Week 2 HW: DNA read, write and edit
Benchling and Silico Gel Art
##DNA desing challenge I chose mCherry because it is a red fluorescent protein derived from Discosoma sp. (a sea anemone). It is widely used in research as a fluorescent marker to visualize cells, proteins, and biological processes in real time under microscopy. It is stable, bright, and non-toxic to cells, making it ideal for cell biology experiments.
Protein sequence
sp|X5DSL3|MCHERRY Fluorescent protein mCherry OS=Discosoma sp. PE=1 SV=1 MVSKGEEDNMAIIKEFMRFKVHMEGSVNGHEFEIEGEGEGRPYEGTQTAKLKVTKGGPLPFAWDILSPQF MYGSKAYVKHPADIPDYLKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGEFIYKVKLRGTNFPSDGPV MQKKTMGWEASSERMYPEDGALKGEIKQRLKLKDGGHYDAEVKTTYKAKKPVQLPGAYNVNIKLDITSHN EDYTIVEQYERAEGRHSTGGMDELYK
Reverse sequence
ATGGTGAGCAAGGGCGAGGAGGATAACATGGCCATCATCAAGGAGTTCATGCGCTTCAAGGTGCACATG GAGGGCTCCGTGAACGGCCACGAGTTCGAGATCGAGGGCGAGGGCGAGGGCCGCCCCTACGAGGGCACC CAGACCGCCAAGCTGAAGGTGACCAAGGGTGGCCCCCTGCCCTTCGCCTGGGACATCCTGTCCCCTCAGT TCATGTACGGCTCCAAGGCCTACGTGAAGCACCCCGCCGACATCCCCGACTACTTGAAGCTGTCCTTCCC CGAGGGCTTCAAGTGGGAGCGCGTGATGAACTTCGAGGACGGCGGCGTGGTGACCGTGACCCAGGACTCC TCCCTGCAGGACGGCGAGTTCATCTACAAGGTGAAGCTGCGCGGCACCAACTTCCCCTCCGACGGCCCCG TAATGCAGAAGAAGACCATGGGCTGGGAGGCCTCCTCCGAGCGGATGTACCCCGAGGACGGCGCCCTGAA GGGCGAGATCAAGCAGAGGCTGAAGCTGAAGGACGGCGGCCACTACGACGCTGAGGTCAAGACCACCTAC AAGGCCAAGAAGCCCGTGCAGCTGCCCGGCGCCTACAACGTCAACATCAAGTTGGACATCACCTCCCACA ACGAGGACTACACCATCGTGGAACAGTACGAACGCGCCGAGGGCCGCCACTCCACCGGCGGCATGGACGA GCTGTACAAG
Codon optimization
Different organisms prefer different codons for the same amino acid. If mCherry’s original codons are rare in the host organism, ribosomes will produce the protein slowly or make errors. Codon optimization replaces rare codons with preferred ones for the chosen host, maximizing expression efficiency and protein yield. I chose E. coli as the expression host because it is the most common, cost-effective, and well-characterized system for protein production in laboratory settings. Using Twist Bioscience’s Codon Optimization Tool while avoiding Type IIs enzyme recognition sites BsaI, BsmBI, and BbsI, the optimized sequence is:
ATG GTT AGC AAA GGT GAA GAA GAC AAC ATG GCG ATC ATC AAA GAG TTC ATG CGC TTT AAA GTT CAT ATG GAA GGC TCG GTC AAC GGC CAC GAG TTT GAG ATC GAA GGC GAA GGC GAA GGC CGT CCG TAT GAA GGC ACG CAG ACG GCC AAA CTG AAA GTC ACC AAA GGC GGC CCG CTG CCG TTT GCG TGG GAC ATC CTG TCA CCG CAG TTC ATG TAC GGC TCC AAA GCC TAT GTC AAA CAC CCG GCA GAT ATT CCG GAT TAC CTG AAA CTG AGC TTC CCG GAA GGC TTT AAA TGG GAG CGT GTG ATG AAC TTT GAA GAT GGC GGT GTG GTG ACC GTG ACC CAG GAC AGC AGC CTG CAG GAC GGT GAG TTT ATC TAC AAA GTG AAA CTG CGT GGC ACC AAC TTC CCC TCT GAT GGC CCG GTG ATG CAG AAA AAA ACC ATG GGT TGG GAA GCC TCA TCA GAG CGC ATG TAC CCG GAA GAC GGT GCG CTG AAA GGT GAG ATC AAA CAG CGT CTG AAA CTG AAA GAC GGC GGG CAC TAT GAT GCG GAA GTG AAA ACC ACC TAC AAA GCG AAG AAG CCG GTT CAG CTG CCG GGC GCC TAC AAC GTT AAC ATC AAG CTG GAT ATC ACC AGC CAC AAC GAA GAC TAC ACC ATT GTT GAG CAG TAT GAG CGT GCT GAA GGC CGC CAC AGC ACC GGC GGT ATG GAT GAG CTG TAT AAA