Week 2 Lab: DNA Gel Art

Part 1. Benchling & In-silico Gel Art

This week’s lab followed the protocol detailed in “Gel Art: Restriction Digests and Gel Electrophoresis”. The first step was to make a free account at benchling.com and import the Lambda DNA as seen in [Figure 1] below.

Figure 1. Imported the Lambda DNA.

The next step was to simulate restriction enzyme digestion with the following enzymes:

EcoRI
HindIII
BamHI
KpnI
EcoRV
SacI
SalI

Figure 2 shows the virtual digest with EcoRI and Figure 3 shows the virtual digest with all the enzymes mentioned above.

Figure 2. EcoRI virtual digest.

Figure 3. Full virtual digest.

The last step was to create a pattern/image in the style of Paul Vanouse’s Latent Figure Protocol artworks. For this I used Ronan’s website which was a helpful tool to iterate designs, especially since the physical lab experiment could not be carried out due to lab and equipment restrictions.

This was my original idea to make a penguin:

Figure 4. Pixel penguin sketch.

The result using Ronan’s website:

Figure 5. Attempt at designing a penguin in the style of latent Figure Protocol.

These are the gel restriction digest per row:

Figure 6. Tables of restriction enzymes used per row and per layer.

Part 4: Prepare a Twist DNA Synthesis Order

After creating my Twist and Benchling account, I built my DNA insert sequence to make MnSOD (see [Figure 7,8]). I went through each piece of the DNA sequence and annotated the parts and finally got a Linear Map of the entire sequence [Figure 9]. Then on Twist, I imported the sequence by uploading the FASTA file from Benchling. Since the order is for a clonal gene, I had to then select a cloning vector like pTwist Amp High Copy. I then proceeded to download construct (GenBank) to get the full plasmid sequence and imported this to Benchling to see the plasmid with the expression cassette [Figure 10].

Figure 7. Annotations for MnSOD.