Protocol is following!

Colony PCR with ALLin™ Red Taq Mastermix, 2X:

aim:
Is the insert DNA in the plasmid present or absent?
Much easier than to isolate, purify the vector

good to know before the start:
- Take typical measures to prevent PCR cross over contamination, keep your bench clean, wear gloves, use sterile tubes and filter pipet tips
- Include a no-template control and positive control in parallel.
- Thaw and keep reagents on ice
- Mix well before use.
- The longer the amplicon, the longer the extension time: Use 15 sec/kb extension.
- Use 90 sec extension for multiplexing
- Run an annealing temperature gradient from 55 °C to 65 °C to choose the best specificity conditions. Do not use fast cycling for multiplexing.
- ALLin™ Red Taq Mastermix, 2X is premixed with red dye and density reagents for direct loading on the gels after the PCR. In a 2% agarose TAE gel the dye migrates with~350 bp DNA, in 1% agarose TAE gel with ~ 600 bp DNA fragments

step by step for E.coli:


- Prepare a PCR master mix (always prepare at least 10 % more, use the excel sheet by Sophia to calculate)
- 20 μl would be good, Fabian suggested 5 μl
Mix gently, avoid bubbles.
- Aliquote the 22.5 μl of PCR master mix into each PCR tube
- Add 2.5 μl of the resuspended colony or overnight culture

Do not forget the negative control!

- Close tube
- Perform the PCR using Thermocycler as follow:

Initial denaturation	1 cycle	95°C	60s
Denaturation	30-40 cycles	95°C	15s
Annealing	30-40 cycles	55-65°C	15s
Extension	30-40 cycles	72°C	15-90s
Final extension	1 cycle	72°C	5 min

- Store probes for short time on ice, for long at -20°C
- Load probes on the agarose gel e.g. 10 μl (so in case you have enough left for another round).

step by step for yeast: - If resuspended colonies are to be used: pipette 50 μl of a 0.02 M NaOH solution into each of a set of appropriately labelled PCR tubes or wells of a PCR plate. Using sterile pipette tips or toothpicks, transfer transformants to individual tubes/wells. The amount of cells resuspended must just be visible. Resuspend cells by pipetting or vortexing and incubate for ≥ 5 min at 37 °C.
If overnight cultures are to be used: pipette 40 μl of a 0.1 M NaOH solution into each of a set of appropriately labelled PCR tubes or wells of a PCR plate. Transfer 10 μl of each overnight culture to be tested to the appropriate tube/well and mix by pipetting up and down. Incubate for ≥ 5 min at 37 °C.
- Prepare a PCR master mix (always prepare at least 10% more, use the excel sheet to calculate) - Aliquot 22.5 μl of PCR master mix into each PCR tube.
- Add 2.5 μl of the resuspended colony or overnight culture mixed with NaOH to the appropriate PCR tube.
- Close the tubes
- Perform the PCR using the following cycling profle:

Initial denaturation	1 cycle	95°C	60s
Denaturation	30-40 cycles	95°C	15s
Annealing	30-40 cycles	55-65°C	15s
Extension	30-40 cycles	72°C	15-90s
Final extension	1 cycle	72°C	5 min

- Load probes on the agarose gel
- Store probes for short time on ice, for long at -20°C

Protocol is following!

What is it ? – standard lab procedure for separating DNA by size (e.g., length in base pairs) for visualization and purification
– uses an electrical field to move the negatively charged DNA through an agarose gel matrix toward a positive electrode
- Shorter DNA fragments migrate through the gel more quickly than longer ones

Why are we doing it ?
– to determine the approximate length of a DNA fragment by running it on an agarose gel alongside a DNA ladder (a collection of DNA fragments of known lengths)

Protocol :
- Pouring a Standard 1% Agarose Gel:


- Microwave for 1-3 min until the agarose is completely dissolved (but do not overboil the solution, as some of the buffer will evaporate and thus alter the final percentage of agarose in the gel. Many people prefer to microwave in pulses, swirling the flask occasionally as the solution heats up.).


Pouring of the gel
- Let agarose solution cool down to about 50°C (about when you can comfortably keep your hand on the flask), about 5 mins.

- Add ethidium bromide (EtBr) to a final concentration of approximately 0.2-0.5 μg/mL (usually about 2-3 μl of lab stock solution per 100 mL gel). EtBr binds to the DNA and allows you to visualize the DNA under ultraviolet (UV) light.

- Pour the agarose into a gel tray with the well comb in place.
- Let the newly poured gel sit at room temperature for 20-30 mins, until it has completely solidified.


Loading Samples and Running an Agarose Gel:

- Add loading buffer to each of your digest samples.
Note: Loading buffer serves two purposes: 1) it provides a visible dye that helps with gel loading and will also allows you to gauge how far the gel has run while you are running your gel; and 2) it contains a high percentage of glycerol, so it increases the density of your DNA sample causing it settle to the bottom of the gel well, instead of diffusing in the buffer. 2. Once solidified, place the agarose gel into the gel box (electrophoresis unit). 3. Fill gel box with 1xTAE (or TBE) until the gel is covered. 4. Carefully load a molecular weight ladder into the first lane of the gel. Note: When loading the sample in the well, maintain positive pressure on the sample to prevent bubbles or buffer from entering the tip. Place the very top of the tip of the pipette into the buffer just above the well. Very slowly and steadily, push the sample out and watch as the sample fills the well. After all of the sample is unloaded, push the pipettor to the second stop and carefully raising the pipette straight out of the buffer. 5. Carefully load your samples into the additional wells of the gel. 6. Run the gel at 80-150 V until the dye line is approximately 75-80% of the way down the gel. Note: Black is negative, red is positive. (The DNA is negatively charged and will run towards the positive electrode.) Always Run to Red. Note: A typical run time is about 1-1.5 hours, depending on the gel concentration and voltage. 7. Turn OFF power, disconnect the electrodes from the power source, and then carefully remove the gel from the gel box. 8. Using any device that has UV light, visualize your DNA fragments. Note: Fabian or Lena will give you a short introduction on how to work with UV light !!! Note: When using UV light, protect your skin by wearing safety goggles or a face shield, gloves and a lab coat. Note: If you will be purifying the DNA for later use, use long-wavelength UV and expose for as little time as possible to minimize damage to the DNA. Note: The fragments of DNA are usually referred to as ‘bands’ due to their appearance on the gel. Analyzing Your Gel: Using the DNA ladder in the first lane as a guide (the manufacturer's instruction will tell you the size of each band), you can interpret the bands that you get in your sample lanes to determine if the resulting DNA bands that you see are as expected or not. For more details on doing diagnostic digests and how to interpret them please see the Diagnostic Digest page. Purifying DNA from Your Gel: If you are conducting certain procedures, such as molecular cloning, you will need to purify the DNA away from the agarose gel. For instructions on how to do this, visit the Gel Purification page

What is the PCR ? Method to make multiple copies of a the specific DNA-sequence Protocol for PCR with Q5 High- Fidelity 2x Master Mix Please note that protocols with Q5 High-Fidelity DNA Polymerase may differ from protocols with other polymerases. Conditions recommended below should be used for optimal performance. Reaction Setup: – assemble all reaction components on ice, work on ice while assembling – preheat the thermocycler to the denaturation temperature( 98 °C) – prior to use all components should be mixed – work quickly when transferring the reactions to a thermocycler 1. on ice Assemble all components for the reaction : Component 25 μl Reaction 50 μl Reaction Final Concentration Q5 High-Fidelity 2X Master Mix 12.5 μl 25 μl 1X 10 μM Forward Primer 1.25 μl 2.5 μl 0.5 μM 10 μM Reverse Primer 1.25 μl 2.5 μl 0.5 μM Template DNA variable variable < 1,000 ng Nuclease-Free Water to 25 μl to 50 μl Notes: Two Primers have to be diluted 1:10 ! Notes: Gently mix the reaction. Collect all liquid to the bottom of the tube by a quick spin if necessary. Overlay the sample with mineral oil if using a PCR machine without a heated lid. 2. Transfer PCR tubes to a PCR machine and begin thermocycling. Steps of PCR: 1.Denaturation : double- stranded template DNA is heated to separate it into two single stands 2. Annealing : temperature is lowered to enable the DNA primers to attach to the template DNA 3. Extending : temperature is raised and the new strand of DNA is made by the polymerases Thermocycling Conditions for a Routine PCR: STEP TEMP TIME Initial Denaturation 98°C 30 seconds 25–35 Cycles 98°C 5–10 seconds *50–72°C 10–30 seconds 72°C 20–30 seconds /kb Final Extension 72°C 2 minutes Hold 4–10°C hold is not necessary 1. Template: Use of high quality, purified DNA templates greatly enhances the success of PCR. Recommended amounts of DNA template for a 50 μl reaction are as follows: DNA AMOUNT DNA Genomic 1 ng–1 μg Plasmid or Viral 1 pg–1 ng 2. Primers: Oligonucleotide primers are generally 20–40 nucleotides in length and ideally have a GC content of 40–60%. Computer programs such as Primer3 can be used to design or analyze primers. The best results are typically seen when using each primer at a final concentration of 0.5 μM in the reaction. 3. Mg ++ and additives: The Q5 High-Fidelity Master Mix contains 2.0 mM Mg ++ when used at a 1X concentration. This is optimal for most PCR products generated with this master mix. 4. Deoxynucleotides: The final concentration of dNTPs is 200 μM of each deoxynucleotide in the 1X Q5 High- Fidelity Master Mix. Q5 High-Fidelity DNA Polymerase cannot incorporate dUTP and is not recommended for use with uracil-containing primers or templates. 5. Q5 High-Fidelity DNA Polymerase concentration: The concentration of Q5 High-Fidelity DNA Polymerase in the Q5 High-Fidelity 2X Master Mix has been optimized for best results under a wide range of conditions. 6. Denaturation: An initial denaturation of 30 seconds at 98°C is sufficient for most amplicons from pure DNA templates. Longer denaturation times can be used (up to 3 minutes) for templates that require it. During thermocycling, the denaturation step should be kept to a minimum. Typically, a 5–10 second denaturation at 98°C is recommended for most templates. 7. Annealing: Optimal annealing temperatures for Q5 High-Fidelity DNA Polymerase tend to be higher than for other PCR polymerases. The NEB T m Calculator should be used to determine the annealing temperature when using this enzyme. Typically use a 10–30 second annealing step at 3°C above the T m of the lower T m primer. A temperature gradient can also be used to optimize the annealing temperature for each primer pair. For high T m primer pairs, two-step cycling without a separate annealing step can be used (see note 10). 8. Extension: The recommended extension temperature is 72°C. Extension times are generally 20–30 seconds per kb for complex, genomic samples, but can be reduced to 10 seconds per kb for simple templates (plasmid, E. coli , etc.) or complex templates < 1 kb. Extension time can be increased to 40 seconds per kb for cDNA or long, complex templates, if necessary. A final extension of 2 minutes at 72°C is recommended. 9. Cycle number: Generally, 25–35 cycles yield sufficient product. For genomic amplicons, 30-35 cycles are recommended. 10. 2-step PCR: When primers with annealing temperatures ≥ 72°C are used, a 2-step thermocycling protocol (combining annealing and extension into one step) is possible. 11. Amplification of long products: When amplifying products > 6 kb, it is often helpful to increase the extension time to 40–50 seconds/kb. 12. PCR product: The PCR products generated using Q5 High-Fidelity 2X Master Mix have blunt ends. If cloning is the next step, then blunt-end cloning is recommended. If T/A-cloning is preferred, the DNA should be purified prior to A-addition, as Q5 High-Fidelity DNA Polymerase will degrade any overhangs generated. Addition of an untemplated -dA can be done with Taq DNA Polymerase ( NEB #M0267 ) or Klenow exo – ( NEB #M0212 )

Protocol is following!

Protocol is following!

Protocol is following!

Protocol is following!

Protocol is following!

Protocol is following!