Supplementary Online Material. An Expanded Eukaryotic Genetic Code 2QH, UK. * To whom correspondence should be addressed.

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1 Supplementary Online Material An Expanded Eukaryotic Genetic Code Jason W. Chin 1, T. Ashton Cropp, J. Christopher Anderson, Mridul Mukherji, Zhiwen Zhang and Peter G. Schultz* Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute North Torrey Pines Road La Jolla CA 92037, USA 1 Current address: MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK * To whom correspondence should be addressed. Schultz@scripps.edu

2 Materials and Methods EcTyrRS library construction To create the EcTyrRS library of mutants the five positions targeted for mutation were first converted to alanine codons to produce the A5RS gene. This was split between two plasmids at a unique Pst I site in the gene. The library was created essentially as described(1). One plasmid contains the 5 half of the A5RS gene, the other plasmid contains the 3 half of the A5RS gene. Mutagenesis was performed on each fragment by PCR with oligonucleotide primers for the amplification of the whole plasmid. The primers are doped, containing NNK (N = A + G + T + C and K = G + T) and Bsa I restriction endonuclease recognition sites. Digestion with Bsa I and ligation yielded two circular plasmids, each containing mutant copies of one half of the EcTyrRS gene. The two plasmids were then digested with Pst I and assembled into a single plasmid by ligation, leading to assembly of the full-length mutant genes. The mutant EcTyrRS genes were excised from this plasmid and ligated into pa5rs/trnacua between EcoR I and Not I sites. The library was transformed into S. cerevisiae Mav203: pgadgal4 (2TAG) using the PEG-lithium acetate method yielding ~ 10 8 independent transformants. Selection and screening of mutant synthetases To select mutant synthetases, cells (10 9 ) were grown for 4h in liquid SD -leu, -trp + 1 mm amino acid. Cells were then harvested by centrifugation, resuspended in 0.9 % NaCl, and plated on SD -leu, -trp, -his + 20 mm 3-AT, + 1 mm unnatural amino acid or SD -leu, -trp, -ura, + 1 mm unnatural amino acid. After 48 to 60 hours at 30 C the cells were scraped from the plates into liquid SD -leu, -trp and grown for 15 h at 30 C. Cells were harvested by centrifugation, resuspended in 0.9 % NaCl and plated on SD -leu, -trp % 5-FOA. After 48 h at 30 C cells were scraped into liquid SD -leu, -trp + 1 mm unnatural amino acid and grown for 15 h. Cells were then harvested by centrifugation, resuspended in 0.9 % NaCl, and plated on SD -leu, -trp, -his + 20 mm 3-AT, + 1 mm unnatural amino acid or SD -leu, -trp, -ura, + 1 mm unnatural amino acid. To screen phenotypes of selected cells, colonies (192) from each selection were transferred to wells of 96 well blocks containing 0.5 ml of SD -leu, -trp and grown at 30 C for 24hrs. Glycerol (50 % v/v; 0.5 ml) was added to each well, and the cells replica plated onto agar (SD -leu, -trp; SD -leu, -trp, -his, + 20 mm 3-AT; SD -leu, -trp, - ura) in the presence or absence of 1 mm unnatural amino acid. X-GAL assays were performed on SD -leu, -trp plates using the agarose overlay method.

3 Expression of mutant SOD containing unnatural amino acids and characterization by mass spectrometry The addition of DNA encoding a C-terminal hexahistidine tag, and mutation of the codon for Trp 33 to an amber codon in the human superoxide dismutase gene was performed by overlap PCR using PS356 (ATCC) as a template. hsod(trp 33 TAG) HIS was cloned between the GAL1 promoter and CYC1 terminator from pyes2.1 (Invitrogen, Carlsbad, CA USA). Mutant synthetase and trna genes on pectyrrs/trnacua derived plasmids were co-transformed with pyes2.1 hsod(trp 33 TAG) HIS into the strain InvSc (Invitrogen). For protein expression cells were grown in SD -trp, -ura + raffinose and expression induced at an OD 660 of 0.5 by the addition of galactose. HSOD mutants were purified by Ni-NTA chromatography (Qiagen, Valencia, CA, USA). For mass spectrometry protein bands were visualized by colloidal Coomassie stain. Gel bands corresponding to wild-type and mutant SOD were excised from polyacrylamide gels, sliced into 1.5-mm cubes, reduced and alkylated, then subjected to trypsin hydrolysis essentially as described(2). Tryptic peptides containing the unnatural amino acid were analyzed by nanoflow reversed-phase HPLC/µESI/MS with an LCQ ion trap mass spectrometer. Liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis was performed on a Finnigan LCQ Deca ion trap mass spectrometer (Thermo Finnigan) fitted with a Nanospray HPLC (Agilent 1100 series). 1. W. P. Stemmer, S. K. Morris, B. S. Wilson, Biotechniques 14, (1993). 2. A. Shevchenko, M. Wilm, O. Vorm, M. Mann, Analytical Chemistry 68, (1996).

4 Supplementary Data Table S1- Sequences of Selected aminoacyl-trna synthetases. Residue # # clones Ec TyrRS Tyr Asn Asp Phe Leu p-iodophers-1 Val Asn Ser Tyr Leu 1/8 p-iodophers-2 Iso Asn Ser Met Leu 1/8 p-iodophers-3 Val Asn Ser Met Ala 6/8 p-ometyrrs-1 Val Asn Ser Met Leu 5/13 p-ometyrrs-2 Thr Asn Thr Met Leu 1/13 p-ometyrrs-3 Thr Asn Thr Tyr Leu 1/13 p-ometyrrs-4 Leu Asn Ser Met Ser 1/13 p-ometyrrs-5 Leu Asn Ser Met Ala 1/13 p-ometyrrs-6 Thr Asn Arg Met Leu 4/13 p-acetylphers-1 a Iso Asn Gly Met Ala 10/10 p-benzoylphers-1 Gly Asn Gly Phe Ala 1/2 p-benzoylphers-2 Gly Asn Gly Tyr Met 1/2 p-azidophers-1 Leu Asn Ser Met Ala 1/6 p-azidophers-2 Val Asn Ser Ala Ala 1/6 p-azidophers-3 Leu Asn Ser Ala Ala 1/6 p-azidophers-4 Val Asn Ser Ala Val 1/6 p-azidophers-5 Ile Asp Asn Phe Val 1/6 p-azidophers-6 Thr Asn Ser Ala Leu 1/6 a These clones also contain a Asp165Gly mutation.

5 Fig. S1. Tandem mass spectrum of the tryptic peptide VY*GSIK containing the unnatural amino acids (denoted Y*) are shown with their expected fragment ion masses. Arrow indicates observed b (blue) and y (red) ions series for each peptide. Unnatural amino acids are denoted by a number (as described in the legend to Figure 1b) in A-E. Control spectra for Y*=W, Y, L are shown in F, G and H respectively. A B

6 C D

7 E F

8 G H