1. Monnat Lab progress monomerizations of Cre, Mso (Hui) 2 nd round designs vs. Anopheles targets (Umut) in vivo recombination reporter assays (Ray, Hui) completed/sequence-verified reporters completed expression vectors functional analyses of Sce/Ani/Cre to discuss: expression vectors/target cells

2. Monomerization of Homing Endonucleases Gene synthesis Scalley-Kim M. et. al. Protein Science (2003), 12: 197-206 Doyon JB et. al. J.A.C.S. (2006), 128: 2477-84. Library size: ~1×10 6

3. The Length and Aa Distribution of Linkers 19 various linkers were identified from Cre library with length from 13 Aa to 73 Aa. 13 various linkers were identified from Mso library with length at 13 and 33 Aa.

4. In Progress Structural analysis by crystallography. Biochemical study: Binding by isothermal titration calorimetry (ITC) and fluorescence anisotropy. Thermal stability by circular dichroism ( CD). Cleavage specificity matrix In vivo function assay using pDR-GFP recombination system. Verification of monomeric HEs as novel platform for future engineering. Introduction of mutations with known specificity changes in single domain. Construction of Cre and Mso heterodimer.

5. TgcgcGTcgCTCAGGgcAaTGAA GELSOLIN CgAtcGcaaCGCAAGTGCaGGAT CHEERIO TTctcCcagCGCAAcTACGTGAA YOLKLESS CAAgAGccatTTAAaAATCTGAA HIV1 WT: CCAAACTGTCTCAAGTTCCGGCG Engineering Targets 9.14 kb 43.6 kb 7.14 kb

6. TgcgcGTcgCTCAGGgcAaTGAA GELSOLIN 1. CgcgcCTGTCTCAAGTTCCGGCG 2. CCAAACTcgCTCAAGTTCCGGCG 3. CCAAACTGTCTCAAGgcaaGGCG CgAtcGcaaCGCAAGTGCaGGAT CHEERIO 4. CCAtcCTGTCTCAAGTTCCGGCG 5. CCAAACcaaCTCAAGTTCCGGCG TTctcCcagCGCAAcTACGTGAA YOLKLESS 6. CCctcCTGTCTCAAGTTCCGGCG 7. CCAAACcagCTCAAGTTCCGGCG CAAgAGccatTTAAaAATCTGAA HIV1 8. CCAAACccatTCAAGTTCCGGCG WT: CCAAACTGTCTCAAGTTCCGGCG Engineering Targets

7. Cleavage Assays substrate products controls + – + – substrate products Design 1Design 2Design 4 Design 5Design 7Design 8 3 kb

8. Universal pDRGFP/HEG-specific reporter plasmids sequence verified: pDRGFP-Sce pDRGFP-Ppo pDRGFP-Ani pDRGFP-AniLib4 pDRGFP-Dre3 pDRGFP-Dre4 pDRGFP-Mso pDRGFP-Ceu pDRGFP-Cpa pDRGFP-Dpa pDRGFP-Cre (Hui) Xba SpeI HE cut site XhoI/KpnI/SacI AflII carb puro GFP 5' iGFP 3'

9. HEG expression vectors HEGpCS2pCMVother I-SceI: pCSce, pCMVSce- I-AniI: pCSAni -pHyperAniK (pCMV+pEF) I-PpoI: -pCNPpo6- I-CreI: pCSCrepCMVCre3- I-SpomI: pCSSpom pCMVSpom-

10. 293T – 72h after transfection -/pEGFP-C1 (FuGENE6) GFP PI (dead) -/pEGFP-C1/CaPO4 15.5% 56.9% -/pDRGFPuniv 0.5%

11. pCMVSce/pDRGFPSce pCSAni/pDRGFPAni pCSAni/pDRGFPLib4 293T – 72h after transfection (FuGene6) 1.5% 0.2% 0.4%

12. %GFP (hrs) cells/plasmid(s)tf487296hrs 293TCaPO40.70.0 + EGFP-C179.0 15.519.8 66.3 + DRGFPuni0.00.7 + Sce/DRSce1.311.7 + Ani/DRAni0.11.7 + EGFP-C1FuGENE656.951.8 + DRGFPuni0.50.8 + Sce/DRSce1.53.2 + Ani/DRAni0.20.5 + Ani/DRLib4Ani0.40.7

13. In vivo Cre Cleavage-Mediated Recombination -/-pEGFP pDRGFP-Cre pDRGFP-Cre/pCSCreWTpDRGFP-Cre/pCSCreD20N

14. Splice site prediction in HE ORFs Prediction of cryptic splice sites in HE ORFs using Alternative splice site predictor (http://www.es.embnet.org/~mwang/assp.html)http://www.es.embnet.org/~mwang/assp.html Berkeley Drosophila genome project splice site prediction (http://www.fruitfly.org/seq_tools/splice.html)http://www.fruitfly.org/seq_tools/splice.html NetGene2 (http://www.cbs.dtu.dk/services/NetGene2/)http://www.cbs.dtu.dk/services/NetGene2/ GenScan (http://genes.mit.edu/GENSCAN.html)http://genes.mit.edu/GENSCAN.html TIGR Gene splicer (http://www.tigr.org/tdb/GeneSplicer/gene_spl.html)

15. Splice site prediction for I-AniI (JO1387) AFN conf. AFAF 314471 AFN const. crypt. sd sa 31 AF 337 AF 424 AFN AF 54361467272 764 A(SSP)F(ruitfly)N(etGene2) const. crypt.