This is the source for 2026a-vithushan-varatharaj's HTGAA Spring 2026 pages.

Hi there, my name is Vithushan Varatharaj - I am a 1st year Biotechnology student at Imperial College London and am very interested on the applications of synthetic biology and the effects modern A.I. has on its processes!

DNA Design Challenge

1. Obtaining the amino acid sequence

Using the Uniprot website I obtained the sequence for Growth Hormone 1

https://www.uniprot.org/uniprotkb/B1A4H0/entry#sequences

The isoform P012141 has been chosen

MATGSRTSLLLAFGLLCLPWLQEGSAFPTIPLSRLFDNAMLRAHRLHQLAFDTYQEFEEAYIPKEQKYSFLQNPQTSLCFSESIPTPSNREETQQKSNLELLRISLLLIQSWLEPVQFLRSVFANSLVYGASDSNVYDLLKDLEEGIQTLMGRLEDGSPRTGQIFKQTYSKFDTNSHNDDALLKNYGLLYCFRKDMDKVETFLRIVQCRSVEGSCGF

2. Reverting to DNA Sequence

• As learnt, since amino acid codes are degenerate this is a rough sketch of what the code could be:

ATGGCTACCGGTAGCCGTACCAGCCTGCTGCTGGCTTTTGGTCTGCTGTGTCTGCCGTGG CTGCAAGAAGGTAGCGCTTTTCCGACCATTCCGCTGAGCCGTCTGTTTGATAATGCTATG CTGCGTGCTCATCGTCTGCATCAACTGGCTTTTGATACCTATCAAGAATTTGAAGAAGCT TATATTCCGAAAGAACAAGTATAGCTTTCTGCAAAATCCGCAAACCAGCCTGTGTTTTAGC GAAAGCATTCCGACCCCGAGCAATCGTGAAACCCAACAAAAAAGCAATCTGGA ACTGCTG CGTATTAGCCTGCTGCTGCTGATTCAAAGCTGGCTGGAACCGGTGCAATTTCTGCGTAGC GTTTTTGCTAACTCGCTGGTGTATGGTGCTAGCGATAGCAATGTGTATGATCTGCTGAAA GATCTGGAAGAAGGTATTCAAACCCTGATGGGT CGTCTGGAAGATGGCTCGCCGCGTACC GGTCAAATTTTTAAACAAACC TATAGCAAATTTGATACCAATAGCCATAATGATAATGCT CTGCTGAAAAATTATGGTCTGCTGTATTGTTTTCGTAAAGATATGGATAAAGTTGAAACC TTTCTGCGTATTGTGCAATGTCGTAGCGTTGAAGGTAGCTGTGGTTTTTAA

-The above codon has already been optimized for the next part*

3.3 Codon Optimization

Although multiple DNA sequences can encode the same protein due to the degeneracy of the genetic code, different organisms preferentially use certain codons over others. This phenomenon, known as codon bias, reflects differences in tRNA abundance within each species. If a gene contains codons that are rare in the host organism, ribosomes may stall during translation, leading to reduced protein yield, misfolding, or incomplete synthesis.

Therefore, codon optimization is necessary to improve translation efficiency and overall protein expression in the chosen host. Optimization involves selecting synonymous codons that are more frequently used in the target organism, balancing GC content, minimizing stable mRNA secondary structures near the ribosome binding site, and removing problematic motifs such as unwanted restriction sites or premature transcriptional signals.

I optimized the hGH coding sequence for Escherichia coli, as it is a widely used and well-characterized host for recombinant protein production. E. coli grows rapidly, is cost-effective, and is commonly used in industrial biotechnology for producing therapeutic proteins. Since codon usage in humans differs significantly from that in bacteria, optimization ensures efficient translation in the bacterial expression system and increases the likelihood of high-yield protein production.

PART 4. Building My First Plasmid

1. using my HG1 gene I uploaded thios to Benchling
2. I added annotations to the different parts of the gene