Part 1: Benchling & In-silico Gel Art

See the Gel Art: Restriction Digests and Gel Electrophoresis protocol for details. Overview:

• [ ] Make a free account at benchling.com
• [ ] Import the Lambda DNA.

• [ ] Simulate Restriction Enzyme Digestion with the following Enzymes: EcoRI, HindIII, BamHI, KpnI, EcoRV, SacI, SalI

• [ ] Create a pattern/image in the style of Paul Vanouse’s Latent Figure Protocol artworks.

In order to create a pattern or image I decided to try the digestion with additional enzymes, not only those assigned in the homework. For that, I decided to try out AbaSI, BbvI and ApoI. Also, I decided to try combinations of digestion enzymes, to see the new patterns that can be created. For example, I tried out EcoRI+KpnI.

From the different restriction enzymes I tried out I chose the combination of EcoRI+KpnI and ApoI. The pattern that was created with these digestions resembles a trident.

Part 3: DNA Design Challenge

3.1.     Choose your protein.

In recitation, we discussed that you will pick a protein for your homework that you find interesting. Which protein have you chosen and why? Using one of the tools described in recitation (NCBI, UniProt, google), obtain the protein sequence for the protein you chose.

For this assignment, I chose the Parasporin-1 protein because of its unique characteristics. This protein comes from Bacillus thuringensis; it was initially described as a Cry protein, part of the group of toxins that act as insecticides. After studying its structure and properties, it was discovered that some of the Cry proteins had cytocidal activities against human cancer cells and were renamed as parasporins. I was able to obtain the protein sequence from NCBI.

Parasporin 1 like protein: Amino acid sequence

MDPFSNYSEQKYPDSNNNQELTVESSSFYSNTTNENAKNYHPIEQDILKFTNQEFSDNPYQHSDVSNSYE
NKKKEIINIDLPYNTNDINSMRNTLCRDLPPETNMSIYDNLRSTVTVPSFSNQFDPIKFLHDIEIAIQTG
SFSALTQSNMNQGGTDINPMLISAFFKVAGSLLPFPLSSLGALASFYVTDSQTGAMANLWRQMVDYVEKR
IDSKILDYHNFIMGAELAALNASLKEYARVVKIFENDMNRIAEPPSTGVITQFRILHDNFIKYIAKLQFS
TNQSDLQYPVLTLPLRAQACVMHLMLLKDATTSVWGQQIDSQQLNGYKAELIRLIKVYTNDVNTTYNQGL
ELEKAKPLNYSDPEEYLQAGRPDISVLRSNFREVMKWNKVAKYKRGMAMSALSLAALFPTFGPNYPKQAL
KVVQSRQIFAPVIGIPGGITSQDHSGTFGSMRFDVKTYDQIDALRRLMELYIQPLKSAYFYIYESDWKVR
ATYVNDYIGKRGSNTGLAWGMWSSDPSVIYTSALGAAGYAPNVVGVRYSHGGSYTKGMAPPNTNAYAPFE
FKYPGYKLHSVSAYGLSKAPDAADSVMFGFRPVLLENEANQLLTDTALQIPAEIGITDVVPAFGRTEEPI
NGQDAIILKKITRGPIPGGSTDCSPWELTHGMCEIDPGPPVPPGPPVPLPHRINYTINSPESGKEYTIWY
RLASNQNSLIALQHRISQYDTNISNTQQDTNSVKGNYGYYTLIKGPTLVLFKGENIISLGMLSGEIALDS
IIFSPVS

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