Week 2 HW: DNA read-write-edit

Part 1: Gel Electrophoresis

Due to no access to equipment and space for gel electrophoresis I simulated the same to understand the process on https://www.labxchange.org/library/items/lb:LabXchange:9548bee3:lx_simulation:1?fullscreen=true

Workflow Design plasmid DNA with protein of interest →Transform bacteria with plasmid DNA→Get many copies of plasmid DNA→introduction of plasmid DNA to cells

Working in Benchling

After signing in I imported it into Benching and ran digests for EcoRI HindIII BamHI KpnI EcoRV SacI SalI

And then ran digests on SalI SacI BamHI KpnI EcoRV BamHI KpnI SacI SalI

to create an Elephant! 🐘

For this, I referred to an iGem video to understand how enzyme digesting works as well https://www.youtube.com/watch?v=7cGev-SKLao

DNA design challenge

Chosen protein : Actin

tr|D3BD07|D3BD07_HETP5 Actin OS=Heterostelium pallidum (strain ATCC 26659 / Pp 5 / PN500) OX=670386 GN=act10 PE=3 SV=1 MEGEDVQALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHTGVMVGMGQKDSYVGDEAQ SKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKM TQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVSHTVPIYEGYALPHAILRLD LAGRDLTDYMMKILTERGYSFTTTAEREIVRDIKEKLAYVALDFENEMQTAASSSALEKS YELPDGQVITIGNERFRCPEALFQPSFLGMESAGIHETTYNSIMKCDVDIRKDLYGNVVL SGGTTMFPGIADRMQKELTALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISK EEYDESGPSIVHRKCF

Reverse translated

ATGGAAGGCGACGTTCAAGCGCTGGTGATCGACAATGGTTCTGGCATGTAAAGCGGGTTTCGCAGGCGACGACGCACCGCGCGCGCGCGTTCTTTCCTTCGATTGTGCGCCGTCGCCGTCATACCGGCGTGATGGTTGTGGGGATGCAGCAAGAGGACTCCTACGTGGGCGACGAGGCGCAGTCGAAAGGTGGGATCCTGACCCTGAAGTACCCGATCGAACACGGGATTGGTGACTAACAATGGGACGATATGAAGGAAATCTGGCACCACACGTTCTTATAACGAATTAAGAGTGGCGCCGGAAGAACCAGTTCCTGTGCTGCTGACCGAGGCGCCGCTGAACCCGAAAGCCAACCGTGAAGAAATGAAGACCAGGATTATGTTTGAACCTTTC AACACGCCGGCGATGTATGTGGCGATTCAAGCGGTGTTGTCGCTGTATGCCTCGGGTCGTACCACC GGTATTGTGATGGATTCTGGCGACGGCGTGTCCCATACGGTGCCCATCTATGAAGGTTATGCCTTACCGCACCGCATCCTCCGCCTGGATCTGGCGGGTCGCGATCTGACTGAC TATATGATGAAGATCCTGACTGAACGTGGTTATTCGTTTACGACCACCGCCGAAAGGGAaatcgtcgacatc aaagagaagctggcgtatgtggcacttgatttcgagaacgagatgcaaacggcggcgTCGTCGTCGTCGCGTTGAA AAGTCG TATGAACTGCCG GACGGCCAGGTCATCACTATCGGTAACGAACGTTTC CGCTGCCCTGCGCTTTCAACCGTCGTTCTTAGGCATGGAAAGCGCGGGCA TACACGAAACCACGTACAACAGCATTATGAAATGC GATGTCGACATT CGCAAGGATCTGTATGGTAACGTGGTCCTGGGCGGCACCACGATGTTCCCGGGCATCGCCGAACG CATGCAAGAAACTGACCACCGCGCTGGCGCCGTCGACCATGAAAATCAAGATCATTGCCGCGCCGGAACGTAAGTCTTGGGTCATCGGCGGC TCGTTGGCCTCGTCGACCTTC CAGCAGATG TGGATCAGCAAAGAAGAG TATGACGAAAGCGGTCCTTCGGTGATCCACCGTAAGTTCTTCGCGAAACCGCAAGATTAA

optimized codon sequence

Optimized DNA Sequence (1122 bp)

atggaaggcgatgtccaggcgctggtgatcgacaacggctccggcatgaaggccggcttcgccggcgatgatgcccccagggcggcggtgtcttcccctcgatcgtgggccgtccgcgtcacaccggtgtgatggtggtgggtatgcagcagaaagattcctatgtgggcgacgaagcgcaatcgaaagggcatcctgaccctgaagtatccgatcgagcatggcatcgtgaacaactgggacatggagaagatctggcaccacatgttctacaacgagctgcgtgtggcgccggaagaaccccacgtgctgctgaccgaggcgccgctgaacccgaaggccaaccgtgaacgcaagatgaagaccaggatcatgatgttcgaacagttcaacacgccggcgatgtatgtggcgattcaagcggtgctgtcgctgtatgcctcgggccgtaccaccggcatcgtgatggactccggcgatggcgtttcccacatcgtgcccatctatgaaggctatgcgctgccgcatgccatcctgcgcctggatctggcgggcagggatctgaccgactacatgatgaagatcctgaccgaacgcggttatagcttcaccaccaccgcggagaagatcgtccgggacatcaagaagaaactggcgtatgtggcgctcgatttcgaaaacgaaatgcaagcgaccgcgagctcgagcgccctggagaagtcgtatgagctgccggacggccaggtgatcaccatcggcaacgaacgcttccgttgccctgccgctgttccagccctcgttcggcatggagagcgccggcatccatgagaccacctacaacagcatcatgaagacctgcgatgtggacatccgcaaggacctgtatggcaacgtggtgctcggcggcaccaccatgttccccggcatcgccgacaggatgcaaaaggagctgaccgccgcgctgccgcccagcaccatgaagatcaagatcatcgcgccgccggagcgtaagtcgtgggtgatcggcggctcgctggcgagcctgagcacgttccagcagatgtggatcagcaaggaggaatacgacgagtcgggcccgagcatcgtgcaccgcaagtgcttcggcaagcgcaagatgaa