose, don't just quote the catalogue.) <br>
#The vector [http://tools.invitrogen.com/content/sfs/manuals/prset_man.pdf pRSET] has several properties that make it useful for protein expression and production in bacteria. Some of these were described in today’s Introduction, namely the T7 promoter and an ampicillin resistance gene. Name 1 other feature contained in the pRSET vector and tell what purpose it serves. (Use your own words to describe the purpose, don't just quote the catalogue.) <br>
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##BL21(DE3) ''E. coli'' are often used for protein expression. In contrast, XL1-Blue ''E. coli'' are ‘workhorse’ cells useful for plasmid propagation. One gene modification in XL1-Blue is the ''hsdR'' mutation. What are the two other modified genes in XL1-Blue that make them ideal for the task of propagating a desired DNA? Briefly explain why each is important. It may help you to refer to the cell manual: [http://www.chem-agilent.com/pdf/strata/200249.pdf  (pdf download)], but be sure to answer the question in your own words. Note that this question is about propagation, not screening.
#Your Module 1 report revision is due by 11 AM next time, to the 20109.submit address and using a Firstinitial_Lastname_LabSection_Mod1-REV.doc naming scheme.
#Your Module 1 report revision is due by 11 AM next time, to the 20109.submit address and using a Firstinitial_Lastname_LabSection_Mod1-REV.doc naming scheme.
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2. The pRSET plasmid with inverse pericam insert, or pRSET-IPC, is 4141 basepairs long and its GenBank file is linked [[Media: S12-M2-20109_pRSET-IPC.gb| here]]. According to the [[Media:S12_pRSET-IPC_1or2-cutters_NEBonly.pdf |cutters list]] that you used on Day 1, restriction site ''PvuI'' occurs at ~1655 bp, and again at ~2700 bp into pRSET-IPC. Thus, digesting this parental plasmid with the ''PvuI'' enzyme should result in two linear fragments of DNA, with about 1045 and 3095 bp sizes. 
 
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A silent mutation can be introduced that results in a new ''PvuI'' site at the 341<sup>st</sup>-342<sup>nd</sup> residues of inverse pericam (ATT &rarr; ATC and TAC &rarr; GAC) , or approximately the 1020<sup>th</sup> basepair of IPC. When IPC is inserted into pRSET, its starting point is ~200bp into the pRSET plasmid. Thus, if the mutated pRSET-IPC plasmid is digested with ''PvuI'', three linear fragments of DNA are the result: 440, 1045, and 2655 bp. To understand these calculations, see also the plasmid maps above. Make sure you can reproduce the numbers in this example before proceeding with your own samples. Plasmid maps can be made using the ''Enzyme Selector'' and ''Graphic Map'' functions in ApE.
 
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For this assignment, you should plan restriction enzyme digests that allow you to distinguish parental and mutant pRSET-IPC for your X#Z mutation and for your positive control. You are probably best off doing a single enzyme digest for this particular experiment. However, in other kinds of experiments (notably cloning) using two enzymes per digest can give more information. We will discuss these types of digests in a future pre-lab if there is time.
 
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Use the tabulated information on the [[Talk:20.109%28S12%29:Start-up_protein_engineering_%28Day1%29 | Day 1 Talk page]] along with the cutters lists from the Day 1 protocol to determine the cut sites relevant for M124S and T79P. For E67K, the students could not create an enzyme site on the 0- or 1-and-2-cutters lists. Instead, they ended up making a site for a 6-cutter (linked [[Media:20109-S12_pRSET-IPC_6-cutters.txt | here]]). The banding pattern should nevertheless be distinguishable for the parent and mutant case, even though not all the bands will be visible.
 
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'''Please clearly show all your work and reasoning throughout this assignment.'''
 
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(A) First, use the [http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/buffer_activity_restriction_enzymes.asp? NEB site] to determine the appropriate buffer and temperature for your two reactions.
 
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(B) Next, you should explicitly show how the digest distinguishes between  parent and mutant. In other words, what are the expected band sizes for each upon digestion?
 
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(C) Finally, to prepare for Day 4 in lab, calculate the amount of enzyme and buffer needed for your digestion master mixes. Refer to [[20.109%28S12%29:Prepare_expression_system_%28Day4%29#Diagnostic_Digests | Part 5 (first sub-part)]] of the Day 4 protocol.
 
3. Please download the midsemester evaluation form [[Media:MidsemesterEval_20.109-S12.doc | found here (DOC download)]]. Complete the questionnaire and then print it out <b>without including your name </b> to turn in. If there is something you'd like to see done differently for the rest of the course, this is your chance to lobby for that change. Similarly, if there is something you think the class has to keep doing, let us know that too. These will be collected in a separate folder from your FNTs, to preserve anonymity.
3. Please download the midsemester evaluation form [[Media:MidsemesterEval_20.109-S12.doc | found here (DOC download)]]. Complete the questionnaire and then print it out <b>without including your name </b> to turn in. If there is something you'd like to see done differently for the rest of the course, this is your chance to lobby for that change. Similarly, if there is something you think the class has to keep doing, let us know that too. These will be collected in a separate folder from your FNTs, to preserve anonymity.

Revision as of 14:42, 18 March 2013

20.109(S13): Laboratory Fundamentals of Biological Engineering

Home        Schedule Spring 2013        Assignments       
DNA Engineering        Protein Engineering        Cell Engineering              


Contents

Introduction

Now that we have prepared DNA encoding your mutant inverse pericams, we would like to produce the proteins themselves. Last time you were here, you transformed competent bacteria (called XL1-Blue) with mutagenized DNA prepared from a template plasmid. Successfully transformed bacteria grew into colonies on amipicillin-containing plates, and yesterday your oh-so devoted teaching staff picked two colonies per mutant to grow in liquid culture. The XL1-Blue cell line, although it now carries the inverse pericam DNA, cannot produce the inverse pericam protein. Today you will extract DNA from the XL1-Blue cells, prepare it for analysis, and transform your IPC mutant plasmids into a new bacterial system that can produce the protein directly.

From Invitrogen manual
From Invitrogen manual

The bacterial expression vector we are using (pRSET) contains the bacteriophage T7 promoter. This promoter is active only in the presence of T7 RNA polymerase (T7RNAP), an enzyme that therefore must be expressed by the bacterial strain used to make the protein of interest. We will use the BL21(DE3)pLysS strain, which has the following genotype: F-, ompT hsdSB (rB- mB-) gal dcm (DE3) pLysS (CamR). In BL21(DE3), T7RNAP is associated with a lac construct, and its expression is under the control of the lacUV5 promoter. Constitutively expressed lac repressor (lacI gene) blocks expression from the lac promoter; thus, the polymerase will not be produced except in the presence of repressor-binding lactose or a small-molecule lactose analogue such as IPTG (isopropyl β-D-thiogalactoside). To reduce ‘leaky’ expression of the protein of interest (in our case, inverse pericam), the pLysS version of BL21(DE3) contains T7 lysozyme, which inhibits basal transcription of T7RNAP. This gene is retained by chloramphenicol selection, while the pRSET plasmid itself (and thus inverse pericam) is retained by ampicillin selection - as you learned last time.

To isolate the inverse-pericam-containing pRSET plasmid from the overnight cultures, you will perform what is commonly called a “mini-prep.” This term distinguishes the procedure from a “maxi-” or “large scale-prep” which involves a larger volume of cells and additional steps of purification. The overall goal of each “prep” is the same--to separate the plasmid DNA from the chromosomal DNA and cellular debris, allowing the plasmid DNA to be studied further. In the traditional mini-prep protocol, the media is removed from the cells by centrifugation. The cells are resuspended in “Solution I” which contains Tris to buffer the cells and EDTA to bind divalent cations in the lipid bilayer, thereby weakening the cell envelope. A solution of sodium hydroxide and SDS is then added. The base denatures the cell’s DNA, both chromosomal and plasmid, while the detergent dissolves the cellular proteins and lipids. The pH of the solution is returned to neutral by the acetic acid and potassium acetate in “Solution III.” At neutral pH the SDS precipitates from solution, carrying with it the dissolved proteins and lipids. In addition, the DNA strands renature at neutral pH. The chromosomal DNA, which is much longer than the plasmid DNA, renatures as a tangle that gets trapped in the SDS precipitate. The plasmid DNA renatures normally and stays in solution, effectively separating plasmid DNA from the chromosomal DNA and the proteins and lipids of the cell.

Production of mutant IPC protein. The mutant DNA and protein are indicated by a green colour. Blue arrows/text indicate steps performed during class time; black arrows indicate steps performed by the teaching staff.
Production of mutant IPC protein. The mutant DNA and protein are indicated by a green colour. Blue arrows/text indicate steps performed during class time; black arrows indicate steps performed by the teaching staff.


Once you have the plasmid DNA isolated, you can prepare it for sequencing and gel analysis, as well as use it immediately for transformation. In order to transform BL21(DE3) cells with your mutant IPC plasmids, you will first have to make the cells competent, i.e., able to efficiently take up foreign DNA. With the XL1-Blue strain, we used commercially available competent cells that did not need further treatment prior to DNA addition. Today, you will make chemically competent cells yourself using calcium chloride, then incubate them with plasmid DNA and heat shock them as before prior to plating. Tomorrow, the teaching staff will pick colonies and set up liquid overnight cultures from your transformed cells. Next time, you will add IPTG to these liquid cultures to induce expression of your mutant proteins, which you will then isolate and characterize. Much of this process is summarized in the figure above.

Protocols

Part 1: Prepare competent BL21(DE3) cells

  1. Pick up one 5 mL tube of BL21(DE3) cells. These cells should be in or near the early- or mid-log phase of growth, which is indicated by an OD600 value of 0.4-0.8.
  2. Measure the OD600 value of a 1:10 dilution of your cells (use a total volume of 650-700 μL). If the cells are not yet dense enough, return them to the rotary shaker in the incubator. Remember to balance with another tube! As a rule, your cells should double every 20-30 min.
    Aspirate the supernatant, as shown, removing as few cells as possible
    Aspirate the supernatant, as shown, removing as few cells as possible
  3. Once your cells have reached the appropriate growth phase, pour them into 3 eppendorf tubes each containing ~ 1.5 mL culture volume. Spin for 1 min at max speed (~16,000 rcf/13,000 rpm), aspirate the supernatants as shown, and resuspend in an equal volume of ice-cold calcium chloride (100 mM). Note: you can balance these tubes in the centrifuge with three-way symmetry.
    • If you are nervous about pouring the liquid, you can use your P1000 to pipet 750 μL into each eppendorf twice. Either way, the eppendorf should be quite full when you try to close the cap. You can wear gloves to keep the bacteria from splashing your skin or you can wash your hands after closing all the caps.
    • You may find it easiest to resuspend the cells in a small volume first (say, 200 μL), then add the remaining volume of CaCl2 (e.g., in two steps of 650 μL) and invert the tubes to mix.
  4. Spin again for 1 min. The resultant pellets should occur as streaks down the side of the eppendorf tube, so be very careful not to disturb the cells when aspirating.
  5. This time, resuspend each pellet in 100 μL of CaCl2, then pool the cells together in one tube.
    • Alternatively, resuspend the first pellet in 300 μL, then use this cell solution to resuspend the next pellet, and the next.
  6. Incubate on ice for 1 hour. You can work on parts 2, 4, and 5 of today's protocols now, as well as assemble the materials for part 3. Among other things, be sure to label four eppendorfs and pre-chill them on ice. The labels should indicate a (-) no DNA control, a (+) M124S/E67K/T79P transformation control, and your two mutant candidate transformations (X#Z -1 and -2).

Part 2: DNA extraction (mini-prep)

  1. Pick up your two candidates cultures, growing in the test tubes labeled with your team colour. Label two eppendorf tubes to reflect your mutations and candidates (X#Z-1, X#Z-2).
  2. Vortex the bacteria and pour ~1.5 mL of each candidate into the appropriate eppendorf tube.
  3. Balance the tubes in the microfuge, spin for one minute, and resuspend the cells in 100 μL of Solution I, changing tips between samples.
    • Note that the word "resuspend" implies aspiration beforehand.
  4. Prepare Solution II by mixing 250 μL of 2% SDS with 250 μL of 0.4M NaOH in an eppendorf tube. Add 200 μL of Solution II to each sample and invert the tubes five or six times to mix. The samples should become less opaque (almost clear) but don't worry if you don't see a big change.
  5. Place the tubes on ice for five minutes.
  6. Add 150 μL of Solution III to each sample and immediately vortex the tubes for 10 seconds at the highest setting. White clumps should appear in the solution.
  7. Spin for 4 minutes to separate the plasmid DNA from cell debris.
    • While the tubes are spinning, label another set of eppendorf tubes with the candidate names and your team color.
  8. A white pellet should be visible when you retrieve your tubes. Transfer 400 μL of each supernatant to the appropriate clean eppendorf tube. It's OK to leave some of the supernatant behind; avoid transferring any of the white pellet.
  9. Add 1000 μL of room temperature 100% ethanol to each supernatant. The tubes will be quite full, so cap tightly before inverting at least five times to thoroughly mix the contents.
  10. Microfuge the samples for 2 minutes. It is important to orient your tubes in the microfuge now since the pellets from this spin may be barely visible.
    • An orientation aligned with the tab of the cap may be easiest to remember.
  11. Remove the supernatants using your P1000, taking care not to disturb the pellet of plasmid DNA that is at the bottom of the tube, and put them in a 15 mL conical waste collection tube. Remove as much of the supernatant as possible, but you do not need to remove every drop since you will be washing the pellet in the next step.
  12. Add 500 μL of 70% ethanol to each pellet. You do not need to fully resuspend the pellet, but you might invert or flick the tube a few times. Spin the samples one minute, orienting the tubes in the microfuge so you will know where to find the pellet.
  13. Immediately remove the supernatant with your P1000, making sure to keep the tip on the side of the tube that doesn't have your pellet. Remove as much liquid as possible, using your P200 set to 100 μL to remove the last few droplets and/or to streak them up the side of the tube to promote evaporation.
  14. To completely dry the pellets, place your rack in the hood with the tube caps open for ~ 10 minutes. When the pellets are completely dry, add 50 μL of sterile water to each sample and vortex for 2 X 30 seconds (with a quick-spin in between and afterward) to completely dissolve the pellets. Store the DNA on ice, and do NOT throw it away after completing Part 3. (The teaching faculty will save the minipreps for potential future use.)

Part 3: Transform BL21(DE3) with mutant DNA

  1. Prewarm and dry 4 LB+Amp/Cam plates by placing them in the 37°C incubator, media side up with the lids ajar. You will perform one transformation for each of your four samples.
  2. When your competent cells are ready, aliquot 70 μL of cells per pre-chilled eppendorf.
  3. Add 2 μL of the appropriate DNA to each tube. Remember, you are testing plasmid DNA that was prepared from two different colonies for your X#Z mutant, along with DNA from a colony that is already known to be M124S/E67K/T79P. You will also perform a no DNA control.
  4. Flick to mix the contents and leave the tubes on ice for at least 5 minutes.
  5. Heat shock the cells on the 42°C heat block for 90 seconds exactly and then put on ice for two minutes.
  6. Move the samples to a rack on your bench, add 0.5 ml of LB media to each one, and invert each tube to mix.
  7. Incubate the tubes in the 37°C incubator for at least 30 minutes. This gives the antibiotic-resistance genes some time be expressed in the transformed bacterial cells.
  8. While you are waiting, prepare 3 large glass test tubes containing LB+Amp/Cam, and label them with your team color and sample name. (You can also finish part 5 of the protocol if you have not yet done so.)
    • Prepare one 7.5 mL stock of LB with Amp and Cam each at 1:1000. Then distribute 2.5 mL each to the 3 tubes.
  9. Also prepare 4 eppendorf tubes containing 180 μL of LB each. You will use these to dilute your transformed cells 1:10 when you retrieve them from the incubator.
    • If you label these tubes with stickers rather than directly on the cap, you can then transfer each sticker to the appropriate plate as you go, saving one labeling step.
    • Note that we are reducing the cell concentration because miniprep DNA is much more concentrated than the DNA resulting from mutagenesis; it also does not require repair, further increasing the transformation efficiency.
  10. Plate 200 μl of each (1:10 diluted) transformation mix on an LB+Amp/Cam plate.
    • Safety reminder: After dipping the glass spreader in the ethanol jar, then pass it through the flame of the alcohol burner just long enough to ignite the ethanol. After letting the ethanol burn off, the spreader may still be very hot, and it is advisable to tap it gently on a portion of the agar plate without cells in order to equilibrate it with the agar.
  11. Once the plates are done, wrap them with colored tape and incubate them in the 37°C incubator overnight. One of the teaching faculty will remove them from the incubator and set up liquid cultures for you to use next time.

Part 4: Count mutant colonies

When you have a spare moment today, count the colonies that arose on your transformed XL1-Blue plate, as well as on your positive and negative control plates. Does the negative control have any colonies? How does your mutation efficiency compare to that of the positive control? Please put your colony counts on today's Talk page.

Part 5: Prepare DNA for Evaluation

Diagnostic Digests

You will perform diagnostic digests on the following samples: the inverse pericam parent plasmid (pRSET-IPC), a known mutant pRSET-M124S or -T79P or -E67K, and two candidates for your X#Z mutation. "Digest 1" (D1) will be used to show that the positive control DNA contains the correct mutation, and "Digest 2" (D2) will be used to test whether your X#Z candidates do. Thus, you will need enough D1 mixture for two reactions (IPC and M124S/T79P/E67K), and enough D2 mixture for three reactions (IPC and the two X#Z candidates). To avoid pipetting very small volumes of enzymes, and in order to have at least a little extra of each reaction (so you don't run out due to pipetting error), make enough of each digest for four reactions.

The table below is for one reaction and assumes that each digest will consist of a single enzyme. Note that enzyme stock concentrations can be found on the NEB product page for that enzyme.

Example Digest 1 Digest 2
Plasmid DNA 4 μL 4 μL 4 μL
10X NEB buffer 2.5 μL of buffer#3 2.5 μL of buffer#_____ 2.5 μL of buffer#_____
Enzyme 2.5 U = 0.25 μL of PvuI 2.5 U = __ μL of _____ 2.5 U = __ μL of _____
H2O For a total volume of 25 μL
  1. Prepare a reaction cocktail for each of the above reactions (digest 1 and digest 2) that includes water, buffer and enzyme. Prepare enough of each cocktail for 4 digests. Leave the cocktails on ice.
  2. Aliquot 4 μL of the appropriate plasmids into five well-labeled eppendorf tubes. The labels should include the plasmid name, the enzyme(s) to be added and your team color.
  3. Add 21 μL of the appropriate cocktail to each tube. Flick the tubes to mix the contents, touch-spin, then incubate the mixtures at 37°C for at least one hour.
    • While your samples are digesting, you can return to Part 3 of the protocol.
  4. Before leaving lab today, please add 2.5 μL of loading dye to each of the digests you have assembled. You should also prepare undigested samples of parent IPC and each mutant candidate, containing 4 μL of plasmid, 21 μL of water, and loading dye. We will store the digests and the remaining DNA at –20°C.

Sequencing Reactions

As we will discuss in lab today, sequencing reactions require a primer for initiation. Legible readout of the gene typically begins about 40-50 bp downstream of the primer site, and continues for ~1000 bp at most. Thus, multiple primers must be used to fully view genes > 1 Kbp in size. How many basepairs long is inverse pericam? (Check the ApE file linked in your previous homework.)

Luckily, we only care about the back end of IPC, i.e., the part containing calmodulin. The primer you will use today starts at base pair 823 of pRSET-IPC, a couple hundred base pairs upstream of CaM. As for the positive controls, everyone will be given the same sequencing data to analyze, because you are all working with DNA from the same three candidates.

The recommended composition of sequencing reactions is ~500 ng of plasmid DNA and 25 pmoles of sequencing primer in a final volume of 15 μL. The miniprep'd plasmid should have ~1 μg of nucleic acid/μL but that will be a mixture of RNA and DNA, so we will guess at the amount of plasmid DNA appropriate for our reactions.

For each reaction, combine the following reagents directly in the appropriate tube within the 8-PCR-tube strip, as noted in the table below:

  • 2.5 μL of your plasmid DNA candidate
  • 12.5 μL of the primer solution on the teaching bench, which contains
    • 5 μL of sequencing primer at 5 *mu;M
    • 7.5 μL sterile water

The side of each tube is numerically labeled and you should use only the two tubes assigned to your group. The teaching faculty will turn in the strips at the Genewiz company drop-off box for sequencing.

Group Label Range Group Label Range
Red 1-2 Blue 9-10
Orange 3-4 Pink 11-12
Yellow 5-6 Purple 13-14
Green 7-8

For next time

Revise for S13

  1. The vector pRSET has several properties that make it useful for protein expression and production in bacteria. Some of these were described in today’s Introduction, namely the T7 promoter and an ampicillin resistance gene. Name 1 other feature contained in the pRSET vector and tell what purpose it serves. (Use your own words to describe the purpose, don't just quote the catalogue.)
    1. BL21(DE3) E. coli are often used for protein expression. In contrast, XL1-Blue E. coli are ‘workhorse’ cells useful for plasmid propagation. One gene modification in XL1-Blue is the hsdR mutation. What are the two other modified genes in XL1-Blue that make them ideal for the task of propagating a desired DNA? Briefly explain why each is important. It may help you to refer to the cell manual: (pdf download), but be sure to answer the question in your own words. Note that this question is about propagation, not screening.
  1. Your Module 1 report revision is due by 11 AM next time, to the 20109.submit address and using a Firstinitial_Lastname_LabSection_Mod1-REV.doc naming scheme.

Closer to below, but that was too long so revise somewhat

Revise for S13

1. The major assessment for this module will be a research article describing your protein design work. For this assignment, you will write a draft of the introduction to your report. Recall that the introduction provides a framework for the story you are about to tell, with respect to both background and motivation. You are encouraged to revisit the scientific writing guidelines and brainstorm using the suggested three-section structure before you begin.

  • What might the big picture section consist of? Will you focus on engineering sensors in general, the utility of sensing calcium specifically, or ... what?
  • What background would the reader like to have as you zoom in?
  • When you define your specific study, be sure to share your hypotheses about both your unique mutant and one of the positive control mutants.
IPC plasmid map (Q2)
IPC plasmid map (Q2)
Mutant plasmid map (Q2)
Mutant plasmid map (Q2)



3. Please download the midsemester evaluation form found here (DOC download). Complete the questionnaire and then print it out without including your name to turn in. If there is something you'd like to see done differently for the rest of the course, this is your chance to lobby for that change. Similarly, if there is something you think the class has to keep doing, let us know that too. These will be collected in a separate folder from your FNTs, to preserve anonymity.

4. Extra credit (1 pt): Consider a mutant pRSET-IPC with a newly introduced NotI restriction site that did not occur at all on the parental plasmid (zero cutter). After digestion, you see banding patterns that indicate an uncut plasmid (supercoiled and circular) rather than a linearized piece of DNA for both the parental and the mutant plasmid. Your lab partner tells you that the mutagenesis reaction must not have worked, and that the so-called mutant couldn't possibly contain a NotI site. What’s an equally valid interpretation of this data?

Reagent list

Microbial work

  • 100 mM CaCl2, sterile
  • LB (Luria-Bertani broth)
    • 1% Tryptone
    • 0.5% Yeast Extract
    • 1% NaCl
    • autoclaved for sterility
  • Ampicillin: 100 mg/mL, aqueous, sterile-filtered
  • Chloramphenicol: 34 mg/mL in ethanol
  • LB+AMP+CAM plates
    • LB with 2% agar and 100 μg/ml Ampicillin and 34 μg/ml Chloramphenicol

DNA Mininprep

  • Solution I
    • 25 mM Tris pH8
    • 10 mM EDTA pH8
    • 5 mM Glucose
  • Solution II
    • 1% SDS
    • 0.2M NaOH
  • Solution III
    • 3M KAc, pH 4.8

Plasmid Digests

  • Parental plasmid (pRSET-IPC)
  • Mutant plasmids (pRSET-M124S or -T79P or -E67K, and your two minipreps)
  • NEB buffers 1-4
  • NEB enzymes

DNA Sequencing materials

  • Sequencing primer "IPC-seq-f-823" dilute to 5 pmol/μL in water (original stock 100 pmol/μL)
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