Team:Bilkent UNAM Turkey/Experiment

We ordered our genes. We optimized codon usage because of gene taken from Enterobacter cloacae. Codon Usage . We optimized our NFSI gene according to C.reinhardtii codon bias table provided by DNA 2.0. This program enables to change synonymous codons without changing amino acid sequence. You can also check the restriction sites while optimizing codons. We also avoided from forbidden restriction sites (EcoRI, XbaI, SpeI, PstI) therefore; we have chosen second frequently used codons for 34., 35., 38. and 45. amino acids. Then we did restriction digestion and gel electrophoresis.
We repeated this step a lot because of failuire.I put right result







We used standard gel purification kit Our ligation style is really similar to iGEM's one.
Our one;

insert volume(µl):X

Cut Vector Volume(µl):X

DEPC-water(µl):8,5-2X

T4 DNA ligase(µl):0,5

Ligation Buffer(µl):1

Total Volume(µl):10

We transformed our plasmid into E.coli with a protocol.
We used invitrogen purification kit to get our plasmid. We sent genes to sequencing and sequencing data should be available on their link. Polymerase Chain Reaction of GFP from pKScGFP For 1.0µl of DNA we added, • 1.0µl of forward primer • 1.0µl of reverse primer • 2.5µl of 10X PCR Buffer • 0.5µl of MgSO4 • 0.5µl of dNTP mix • 18.375µl of ddH2O • 0.125µl of Taq polymerase Parameters in thermal cycler were chosen as below: Denaturation is 95oC for 4min Annealing is 30 cycles: • 95oC 1min • 65oC 1min • 72oC 2min Extension 72oC for 10min 4oC hold GFP fusion GFP fusion with nfsI gene on our Biobrick is our plannned future work. Restriction Enzyme Digestion We obtained nfsI gene synthetically with prefix and suffixes. Synthetic nfsI gene was restriction digested via XhoI/BamHI to create sticky ends at prefix and suffixes. We used pRbcRL as our backbone and as an algal expression plasmid. We restriction digested luciferase gene via XhoI/BamHI restriction enzymes and created a cut vector backbone with sticky ends. DNA ligation Then we ligated nfsI gene to the cut vector of pRbcRL (pRbc plasmid backbone) with insert:backbone ratios of 10:1, 3:1 and 1:1. All of them gave good results. For 10:1 nfsI:pRbc ligation tube, Solution Volume (µl) pRbc backbone 1.7 Insert nfsI 17.2 T4 ligase buffer (10X) 1 T4 DNA ligase 0.5 ddH2O - Total 20 For 3:1 nfsI:pRbc ligation tube, Solution Volume (µl) pRbc backbone 1.7 Insert nfsI 5.2 T4 ligase buffer (10X) 1 T4 DNA ligase 0.5 ddH2O 1.6 Total 10 For 1:1 nfsI:pRbc ligation tube, Solution Volume (µl) pRbc backbone 1.7 Insert nfsI 1.7 T4 ligase buffer (10X) 1 T4 DNA ligase 0.5 ddH2O 5.1 Total 10