Supplementary Data. Santiago Grijalvo and Ramón Eritja *

Transcription

1 Supplementary Data Synthesis and in vitro Inhibition Properties of Oligonucleotide Conjugates Carrying Amphipathic Proline-rich Peptide Derivatives of the Sweet Arrow Peptide (SAP) Santiago Grijalvo and Ramón Eritja * Institute for Research in Biomedicine (IRB Barcelona); Institute for Advanced Chemistry of Catalonia (IQAC); Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN); Spanish Research Council (CSIC); Cluster Building, Baldiri Reixac 10, E Barcelona, Spain. * recgma@cid.csic.es S-1

2 Summary Table 1. MALDI-TOFF mass spectrometry... S-4 SAP-oligonucleotide conjugates. HPLC chromatograms and MALDI-TOF mass spectrometry spectra 6a... S-5 6b S-6 9a S-7 9b S-8 13a..... S-9 13b S-10 14a S-11 14b S-12 SAP-antisense phosphorothioate conjugates. HPLC chromatograms and MALDI- TOF mass spectrometry spectra 6c S-13 6d... S-14 9c S-15 9d S-16 13c..... S-17 14c S-18 Scr-Orn..... S-19 Polyacrylamide gel electrophoresis (PAGE) Fig. 1S Analysis of the formation of complexes between unmodified antisense phosphorothioate and SAP peptide by native PAGE.. S-20 Fig. 2S Denaturing PAGE of the SAP-antisense oligonucleotide phosphorothioate conjugates synthesized in this study.. S-20 S-2

3 Cell culture Fig. 3S Gene-specific silencing activities of antisense phosphorothioate oligonucleotide conjugates without lipofectamine at 300 nm oligonucleotide concentration S-21 Fig. 4S Dose-response experiments of SAP: antisense phosphorothioate complexes at 150 nm and 300 nm oligonucleotide concentration.... S-22 Fig. 5S Gene-specific silencing activities for antisense phosphorothioate oligonucleotide conjugates using SAP peptide as a transfecting agent. S-23 S-3

4 Table 1S. MALDI-TOFF mass spectrometry Sequence SAP-ODN MW (calc) MW (found) (5 ->3 ) conjugate A 6a A 6b B 6c B 6d A 9a A 9b B 9c * B 9d 7968 n.d. A 13a A 13b B 13c A 14a A 14b B 14c * B Scr-Orn * A unmodified n.d n.d. B unmodified Sequence A (phosphate form): 5 -CGCGAATTCGCG-3 Sequence B (phosphorothioate form): 5 - AGGTCTTGTTTCCTTTGC-3 n.d. not determined; *the mass corresponds to the removal of the whole peptide and the two spacers S-4

5 SAP-ODN conjugates. HPLC chromatograms and MALDI-TOFF mass spectrometry spectra (VKLPPP) 3 GCGCTTAAGCGC 6a S-5

6 (VKLPPP) 3 GCGCTTAAGCGC 6b S-6

7 (VOrnLPPP) 3 CGCGAATTCGCG 9a S-7

8 (VOrnLPPP) 3 CGCGAATTCGCG 9b S-8

9 (VHArgLPPP) 3 CGCGAATTCGCG 13a S-9

10 (VHArgLPPP) 3 CGCGAATTCGCG 13b S-10

11 (VArgLPPP) 3 CGCGAATTCGCG 14a S-11

12 (VArgLPPP) 3 CGCGAATTCGCG 14b S-12

13 SAP-antisense phosphorothioate conjugates. HPLC chromatograms and MALDI-TOFF mass spectrometry spectra (VKLPPP) 3 CGTTTCCTTTGTTCTGGA 6c S-13

14 (VKLPPP) 3 CGTTTCCTTTGTTCTGGA 6d S-14

15 (VOrnLPPP) 3 CGTTTCCTTTGTTCTGGA 9c S-15

16 (VOrnLPPP) 3 CGTTTCCTTTGTTCTGGA 9d S-16

17 (VHArgLPPP) 3 CGTTTCCTTTGTTCTGGA 13c S-17

18 (VArgLPPP) 3 CGTTTCCTTTGTTCTGGA 14c S-18

19 (Val Orn Leu Pro Pro Pro)3 Scr-Orn S-19

20 Polyacrylamide gel electrophoresis (SDS-PAGE) Fig. 1S. Native SDS-PAGE gel shift assay to analyze the ability of SAP peptide to form complexes with unmodified oligonucleotide phosphorothioate (wt). SAP peptide shows the highest propensity for the formation of the complex with the phosphorothioate oligonucleotide at a 10-fold molar excess of SAP Fig. 2S 7M urea PAGE of SAP-antisense phosphorothioate conjugates 20 % Polyacrylamide, 8M urea gel electrophoresis of SAP-antisense phosphorothioate conjugates. The gel was stained with STAINS-ALL. Lane 1: SAP-antisense phosphorothioate 6c; Lane 2: 6d; Lane 3: 9c; Lane 4: 9d; Lane 5: 13c; Lane 6: 14c S-20

21 Cell Culture Fig. 3S Gene-specific silencing activities of antisense phosphorothioate oligonucleotide conjugates without lipofectamine at 300 nm oligonucleotide concentration Gene-specific silencing activities for unmodified phosphorothioate oligonucleotide (wt), and SAP-antisense phosphorothioate conjugates (6c, 15, 9c, 16, 13c and 14c; 300 nm per well) targeting the Renilla luciferase mrna expressed in SH-SY5Y cells. Transfection of antisense oligonucleotides was carried out without using Lipofectamine S-21

22 Fig. 4S Dose-response experiments of SAP: antisense phosphorothioate complexes at 150 nm and 300 nm oligonucleotide concentration Gene-specific silencing activities for unmodified antisense oligonucleotide (wt) complexed with SAP peptide. The concentration of antisense oligonucleotide was 150 nm and 300 nm, respectively. The molar peptide: antisense oligonucleotide ratio used was 4:1, 6:1 and 10:1 targeting the Renilla luciferase mrna expressed in SH-SY5Y cells. Transfection was carried out using SAP peptide as transfecting agent. The bar wt represents the value of the luciferase activity without using SAP peptide as transfecting agent. A scramble sequence combined with SAP peptide in a 6:1 M ratio gave no Renilla luciferase inhibition. S-22

23 Fig. 5S Gene-specific silencing activities for antisense phosphorothioate oligonucleotide conjugates using SAP peptide as a transfecting agent at a molar ratio of 6:1 (SAP peptide / oligonucleotide). A B Gene-specific silencing activities for phosphorothiote oligonucleotide conjugates (wt, 6c, 6d, 9c, 9d, 13c, 14c and Scr-Orn) targeting the Renilla luciferase mrna expressed in SH-SY5Y cells. Transfection of antisense oligonucleotides was carried out using SAP peptide as transfecting agent in a 6-fold molar excess (peptide:sap-antisense conjugate) (A) Experiment was performed at 150 nm oligonucleotide concentration; (B) Experiment was performed at 300 nm oligonucleotide concentration. Scrambled sequence (Scr-Orn) gave no Renilla luciferase inhibition. S-23