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1 Abs. (260 nm) Abs. (260 nm) Abs. (260 nm) Abs. (260 nm) Electronic upporting Information (EI) 1. PLC and Mass pectrometry Analysis (MALDI-TF) of (T 12 )TA_I and (T 12 )TA_III(a) (c) ligonucleotides Figure 1. PLC profiles of the mixtures obtained after different cleavage conditions of oligonucleotides (A) (T 12 )TA_I; (B) (T 12 )TA_III(a); (C) (T 12 )TA_III(b) and (D) (T 12 )TA_III(c). Black lines correspond to the samples treated for 4 h at r.t., blue lines to the samples treated for 1 h at 55 C and green lines to the samples treated o.n. at 55 C. stands for TA-terminated oligonucleotides, stands for a β-elimination side product and stands for and amide bond-cleavage side product. A) B) 2.5 r.t._ 4h 0.5 r.t._ 4h ºC_ 1h 55ºC_ o.n ºC_ 1h 55ºC_ o.n t (minutes) t (minutes) C) 1.8 r.t._ 4h D) 1.2 r.t._ 4h ºC_ 1h 55ºC_ o.n ºC_ 1h 55ºC_ o.n t (minutes) t (minutes) Base 5' 3' ligonucleotide P R 5' 3' ligonucleotide b-elimination product P 5' 3' Amide bond-cleavage ligonucleotide

2 2 Table 1. Mass spectrometry analysis (MALDI-TF) of the main products and the main side products resulting from the cleavage of (T 12 )TA_I and (T 12 )TA_III(a) (c). (T 12 )TA_I (T 12 )TA_III(a) (T 12 )TA_III(b) (T 12 )TA_III(c) t R (min) Mass Found Mass Calcdt. Compound (T 12 )TA_I (+1 ) oxidation product (+2 ) (+3 ) oxidation products (+4 ) β-elimn. product (T 12 )TA_III(a) (+1 ) oxidation product (+2 ) oxidation product (+4 ) (+5 ) (+6 ) oxidation products β-elimn. product (T 12 )TA_III(b) (+1 ) oxidation product amide bond cleavage (T 12 )TA_III(c) (+1 ) oxidation product (+2 ) oxidation product (+4 ) (+5 ) oxidation products (+6 ) β-elimn. product Table 2. Expected conjugates and by-products resulting from the different cleavage conditions of (T 12 )TA_I and (T 12 )TA_III(a) (c). The % of each compound was determined by the PLC analysis. (T 12 )TA_I (T 12 )TA_III(a) (T 12 )TA_III(b ) (T 12 )TA_III(c) Treatment ligonucleotide (%) β-elim. (%) xidation (%) Amide Bond Cleavage (%) 4 h r.t h 55 C o.n. 55 C h r.t h 55 C o.n. 55 C h r.t h 55 C o.n. 55 C h r.t h 55 C o.n. 55 C

3 3 Figure 2. MALDI-TFF mass spectrometry of the main products and the main side products resulting from the cleavage of (T 12 )TA_I and (T 12 )TA_III(a) (c). (T 12 )TA_I (T 12 )TA_III(a)

4 4 Figure 2. Cont. (T 12 )TA_III(b) (T 12 )TA_III(c)

5 5 Figure 2. Cont. b-elim ination product ample (T 12 )TA_III(b) Am ide bond-cleavage product

6 6 Figure 2. Cont. Exam ple of oxidation product ample: (T 12 )TA_III(c) Exam ple of oxidation product ample: (T 12 )TA_III(a)

7 7 2. Mass pectrometry Analysis (MALDI-TF) and PLC Chromatograms of the Purified TA-Terminated ligonucleotides Used to Functionalize Aup Table 3. PLC, Uv-vis and mass spectrometry analysis (MALDI-TFF) of the purified TA-terminated oligonucleotides. ligonucleotide Mw (calcd) Mw (found) t R (min) λ max. (nm) TA_I TA_II TA_III(a) TA_III(b) TA_III(c) 'TA_I ALK_D (F)TA_I , 490 (F)TA_II , 490 (F)TA_III(a) , 490 (F)TA_III(b) , 490 (F)TA_III(c) , 490 (F)ALK_D , 490

8 Threoninol-Based ligonucleotides Containing Modified Thioctic Acid Moieties at Their 3'-Termini TA-10a TA_I 5' 3' ligonucleotide

9 9 5' 3' ligonucleotide TA_II TA-11 5 P

10 10 5' 3' ligonucleotide TA-10c TA_III(a) 3

11 11 5' 3' ligonucleotide TA-10d TA_III(b)

12 12 TA-10b TA_III(c) 5' 3' ligonucleotide

13 13 5 TA_I ligonucleotide 5' 3'

14 14 ALK_D D-1 5' 3' ligonucleotide

15 Threoninol-Based ligonucleotides Containing Modified Thioctic Acid Moieties at Their 3'- Termini and Fluorescein at 5'-Termini (F)TA_I TA-12a F 5' 3' ligonucleotide C = F

16 16 F 5' 3' ligonucleotide TA-13 (F)TA_II 5 P

17 17 F 5' 3' ligonucleotide 3 TA-12c (F)TA_III(a)

18 18 F 5' 3' ligonucleotide (F)TA_III(b) TA-12d

19 19 F 5' 3' ligonucleotide TA-12b (F)TA_III(b)

20 20 (F)ALK_D D-2 F 5' 3' ligonucleotide

21 21 3. PLC and Mass pectrometry Analysis (MALDI-TF) btained from the Treatment of TA_Terminated ligonucleotides with Cathepsin B Table 4. Results obtained with the different TA-terminated oligonucleotides in the presence of Cathepsin B and mass spectrometry analysis (MALDI-TF). Reaction Time (h) % Amide Bond Cleavage t R (min.) Mass Found Mass Calcdt TA_III(b) TA_III(a) TA_III(c)

22 Abs. (260 nm) Abs. (260 nm) Abs. (260 nm) Abs. (260 nm) Abs. (260 nm) 22 Figure 5. PLC profiles obtained after treatment the TA-terminated oligonucleotides with Cathepsin B: (A) TA_III(b) at different times; (B) TA_III(c); (C) TA_III(a); (D) TA_II and (E) TA_I at 72 h (red lines). In all cases the black lines stand for a negative control (the same experimental conditions but without the enzyme). stands for the TA-terminated oligonucleotide and stands for the cleavage product generated in each case. A) 0.20 TA_III(b) o CTB, t=72h + CTB, t=4h + CTB, t=24h + CTB, t=72h B) TA_III(c) o CTB, t=72h + CTB, t=72h t (minutes) t (minutes) C) D) 0.20 TA_III(a) o CTB, t=72h + CTB, t=72h 0.15 TA_II o CTB, 72h + CTB, t=72h t (minutes) t (minutes) E) Cathepsin B TA_I o CTB, 72h + CTB, t=72h Cathepsin B t (minutes) Cathepsin B

23 23 Figure 6. MALDI-TFF mass spectrometry of the amide bond cleavage products. Cathepsin B Cathepsin B

24 24 Figure 6. Cont. Cathepsin B Cathepsin B Cathepsin B

25 25 4. Characterization ( 1 -MR, 13 C-MR and 31 P-MR) of the ynthesized Threoninol-Based Analogues 1 ppm (f1) ppm (f1)

26 26 7a ppm (t1) ppm (t1)

27 27 7b ppm (f1) ppm (f1)

28 28 7c ppm (t1) ppm (t1)

29 29 8a ppm (t1) ppm (f1)

30 30 8b ppm (f1) ppm (f1)

31 31 8c ppm (t1) ppm (t1)

32 32 2 ppm (t1) ppm (t1)

33 33 9a mercury400_0531-treo-lipo-dmt-1.fid.mrc Chemical hift (ppm) ppm (f1)

34 34 9b ppm (f1) ppm (f1)

35 35 9c ppm (t1) ppm (t1)

36 36 12 P C ppm (f1) ppm (f1)

37 37 ppm (f1)

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