1. Gel electrophoresis is a method to analyze DNA fragments by size using an electric current to separate fragments in an agarose or polyacrylamide gel. 2. Verifying a cloning project with virtual gel electrophoresis involves digesting the cloning vector and insert with restriction enzymes, simulating the fragments in a gel, and comparing to expected fragment sizes. 3. The steps are to open the cloning project sequence, run an in silico restriction digest using selected enzymes, view the predicted fragment sizes, and run a gel simulation to visualize fragment migration in the virtual gel.

1. Verifying Your Cloning Project
Virtual Gel Electrophoresis

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A short guide for Virtual Gel Digest and Gel Simulation
GEL ELECTROPHORESIS
An analysis method that indicates the relative sizes of fragments, useful for
restriction mapping and analyzing PCR fragments

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Gel Electrophoresis
An electric current is applied to charged particles in a gel of agar or
polyacrylamide.
The electric field created in the gel causes the
negative DNA to move to the positive electrode.
Large molecules move more slowly through
the gel while small molecules more quickly.
This is caused by the sieving effect that lets
small fragments easily move through the
pores of the gel.

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A short guide for the Restriction Ligation Cloning Method
The Cloning Strategy
1. DNA target isolation by Restriction Enzyme digest and PCR
2. Restriction Enzyme digest of a cloning vector
3. Ligation of the DNA of interest and the cloning vector
4. Transformation with the ligation products
5. Growth on agar plates with selection for antibiotic resistance
6. Isolation of desired DNA clone
7. Verification of the cloning process (with virtual gel experiment)

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How to verify cloning with Genome Compiler
In order to verify a cloning procedure, all you have to do is 5 simple steps:
1. Open your Cloning Project sequence
2. Open the Digest tool
3. Set parameters and Run Digest
4. View Digest Results table
5. Run Gel Simulation and Save Gel image
It’s that simple! Let’s go through the steps…

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1. Open your cloning project sequence
• Start by opening your cloned vector (generated via one of Genome
Compiler’s cloning wizards or a vector you already prepared – see this
step by step course)
• The materials for the practice:
 pcDNA3.1 C-HA plus Gene A - cloned using the
restriction ligation wizard in Genome Compiler.
The folder can be opened from the
Sample Projects folder, inside the
Materials Box:

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2. Open the Digest tool
Open Genome
Compiler’s
Digest tool from
the tool bar

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3. Set Parameters and Run Digest
• Change the preset along the top to “All”
• Select the restriction sites to use in
your analysis.
• Use the filters to help refine your search.
• For this example, select BlpI and AflII
• Then select Run Digest

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4. View Digest Results Table
• View the fragments generated from
digestion with your selected enzymes
• Select them in the table to see them
• From here you can also change the
project topology and initiate the
virtual gel simulation (marked in
green)

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Adjust Ladder
• There are multiple options of ladders on
which to run your gel
If there are any fragments that fall outside of the
ladder limits, a warning message will appear.
Use this information to choose the correct ladder for your project
Don’t see your ladder? just contact us and we will add it!
• You have the option to save this virtual gel as a picture on your
computer that you can later use as a template to check your
physical gel electrophoresis

11. Learn more about Genome Compiler
www.genomecompiler.com