upporting Information Design of equence-pecific D inding Molecules for D Methyltransferase Inhibition JeenJoo. Kang, Jordan L. Meier, and Peter. Dervan* Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, C 9. Table of Contents for upporting Information Page upplemental Figure : Full Chemical structures of polyamides upplemental Figure : Methylation inhibition assay with lambdaphage D upplemental Table : Motif logos from ind-n-eq with E-values Mass spectrometry data for Py-Im polyamides
Figure. (a) Full chemical structures of Py-Im polyamides with ball-and-stick representations. (b) tructures of Py-Im polyamides previously reported to bind methylated -CGCG- oligonucleotides. (c) tructure of distamycin D. 8 D b b C 9b
Lane Lane Lambdaphage D Incubation 8. Kb Restriction sites Methylation DMT Methylation-sensitive restriction digest Me-CpG CpG Restriction sites locked by methylation Intact D inhibition of methylation DMT garose gel Electrophoresis D isolation Methylation-sensitive restriction digest Lane Inhibitor D Methyltransferase Restriction Enzyme -. 9.8... garose gel Electrophoresis size (bp).k 9.8k.k.k.k 8.k Lane D Methyltransferase Restriction Enzyme b b Distamycin D 8 9 - - b nm µm b nm µm D nm µm - λ indiii ladder,9 9,,,, Figure. (a) cheme of in vitro assay of D methyltranferase inhibition. Generic polyamide shown in ball-and-stick notation, CpG sites represented by red squares. (b) Inhibition of methyltransferase activity reflects sequence-specificity of Py-Im polyamides. Lambdaphage D was incubated with M.ssI and subject to methylation-sensitive restriction digest at -CGCGT- sites by MluI. D is pm in match sites. Positive control lane was not subject to methylation and completely digested while negative control lane shows minimal digestion. Increasing concentration of b inhi methylation at the restriction sites as visualized by additional, smaller restriction fragments. b and b was titrated from nm to µm at ten-fold dilutions and distamycin ranged from nm to µm at ten-fold dilutions. Visualized on.% agarose gel with YR gold.
Table. Motif logos from ind-n-eq with E-values ind-n-eq E-value specificity (forward/reverse) T G C G T.e- T G C G T T.e-8 C G C G TT.e-9 GT G C G 8.e- C G TC T G T.9e- G C G C T.e-9 C G C G T.e- 8 C G T C T G T.9e-
Mass pectrometry (MLDI-TF) for Py-Im polyamides PyImβIm-γ-PyImβImβ-()-PEG-iotin () Calculated for C 8 [Mass]: 8.8, found 8. PyImβIm-(R) α - γ-pyimβimβ-()-peg-iotin () Calculated for C 9 [Mass]:.8, found.8 PyImPyIm-γ-PyImβImβ-()-PEG-iotin () Calculated for C 9 [Mass]: 89.8, found 89.. PyImβIm-(R) β - γ-pyimβimβ-()-peg-iotin () Calculated for C 9 [Mass]:.8, found.8. ImβImPy-γ-ImβImPyβ-()-PEG-iotin () Calculated for C 8 [Mass]: 8.8, found 9. ImβImPy-(R) α - γ-imβimpyβ-()-peg-iotin () Calculated for C 9 [Mass]:.8, found.9. ImPyImPy-γ-ImβImPyβ-()-PEG-iotin () Calculated for C 9 [Mass]: 89.8, found 9.. ImβImPy-(R) β - γ-imβimpyβ-()-peg-iotin (8) Calculated for C 9 [Mass]:.8, found.. PyImβIm-γ-PyImβImβ-()- (b) Calculated for C [Mass]:., found.. PyImPyIm-γ-PyImβImβ-()- (b) Calculated for C [Mass]:., found.. PyImPyIm-(R) α - γ-pyimβimβ-()- (9b) Calculated for C [Mass]:., found..