Supporting Information 2-(4-Tolylsulfonyl)ethoxymethyl(TEM) - A ew 2 -H Protecting Group For Solid Support RA Synthesis Chuanzheng Zhou, Dmytro Honcharenko and Jyoti Chattopadhyaya* Department of Bioorganic Chemistry, Box 581, Biomedical Center, Uppsala University, S-751 23 Uppsala, Sweden jyoti@boc.uu.se content General Experimental Methods Synthetic cycle and reagents HPLC profiles of crude 1-4 MS spectrum of synthesized oligo-ras S2 S1 S4 S5 31 P and 1 H MR spectra of phosphoramidite S11 1 H and 13 C MR spectra of 5 --DMTr-2 -TEM ribonucleoside S19 HPLC profiles of crude 3 and 4 under different unblocking conditions Rase H digestion of 15 mer DA/RA duplex Compare the purity of purified RA with that of the crude 12 S23 S35 S36 S1
General Experimental Methods Chromatographic separations were performed on Merck G60 silica gel. Thin layer chromatography (TLC) was performed on Merck pre-coated silica gel 60 F 254 glassbacked plates. 1 H MR spectra were recorded at 270 MHz, using TMS (0.0 ppm) as internal standards. 13 C MR spectra were recorded at 67.9 MHz, using the central peak of CDCl 3 (76.9 ppm) as an internal standard. 31 P MR spectra were recorded at 109.4 MHz using 85% phosphoric acid as external standard. Chemical shifts are reported in ppm ( scale). The C2, C3, H1, H2, H3 are assigned according to H-H cosy and C-H cosy. MALDI-TF mass spectra were recorded in positive ion mode. For oligo-ras, the mass spectrometer was externally calibrated with standard oligonucleotide using 3- HAP and ammonium citrate as co-matrix. For other compounds, the mass spectrometer was externally calibrated with peptide mixture using THPA and ammonium citrate as matrix. Table S1. Synthetic cycle and reagents. function reagents Time (s) 1 coupling 0.1 M amidite in CH 3 C + 0.25M ETT in 120 CH 3 C 15 2 capping 0.1 M Ac 2 in THF + -Methylimidazole/THF/Pyridine 3 oxidation 0.02 M I 2 in THF-H 2 -Pyridine (7:1:2) 8 4 deblocking 3% DCA in CH 2 Cl 2 98 S2
A B C 2 --TEM uridine, 15 uridine Figure S1.1. compound 15 was treated with A) 25% H 3 /MeH at 55 for 21h; B) 33% MeH 2 /EtH at r.t. for 24h; C) 25% H 3 /MeH at r.t. for 24h. S3
A) 1 B) 2 C) 3 D) 4 Figure S1.2. HPLC profiles of crude products. HPLC conditions: A) 1. AE HPLC, 0-40 min, buffer A A/B 2/8. B) 2. anion exchange column, 0-60 min, buffer A/B form 6/4 to2/8. 3 and 4 : RP column, 0-40 min, buffer C C/D 8/2. S4
MS spectra of synthesized oligo-ras. Figure S1.3. MALDI-TF MS spectrum of 1. Figure S1.4. MALDI-TF MS spectrum of 2. S5
Figure S1.5. MALDI-TF MS spectrum of 3. Figure S1.6. MALDI-TF MS spectrum of 4. S6
Figure S1.7. MALDI-TF MS spectrum of 5. Figure S1.8. MALDI-TF MS spectrum of 6. S7
Figure S1.9. MALDI-TF MS spectrums of 7. Figure S1.10. MALDI-TF MS spectrums of 8... S8
Figure S1.11. MALDI-TF MS spectrums of 9. Figure S1.12. MALDI-TF MS spectrums of 10. S9
Figure S1.13. MALDI-TF MS spectrums of 11. Figure S1.14. MALDI-TF MS spectrums of 12. S10
31 P and 1 H MR spectra of phosphoramidite. Figure S2.1. 31 P MR spectrum of uridine phosphoramidite. S11
Figure S2.2. 1 H MR spectrum of uridine phosphoramidite. S12
Figure S2.3. 31 P MR spectrum of cytidine phosphoramidite. S13
Figure S2.4. 1 H MR spectrum of cytidine phosphoramidite. S14
Figure S2.5. 31 P MR spectrum of adenosine phosphoramidite. S15
Figure S2.6. 1 H MR spectrum of adenosine phosphoramidite. S16
Figure S2.7. 31 P MR spectrum of guanosine phosphoramidite. S17
Figure S2.8. 1 H MR spectrum of guanosine phosphoramidite. S18
1 H and 13 C MR spectra of 5 --DMTr-2 -TEM nucleoside. 35000 H 30000 DMTr 25000 H S 20000 15000 10000 50000 0 8.0 ppm (t1) 7.0 6.0 5.0 4.0 3.0 70000 H DMTr H S 60000 50000 40000 30000 20000 10000 0-1000 ppm (t1) 150 100 50 Figure S2.9. 1 H and 13 C MR spectra of 5 --DMTr-2 -TEM uridine. S19
H 25000 DMTr H S 20000 15000 10000 50000 0 9.0 ppm (t1) 8.0 7.0 6.0 5.0 4.0 3.0 H 8000 7000 DMTr 6000 H S 5000 4000 3000 2000 1000 0 ppm (t1) 150 100 50 0 Figure S2.10. 1 H and 13 C MR spectra of 5 --DMTr-2 -TEM cytidine. S20
30000 H 25000 DMTr 20000 H S 15000 10000 50000 0 ppm (t1) 8.0 7.0 6.0 5.0 4.0 3.0 H 1500 DMTr H S 1000 500 0 ppm (t1) 150 100 50 0 Figure S2.11. 1 H and 13 C MR spectra of 5 --DMTr-2 -TEM adenosine. S21
H 30000 DMTr C H 25000 H S 20000 15000 10000 50000 0 9.0 ppm (t1) 8.0 7.0 6.0 5.0 4.0 3.0 8000 DMTr H H C H S 7000 6000 5000 4000 3000 2000 1000 0-1000 ppm (t1) 150 100 50 0 Figure S2.12. 1 H and 13 C MR spectra of 5 --DMTr-2 -TEM guanosine. S22
HPLC profiles of crude 3 and 4 under different unblocking conditions. Figure S3.1 S23
Figure S3.2 S24
Figure S3.3. S25
Figure S3.4. S26
Figure S3.5. S27
Figure S3.6. S28
Figure S3.7. S29
Figure S3.8. S30
Figure S3.9. S31
Figure S3.10. S32
Figure S3.11. S33
Figure S3.12 S34
Pure RA Synthesized crude RA 1 2 3 4 5 6 7 8 2 3 4 5 6 7 8 G15 A14 A13 G12 U11 A10 A9 A8 A7 A6 A5 G4 A3 A2 G1 Figure S4. Rase H digestion of 15 mer DA/RA duplex. Lanes 1 8 represent digestion of RA after 0, 2, 5, 10, 15, 25, 40, 60 min of incubation with enzyme. Conditions of cleavage reactions: pure RA (0.1 μm) or crude RA (0.1 μm) and complementary DA (1 μm) in buffer containing 20 mm Tris-HCl (ph 8.0), 20 mm KCl, 10 mm MgCl 2 and 0.1 mm DTT at 21 ; 0.06 U of Rase H in a total reaction volume of 30 μl. S35
a Pure 12 crude 12 a b b Figure S5. Compare the purity of purified RA ( 12) with that of the crude 12. The pure RA ( 12) was from IBA BioTAGnology (received as a crude form and purified by PAGE). The crude 12 was synthesized by TEM strategy. a: Xylene cyanol blue; b: Bromophenol blue. S36