Z Biotechnology, Santa Cruz, CA) and horseradish peroxidaseconjugated goat polyclonal secondary antibodies to mouse IgG1 heavy chain (Abcam, Cambridge, UK). Chemiluminescence was detected with SuperSignal West Pico Chemiluminescent Substrate (Thermo Scientific, Rockford, IL). Absolute quantities of expressed proteins were estimated by purification of WT and mutated GFP by Ni-NTA agarose (Qiagene), concentration by Amicon Ultracentrifuge device 10 kDa MWCO (Millipore) and resolving by SDS-PAGE. Proteins of interest were visualized by Coomassie staining using SimplyBlue SafeStain (Invitrogen), the Epigenetic Reader Domain desired proteins bands were cut from the gel and eluted using Model 422 Electro-Eluter (Bio-Rad). The concentration of proteins were measured by Implen Nanophotometer (Labfish, Germany). The relative quantity of expressed proteins was analyzed by densitometry using GeneTools software (SynGene, Cambridge, UK). All of the proteins expressed using the RTS 100 E. coli HY Kit were purified according to the manufacturer’s manual using Ni-NTA Spin Columns (Qiagen, Hilden, Germany).Preparation of MjtRNACUA, tRNACUAOptcDNA copies of all the RNA molecules under regulation of the T7 promoter were obtained by annealing the following two synthetic oligonucleotides: MjtRNACUA Forward 5′?TAATACGACTCACTATACCGGCGGTAGTTCAGCAGGGCAGAACGGCGGACTCTAAATCCGCATGGCGCTGGTTCAAATCCGGCCCGCCGGACCA?’ and MjtRNACUA Reverse 5′?TGGTCCGGCGGGCCGGATTTGAACCAGCGCCATGCGGATTTAGAGTCCGCCGTTCTGCCCTGCTGAACTACCGCCGGTATAGTGAGTCGTATTA ?’; and tRNACUAOpt Forward 5′?TAATACGACTCACTATACCGGCGGTAGTTCAGCAGGGCAGAACGGCGGACTCTAAATCCGCATGGCAGGGGTTCAAATCCCCTCCGCCGGACCA?’ and tRNACUAOpt Reverse 5′ GGTCCGGCGGAGGGGATTTGAACCCCTGCCATGCGGATTTAGAGTCCGCCGTTCTGCCCTGCTGAACTACCGCCGGTATAGTGAGTCGTATTA?’. Obtained products were used for in vitro RNA transcription by TranscriptAid High Yield Transcription Kit (Fermentas, Vilnius, Lithuania). Purified RNA molecules were heated to 90uC for 2 minutes, placed on ice for 2 minutes, and folded by addition of RNA Structuring Buffer (10 mM Tris-HCl, pH 7, 0.1 M KCl, 10 mM MgCl) and kept at 37uC for 20 minutes.Preparation of M. jannaschii Tyrosyl-tRNA Synthetase and its Evolved DerivativesE. coli BL21 (DE3) cells transformed with one of the above plasmids were grown to an OD600 of 0.5?.7 in 1 L Luria-Bertani (LB) medium. Isopropyl-?D-thiogalactoside (IPTG) was added to a final concentration of 1 mM and the cells were grown for additional 4? h at 37uC. Cells were harvested at 8,000 g for 10 min at 4uC. The cell pellet was resuspended in 4 mL of lysis buffer (300 mM NaCl, 10 mM imidazole, 50 mM NaH2PO4, pH 8.0) per gram of cell paste. A cell lysate was prepared using BugBuster Protein Extraction Reagent (Novagen, Darmstadt, Germany) with addition of benzonase nuclease (Novagen) and Protease Inhibitor Cocktail Set III (Merck, Darmstadt, Germany). The lysate was centrifuged at 16,000 g at 4uC for 30 minutes. The His-tagged synthetase was then purified using Ni-NTA agarose (Qiagen). The Ni-NTA agarose beads were Autophagy washed twice with wash buffer (300 mM NaCl, 20 mM imidazole, 50 mMProteolysis and Mass SpectrometryThe trypsin cleavage sites in WT GFP were predicted 23977191 by PeptideCutter (http://web.expasy.org/peptide_cutter/). In-gel digestion of purified GFP containing UAA, was performed using Trypsin Gold (Promega, Madison, WI) according to a modified manufacturer’s procedure. Briefly, the gel bands corresponding in size to GFP were finely sliced, washed for 5 minutes with water, 15 minutes w.Z Biotechnology, Santa Cruz, CA) and horseradish peroxidaseconjugated goat polyclonal secondary antibodies to mouse IgG1 heavy chain (Abcam, Cambridge, UK). Chemiluminescence was detected with SuperSignal West Pico Chemiluminescent Substrate (Thermo Scientific, Rockford, IL). Absolute quantities of expressed proteins were estimated by purification of WT and mutated GFP by Ni-NTA agarose (Qiagene), concentration by Amicon Ultracentrifuge device 10 kDa MWCO (Millipore) and resolving by SDS-PAGE. Proteins of interest were visualized by Coomassie staining using SimplyBlue SafeStain (Invitrogen), the desired proteins bands were cut from the gel and eluted using Model 422 Electro-Eluter (Bio-Rad). The concentration of proteins were measured by Implen Nanophotometer (Labfish, Germany). The relative quantity of expressed proteins was analyzed by densitometry using GeneTools software (SynGene, Cambridge, UK). All of the proteins expressed using the RTS 100 E. coli HY Kit were purified according to the manufacturer’s manual using Ni-NTA Spin Columns (Qiagen, Hilden, Germany).Preparation of MjtRNACUA, tRNACUAOptcDNA copies of all the RNA molecules under regulation of the T7 promoter were obtained by annealing the following two synthetic oligonucleotides: MjtRNACUA Forward 5′?TAATACGACTCACTATACCGGCGGTAGTTCAGCAGGGCAGAACGGCGGACTCTAAATCCGCATGGCGCTGGTTCAAATCCGGCCCGCCGGACCA?’ and MjtRNACUA Reverse 5′?TGGTCCGGCGGGCCGGATTTGAACCAGCGCCATGCGGATTTAGAGTCCGCCGTTCTGCCCTGCTGAACTACCGCCGGTATAGTGAGTCGTATTA ?’; and tRNACUAOpt Forward 5′?TAATACGACTCACTATACCGGCGGTAGTTCAGCAGGGCAGAACGGCGGACTCTAAATCCGCATGGCAGGGGTTCAAATCCCCTCCGCCGGACCA?’ and tRNACUAOpt Reverse 5′ GGTCCGGCGGAGGGGATTTGAACCCCTGCCATGCGGATTTAGAGTCCGCCGTTCTGCCCTGCTGAACTACCGCCGGTATAGTGAGTCGTATTA?’. Obtained products were used for in vitro RNA transcription by TranscriptAid High Yield Transcription Kit (Fermentas, Vilnius, Lithuania). Purified RNA molecules were heated to 90uC for 2 minutes, placed on ice for 2 minutes, and folded by addition of RNA Structuring Buffer (10 mM Tris-HCl, pH 7, 0.1 M KCl, 10 mM MgCl) and kept at 37uC for 20 minutes.Preparation of M. jannaschii Tyrosyl-tRNA Synthetase and its Evolved DerivativesE. coli BL21 (DE3) cells transformed with one of the above plasmids were grown to an OD600 of 0.5?.7 in 1 L Luria-Bertani (LB) medium. Isopropyl-?D-thiogalactoside (IPTG) was added to a final concentration of 1 mM and the cells were grown for additional 4? h at 37uC. Cells were harvested at 8,000 g for 10 min at 4uC. The cell pellet was resuspended in 4 mL of lysis buffer (300 mM NaCl, 10 mM imidazole, 50 mM NaH2PO4, pH 8.0) per gram of cell paste. A cell lysate was prepared using BugBuster Protein Extraction Reagent (Novagen, Darmstadt, Germany) with addition of benzonase nuclease (Novagen) and Protease Inhibitor Cocktail Set III (Merck, Darmstadt, Germany). The lysate was centrifuged at 16,000 g at 4uC for 30 minutes. The His-tagged synthetase was then purified using Ni-NTA agarose (Qiagen). The Ni-NTA agarose beads were washed twice with wash buffer (300 mM NaCl, 20 mM imidazole, 50 mMProteolysis and Mass SpectrometryThe trypsin cleavage sites in WT GFP were predicted 23977191 by PeptideCutter (http://web.expasy.org/peptide_cutter/). In-gel digestion of purified GFP containing UAA, was performed using Trypsin Gold (Promega, Madison, WI) according to a modified manufacturer’s procedure. Briefly, the gel bands corresponding in size to GFP were finely sliced, washed for 5 minutes with water, 15 minutes w.
