Week 2: DNA Read, Write, and Edit

Benchling Gel Art

DNA Design Challenge

When looking into proteins to explore further, I chose to focus on proteins related to the structure of diatom silica walls. These proteins would be exciting to understand to get a better picture of how diatoms would form the lacy micropatterns for the rubble-diatom material proposal for the final project. While there are a few different proteins key to the biosilica formation, and silaffins drive the lacy patterns and micropore structure.

In the NCBI database chose: silaffin protein (Thalassiosira pseudonana CCMP1335)

Silaffin from Uniprot

MKVTTSIITLLFASCGAADVQRVLEDVTEPAVTTPAATPAPITPEPATPAPTICEGRNFY RDDDTGKCSNEATGGIYGTLIECCVAISGSDSCPYVDICNTLQPSPSPETNEPSAKPITA APISSAPVSAAPVTSAPVAAPVETTSMTGPTTIVASIVSTNAPSSTNAPSSSLEAVVTRI PVETTNTASPTTTAASIVSTNAPSSSPEAVVTPRPTFRPSPKGTESNTFPASIASDVMFD PARSEPTFTPTSSSQPSSSEPTLSPSVSKEPTRYPTSSPSHSPTKSPSKSPSSSPTTSPS ASPTETPTETPTESPTELPTLSPTEFPSLSPTLSPTWSPTGYPTLAPSPSPSISSAPSVS SAPSSSPSISSAPSVSSAPSKNFGFLPGRNEMPTISPTEDHYFFGKSHKSHKSKATKTLK VSKSGKSSKSSKSSGSRPLFGVSQLSEGIAAGYAKSSGRSSQQAVGSWMPVAAACILGAL SFFLN

Reverse Translate Protein to DNA sequence

atgaaagtgaccaccagcattattaccctgctgtttgcgagctgcggcgcggcggatgtgcagcgcgtgctggaagatgtgaccgaaccggcggtgaccaccccggcggcgaccccggcgccgattaccccggaaccggcgaccccggcgccgaccatttgcgaaggccgcaacttttatcgcgatgatgataccggcaaatgcagcaacgaagcgaccggcggcatttatggcaccctgattgaatgctgcgtggcgattagcggcagcgatagctgcccgtatgtggatatttgcaacaccctgcagccgagcccgagcccggaaaccaacgaaccgagcgcgaaaccgattaccgcggcgccgattagcagcgcgccggtgagcgcggcgccggtgaccagcgcgccggtggcggcgccggtggaaaccaccagcatgaccggcccgaccaccattgtggcgagcattgtgagcaccaacgcgccgagcagcaccaacgcgccgagcagcagcctggaagcggtggtgacccgcattccggtggaaaccaccaacaccgcgagcccgaccaccaccgcggcgagcattgtgagcaccaacgcgccgagcagcagcccggaagcggtggtgaccccgcgcccgacctttcgcccgagcccgaaaggcaccgaaagcaacacctttccggcgagcattgcgagcgatgtgatgtttgatccggcgcgcagcgaaccgacctttaccccgaccagcagcagccagccgagcagcagcgaaccgaccctgagcccgagcgtgagcaaagaaccgacccgctatccgaccagcagcccgagccatagcccgaccaaaagcccgagcaaaagcccgagcagcagcccgaccaccagcccgagcgcgagcccgaccgaaaccccgaccgaaaccccgaccgaaagcccgaccgaactgccgaccctgagcccgaccgaatttccgagcctgagcccgaccctgagcccgacctggagcccgaccggctatccgaccctggcgccgagcccgagcccgagcattagcagcgcgccgagcgtgagcagcgcgccgagcagcagcccgagcattagcagcgcgccgagcgtgagcagcgcgccgagcaaaaactttggctttctgccgggccgcaacgaaatgccgaccattagcccgaccgaagatcattatttttttggcaaaagccataaaagccataaaagcaaagcgaccaaaaccctgaaagtgagcaaaagcggcaaaagcagcaaaagcagcaaaagcagcggcagccgcccgctgtttggcgtgagccagctgagcgaaggcattgcggcgggctatgcgaaaagcagcggccgcagcagccagcaggcggtgggcagctggatgccggtggcggcggcgtgcattctgggcgcgctgagcttttttctgaac

reverse translation into a base sequence of most likely codons from https://www.bioinformatics.org/sms2/rev_trans.html