20.109(S13):DNA cloning (Day4)

Introduction

background on this cloning system -- vector arms and strain

transformation

Protocols

Part 1: Gel electrophoresis of PCR products

You will use a 1% agarose gel to run your three PCRs from last time, as well as a reference lane of molecular weight markers (also called a DNA ladder).

1. Add 3 μL of loading dye to each of three eppendorf tubes. No need to change tips in between.
   • Loading dye contains xylene cyanol as a tracking dye to follow the progress of the electrophoresis (so you don’t run the smallest fragments off the end of your gel!) as well as glycerol to help the samples sink into the well.
2. Now add 30 μL of each reaction from last time (your sample, your partner's sample, and the no template control) to individual eppendorf tubes and label them.
   • If a reaction has less than 30 μL due to evaporation, take the maximum amount you can and write it down.
3. Flick the eppendorf tubes to mix the contents, then quick spin them in the microfuge to bring the contents of the tubes to the bottom.
   • Remember: to quick-spin, hold down the "short" button on your centrifuge for 3-5 seconds, then release.
4. Load the gel according to the table below. Up to 4 groups will share each gel: 2 groups per lane.
   • To load your samples, draw 30 μL into the tip of your P200. Lower the tip below the surface of the buffer and directly over the well. You risk puncturing the bottom of the well if you lower the tip too far into the well itself (puncturing well = bad!). Slowly expel your sample into the well. Do not release the pipet plunger until after you have removed the tip from the gel box (or you'll draw your sample back into the tip!).
5. Once all the samples have been loaded, we will attach the gel box to the power supply and run at 110 V for 45 minutes.
   • Need to check what voltage/time works well for a lower % gel; have been using higher % during pilots due to microsporidia work.
6. Later you will be shown how to photograph your gel and excise the relevant bands of DNA. Begin by anticipating where you expect to see your sample band relative to the bands of the DNA ladder, described here.
7. While the gel runs, weigh two eppendorfs and label each tube with its weight. By preparing these in advance, we won't encounter unnecessary delays during purification.

Loading a gel

Lane	Sample (30 μL)	Lane	Sample (30 μL)
1	DNA ladder (load 10 μL)	6	DNA ladder (load 10 μL)
2	Group 1, NTC	7	Group 2, NTC
3	Group 1, sample A	8	Group 2, sample A
4	Group 1, sample B	9	Group 2, sample B
5	BLANK	10	BLANK

Part 2: Purify 16S PCR band from gel

To purify your DNA from the agarose, you will use a kit from the Qiagen company. As we learned during the DNA extraction step on Day 2, reagents in such commercial kits can have uninformative names and their contents are in part proprietary.

1. Estimate the volume of your gel slices by weighing them.
   • The easiest way to do this is to pre-weigh an eppendorf tube for each slice, then weigh it again after adding the gel, and take the difference.
   • What can you assume about the density of agarose and why?
2. Add 3 volumes of QG for every 1 volume of agarose.
3. The maximum advised volume is 550 μL. If you have a greater volume, continue for now, but first read step 6 to understand how to proceed later. Feel free to ask the teaching faculty for clarification.
4. Incubate in the 50°C water bath for 10 minutes, until the agarose is completely dissolved. Every few minutes, you should remove your tubes from the 50°C heat and flick or vortex them for a few seconds to help dissolve the agarose.
5. Add 1 volume — original gel volume, not current solution volume — of isopropanol to each eppendorf tube and pipet well to mix.
6. Get two QIAquick columns and two collection tubes from the teaching faculty. Label the spin-columns (not the collection tubes!) with your sample IDs and then pipet the appropriate dissolved agarose mixture to the top of each one. Microfuge the column in the collection tube for 60 seconds at maximum speed (approx. 16,000 rcf). The maximum capacity of the QIAquick columns is 800 uL! If you have more than 800 uL in your mixture, you will need to repeat this step using the same column.
7. Discard the flow-through in the sink and replace the spin-columns in their collection tubes. Add 500 μL of QG to the top of the column and spin as before.
8. Discard the flow-through again, then add 750 μL of PE to the top of the column and incubate for 5 min at room temperature.
9. Spin for 1 min as before.
10. Discard the flow-through in a temporary waste container such as a 15 mL conical tube (PE contains ethanol) and replace the spin-columns in their collection tubes.
11. Add nothing to the top but spin for 60 seconds more to dry the membrane.
    • This step completely removes remaining ethanol that could interfere with future reactions.
12. Trim the caps off two new eppendorf tubes and prepare sticky labels (in your team color) for the top: write the date, your section day, and the sample ID. You may also want to label the side of each tube, so you don't lose track of which sample is which in the following step.
13. Place the labeled spin-column in its matching trimmed eppendorf tube and add 30 μL of pH 7 water to the center of the membrane.
    • Do not add regular distilled water, as this is at a lower pH, which will lower elution efficiency.
14. Allow the columns to sit at room temperature for one minute and then spin as before. The material that collects in the bottom of the eppendorf tubes is your purified 16S DNA.

Part 3: Ligate purified product to vector arms

1. Prepare a clearly labeled eppendorf tube for each cloning reaction.
2. In the following order, combine 3 μL cloning buffer, 2 μL purified DNA, and 1 μL of vector mix.
3. Incubate at room temperature for 5 min, and then move to ice if you are not yet ready to proceed with the next step. Meanwhile, obtain an aliquot of competent cells from the teaching faculty and let them slowly thaw on ice. Label the side of each tube (and also the top if you like).
4. When both cells and reaction are ready, add 1 μL of the reaction to the cells. Do not pipet up-and-down more than once! Instead, gently mix the cells and DNA by twirling the tube in your fingers.
   • Hold the tube near the top, so that the cells at the bottom stay cold.
5. Incubate the mixture on ice for 20 min.
6. Place the tubes in the 42 °C heat block for exactly 45 seconds, and transfer immediately immediately to ice for 2 min more.
7. Add 250 μL of warm LB to each sample; do not pipet to mix.
8. Place the tubes on the nutator in the 37 °C incubator, and rock them for about 1 hr.
9. Pre-warm 3 LB-Amp-Xgal plates in the incubator at least 20 min prior to using them in the next step.

Part 4: Transform ligated product into cloning strain

old text to work with

1. Plate 250 μL of each transformation mix on LB+AMP plates. After dipping the glass spreader in the ethanol jar, you should 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 (if it sizzles, it's way too hot). Once the plates are ready, wrap them together with one piece of 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 5: Set up microsporidia PCR on this day also? During 1 hr incubation?

need to do microsporidia PCR on separate day because the Ta etc. is different --> need to find notes on where I planned to put that. possibly Day 2? primers should have arrived by then. or maybe wait until Day 4? don't want to have them balancing lab steps too soon.

1. Begin by carefully labeling each PCR tube that you will use with the date, sample name, and a unique symbol and/or color for quick identification. Filling in the cap tab with your team color will usually suffice. Pre-chill the tubes on a cold block.
2. You and your partner can now prepare and share a so-called "master mix," which contains every PCR ingredient except the template and the polymerase. Prepare enough for the number of reactions you need to run, plus an additional 10%. Feel free to use the table below for your calculations.
   • When the master mix is not in use, keep it on ice.
3. Combine 5 μL of template, 45 μL of master mix, and 1 μL of PfuUltra polymerase in a PCR tube. When everyone's reactions are ready, they will undergo the cycling conditions listed below.
   • Add the master mix first, because the template alone may freeze. Then add template and polymerase, and finally (gently!) mix the reaction with a larger pipet.

Reagent	Amount for 1 reaction (μL)	Amount for ? reactions + 10%
PfuUltra buffer (10X stock)	5
Primer mix [TO WHAT EXTENT PREPARED FOR THEM?]	5 of each (Fx and Rx)
dNTPs	1
10% BSA (100X stock)	0.5
Water	28.5
DNA template	5	N/A

Segment	Cycles	Temperature (° C)	Time
1	1	95	3 min
2-4	40	95	1 min
		58	1.5 min
		72	2 min
5	1	72	10 min
6	1	4	indefinite

For next time

Reagent list

• StrataClone Blunt PCR Cloning kit from Agilent