Week 2 HW: DNA Read Write and Edit

Part 1

Part 2 Gel Art

Part 3

3.1. Choose your protein.

I’ve chosen Brick1 protein from Arabidopsis thaliana.

AEC07332.1 BRICK1 Arabidopsis thaliana MAKAGGITNAVNVGIAVQADWENREFISHISLNVRRLFEFLVQFESTTKSKLASLNEKLDLLERRLEMLE VQVSTATANPSLFAT

3.2. Reverse Translate: Protein (amino acid) sequence to DNA (nucleotide) sequence.

AEC07332.1 BRICK1 Arabidopsis thaliana ATGGCTAAGGCTGGGGGGATCACCAATGCGGTAAACGTTGGAATTGCAGTCCAGGCCGATTGGGAAAATAGAGAGTTCATTAGCCACATATCCCTGAATGTTCGCCGATTATTTGAATTCCTAGTACAATTTGAGTCCACAACAAAGTCGAAGCTAGCTAGCCTCAATGAGAAGCTGGACCTGTTGGAACGTCGACTCGAAATGCTGGAAGTACAGGTCTCCACTGCCACGGCGAACCCTAGTCTGTTTGCAACG

Using https://proteiniq.io/app/protein-to-dna

3.3. Codon optimization.

Original Sequence: GC=48.63%, CAI=0.65

ATGGCTAAGGCTGGGGGGATCACCAATGCGGTAAACGTTGGAATTGCAGTCCAGGCCGATTGGGAAAATAGAGAGTTCATTAGCCACATATCCCTGAATGTTCGCCGATTATTTGAATTCCTAGTACAATTTGAGTCCACAACAAAGTCGAAGCTAGCTAGCCTCAATGAGAAGCTGGACCTGTTGGAACGTCGACTCGAAATGCTGGAAGTACAGGTCTCCACTGCCACGGCGAACCCTAGTCTGTTTGCAACG

Improved DNA: GC=58.82%, CAI=0.95

ATGGCTAAGGCCGGGGGCATCACCAACGCCGTGAATGTGGGCATCGCCGTGCAGGCCGACTGGGAAAACCGGGAGTTCATCTCCCACATTTCTCTGAACGTGAGAAGACTGTTCGAGTTCCTGGTGCAGTTCGAGAGCACCACCAAGTCCAAGCTGGCAAGCCTGAACGAGAAGCTGGACCTGCTGGAGCGGAGACTGGAAATGCTGGAGGTGCAGGTGAGCACCGCCACCGCTAACCCTTCTCTGTTCGCAACC

Benchling also has a codon optimisation tool but I used the tool found on https://en.vectorbuilder.com

3.4. You have a sequence! Now what?

This protein could be overexpressed in yeast cells and then harvested by lysing the cells. I’m not sure about cell-free methods that could be used.

3.5. [Optional] How does it work in nature/biological systems?

A single gene encodes proteins as shown below. Here is the AtBRICK1 mRNA, the highlighted part is the actual part that will encode the protein. The rest are untranslated regions which carry regulatory elements amongst other things.