Homework #2🧬

Part 1: Benchling & In-silico *Gel Art

Overview:*

• [ ] 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.

Attempt 1

Attempt 2

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

• Protein: Escherichia coli strain 29 beta-lactamase (TEM-1)

I find this protein particularly interesting because of its crucial role in antibiotic resistance, specifically against beta-lactam antibiotics. I consider studying TEM-1 beta-lactamase to be highly relevant in epidemiology, especially for monitoring and controlling antibiotic-resistant bacterial strains. Also, since I work mostly with E. coli, I am especially interested in how this resistance mechanism works in this organism.

[NCBI FASTA] - AKO62427.1 beta-lactamase [Escherichia coli]

MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGESGNYG

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

The Central Dogma discussed in class and recitation describes the process in which DNA sequence becomes transcribed and translated into protein. The Central Dogma gives us the framework to work backward from a given protein sequence and infer the DNA sequence that the protein is derived from. Using one of the tools discussed in class, NCBI or online tools (google “reverse translation tools”), determine the nucleotide sequence that corresponds to the protein sequence you chose above.

• Tool: Reverse translate Gene Corner https://www.genecorner.ugent.be/rev_trans.html

Escherichia coli strain 29 beta-lactamase (TEM-1) gene

atgagcattcagcattttcgcgtggcgctgattccgttttttgcggcgttttgcctgccggtgtttgcgcatccggaaaccctggtgaaagtgaaagatgcggaagatcagctgggcgcgcgcgtgggctatattgaactggatctgaacagcggcaaaattctggaaagctttcgcccggaagaacgctttccgatgatgagcacctttaaagtgctgctgtgcggcgcggtgctgagccgcgtggatgcgggccaggaacagctgggccgccgcattcattatagccagaacgatctggtggaatatagcccggtgaccgaaaaacatctgaccgatggcatgaccgtgcgcgaactgtgcagcgcggcgattaccatgagcgataacaccgcggcgaacctgctgctgaccaccattggcggcccgaaagaactgaccgcgtttctgcataacatgggcgatcatgtgacccgcctggatcgctgggaaccggaactgaacgaagcgattccgaacgatgaacgcgataccaccatgccggcggcgatggcgaccaccctgcgcaaactgctgaccggcgaactgctgaccctggcgagccgccagcagctgattgattggatggaagcggataaagtggcgggcccgctgctgcgcagcgcgctgccggcgggctggtttattgcggataaaagcggcgcgggcgaacgcggcagccgcggcattattgcggcgctgggcccggatggcaaaccgagccgcattgtggtgatttataccaccggcgaaagcggcaactatggc

3.3. Codon optimization.

Once the nucleotide sequence of your protein is determined, you need to codon optimize your sequence. You may, once again, utilize Google for a “codon optimization tool”.

• Tool: Codon Optimization IDT https://www.idtdna.com/CodonOpt

ATG TCA ATA CAA CAC TTC CGG GTG GCG CTT ATC CCA TTC TTT GCG GCG TTT TGC CTT CCT GTG TTT GCA CAT CCA GAG ACG TTA GTT AAG GTC AAA GAT GCA GAG GAT CAA CTT GGT GCT CGG GTC GGC TAC ATT GAG CTT GAC TTA AAC TCC GGT AAA ATT TTG GAG TCA TTT AGA CCC GAG GAA CGC TTC CCC ATG ATG TCA ACC TTT AAA GTC CTT TTG TGC GGA GCT GTG CTG AGC CGT GTT GAT GCA GGT CAG GAA CAG TTA GGT AGA CGT ATC CAT TAC TCA CAG AAC GAC CTG GTG GAA TAC TCG CCA GTT ACT GAA AAA CAT CTG ACG GAT GGG ATG ACG GTT CGT GAA TTA TGC TCT GCT GCA ATA ACC ATG TCA GAT AAT ACC GCT GCG AAT TTG TTG TTA ACA ACT ATT GGG GGG CCA AAA GAG TTG ACG GCG TTT TTG CAT AAT ATG GGC GAT CAT GTT ACT CGT CTT GAT CGC TGG GAG CCC GAA CTG AAT GAA GCT ATC CCC AAC GAT GAG AGA GAT ACT ACC ATG CCG GCC GCA ATG GCA ACG ACC TTA AGA AAG TTG TTG ACC GGG GAG TTA CTT ACG TTA GCT TCC CGG CAA CAA TTA ATC GAC TGG ATG GAA GCG GAT AAA GTG GCC GGG CCG CTG TTG CGT TCG GCT TTA CCG GCA GGA TGG TTC ATC GCA GAT AAG TCA GGC GCA GGA GAG CGG GGA TCA AGA GGG ATC ATC GCA GCC TTA GGA CCT GAC GGC AAA CCG AGC AGA ATA GTG GTG ATC TAC ACG ACC GGG GAG AGC GGG AAT TAT GGC