Week 2/Part-1 HW: DNA Write, Read, and Edit

Part 0: Basics of Gel Electrophoresis

  • Watch all lecture and recitation videos.
    • Optionally watch bootcamp

Part 1: Benchling & In-silico Gel Art

See the Gel Art: Restriction Digests and Gel Electrophoresis protocol for details.

Overview:

  • Make a free account at benchling.com
  • Import the Lambda DNA.
  • Simulate Restriction Enzyme Digestion with the following Enzymes:
    • EcoRI
    • HindIII
    • BamHI
    • KpnI
    • EcoRV
    • SacI
    • SalI
  • Create a pattern/image in the style of Paul Vanouse’s Latent Figure Protocol artworks. You might find Ronan’s website a helpful tool for quickly iterating on designs!

Import Lambda DNA to Benchling site Import Lambda DNA to Benchling site Fig. 1 Import Lambda DNA Sequence

On the left-hand side of the website display when you access benchling.com and create an account, choose create tabs (symbolized as: +) → choose DNA/RNA sequence → Import DNA/RNA sequence, then, you can upload any DNA files that you have downloaded from database (NCBI or Genbank in FASTA format etc) → choose nucleotide type, drag and drop files to upload and then done!

Digest enzyme feature Digest enzyme feature Find and run enzyme digest Find and run enzyme digest Figure 2. Selecting Enzymes

Now, on the right-hand side of the website display, choose the digest tool (symbolized with scissors) → find and choose the enzyme you want to try → click run digest

if you find a Hi-Fidelity options on the Enzyme details information, this means that this restriction enzymes have a very low probability of cutting at off-target sites.

Run virtual enzyme digest Run virtual enzyme digest Fig 3. Perform Digest

After you click run digest, the digest tab and virtual digest tab will appear. Switch the ladder to NEB 2-Log. Now you can download the visual depiction of your restriction digest of your own by clicking on the Download PNG (next to the ladder options)

Visual Depiction of your Restriction Digest Visual Depiction of your Restriction Digest Figure 4. Virtual Depiction of your Restriction Digest

This is my random trial, first timers of using benchling-things and the restrictions enzymes.