SUPPORTING INFORMATION

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1 SUPPRTING INFRMATIN Per(-guanidino--deoxy)cyclodextrins: Synthesis, characterisation and binding behaviour toward selected small molecules and DNA. Nikolaos Mourtzis, a Kyriaki Eliadou, a Chrysie Aggelidou, Vassiliki Sophianopoulou b Irene M. Mavridis, a Konstantina Yannakopoulou a * a Institute of Physical Chemistry, b Institute of Biology, National Center for Scientific Research Demokritos Aghia Paraskevi 0, Athens, Greece dyanna@chem.demokritos.gr Experimental Section General. The D and D NMR spectra were acquired at 00 MHz in DMS-d or D, as indicated. Some C NMR spectra were acquired on an AC 0 instrument at.9 MHz. The D spectra CSY and HSQC were acquired using the pulse sequences provided by the instrument s software employing gradient selection. Dimethylformamide (DMF) was dried over CaH for 8 h and then distilled under reduced pressure. Cyclodextrins were dried under vacuum at 80 ºC overnight. Triphenyl phosphine was freshly recrystallized from hexane. N,N- Diisopropylethylamine (DIPEA) and pyrazole-h-carboxamidine hydrochloride were used as received. REFERENCES ARE NUMBERED AS IN THE MAIN TEXT. Hexakis(-bromo--deoxy)-α-cyclodextrin (a). It was prepared according to ref. a in 8% yield (presence of ~% residual Ph P); mp = 9-97 ºC; lit 7a mp = ºC; mp lit 7c mp = 9-9 ºC; H (DMS-d, 00 MHz) δ.8 (d, J =.8 Hz, H, H),. (d, J =. Hz, H,

2 H),.9 (d, J =.7 Hz, H, H), (m, H, H, H),.8 (t, J = 8., H, H),.7 (dd, J = 7. Hz, J =. Hz, H, H ),. (t, J = 8.9 Hz, H, H),.. (m, H, H) ppm; C (DMS-d, MHz) δ 0.7 (C), 8.9 (C), 7.7 (C), 7. (C), 7. (C),.8 (C) ppm, in agreement with the corresponding lit. 7a data. Heptakis(-bromo--deoxy)-β-cyclodextrin (b). It was prepared according to ref. a in 8% yield (presence of ~% residual Ph P); mp = ºC; lit 7a mp = ºC; lit 7c mp =0-0 ºC; lit 7d mp =00 ºC; H NMR (DMS-d, 00 MHz) δ.0 (d, J =. Hz, 7H, H),.89 (br s, 7H, H),.98 (d, J =.9 Hz, 7H, H),.00 (d, J = 0. Hz, 7H, H),.8 (t, J = 7.9 Hz, 7H, H),.9 -. (m, H, H, H),.0-. (m, H, H, H) ppm; C (DMS-d,.9 MHz) δ 0.08 (C), 8.9 (C), 7. (C), 7.0(C), (C),. (C) ppm, in agreement with the corresponding lit. 7a data. ctakis(-bromo--deoxy)-γ-cyclodextrin (c). It was prepared according to ref. a in 8% yield (presence of ~% residual Ph P); mp = 9-98 ºC; lit c mp = 0-0 ºC; H NMR (DMS-d, 00 MHz) δ.00 (d, J =. Hz, 8H, H,),.97 (br s, 8H, H),.0 (d, J =. Hz, 8H, H),.98 (d, J = 0.0 Hz, 8H, H),.8 (t, J = 8.0 Hz, 8H, H),.8 (dd, J = 8.0 Hz, J = 0.0 Hz, 8H, H ),. (t, J = 8.8 Hz, 8H, H),.0-. (m, H, H, H) ppm; C (DMS-d, MHz) δ 0.9 (C), 8.9 (C), 7. (C), 7.0 (C), (C),. (C-Br) ppm, in agreement with the corresponding lit. 7e data. Hexakis(-azido--deoxy)-α-cyclodextrin (a). It was prepared according to ref. 8 in 98% yield; mp = - ºC; H NMR (DMS-d, 98K, 00 MHz) δ. (d, J = 7.0 Hz,, H, H),.7 (d, J =. Hz, H, H),.88 (d, J =. Hz, H, H),.8-.7 (m, H, H), (m, H, H, H),.8 (dd, J =. Hz, J = 7.0 Hz, H, H ),.-.0 (m, H, H, H, partially overlapping with the residual HD signal) ppm; C NMR (DMS-d,

3 MHz) δ 0.79 (C), 8. (C), 7.7 (C), 7.9 (C), 70. (C),.7 (C) ppm, in agreement with the corresponding lit.,7e data.; IR (KBr pellet): 8 (br, str, H); 90 (str, CH.); 097 (str, -N ); (str) cm-. Heptakis(-azido--deoxy)-β-cyclodextrin (b); It was prepared according to ref. 8; Yield 9% mp = - ºC; lit. a mp = 0- ºC (dec); H NMR (DMS-d, 98K, 00 MHz) δ.90 (br s, H, H),.7 (br s, H, H),.9 (d, J =.7 Hz, 7H, H),.78 (d, J =. Hz, 7H, H),.7 (t, J = 9. Hz, 7H, H),.0 (m, H, H, H),.7 (m, 7H, H), partially overlapping with. (m, 7H, H) ppm; C NMR (DMS-d, 98K, MHz) δ 0. (C), 8. (C), 7.77 (C), 7.9 (C), 70. (C),. (C-N ) ppm, in agreement with lit. 8 C NMR data in the same solvent; IR (KBr pellet): 77 (br, str -H); 90 (str, C-H.); 099 (str, -N ); (str) cm -. ctakis(-azido--deoxy)-γ-cyclodextrin (c). It was prepared according to ref. 8 in 7% yield; mp = 0- ºC; H NMR (DMS-d, 98K, 00 MHz) δ.9 (d, J = 7. Hz, 8H, H),.8 (d, J =.0 Hz, 8H, H),.9 (d, J =. Hz, 8H, H),.7 (m, 8H, H),.7 (d, J =. Hz, 8H, H),.8 (8H, H ) overlapping with.7 (H, 8H),.9 (m, 8H, H), overlapping with. (t, J = 8.8 Hz, 8H, H) ppm; C NMR (DMS-d, 98K, MHz) δ 0.9 (C), 8. (C), 7. (C), 7.0 (C), 70.0 (C),.07 (C-N ) ppm, in agreement with lit. a, 7e data. IR (KBr pellet): 8 (br, str, H); 9 (str, CH.); 098 (str, -N ); (str) cm -. Hexakis(-amino--deoxy)-α-cyclodextrin (a). It was prepared according to ref. 8 in 70% yield (free base); mp = ºC (dec); H NMR (D /DCl, 98K, 00 MHz) δ. (d, J =. Hz, H, H),.9 (m, H, H),.0 (t, J = 9.0 Hz, H, H),.7 (dd, J =. Hz, J = 0. Hz, H, H),.9 (t, J = 9.0 Hz, H, H),. (dd, J =.0 Hz, J =. Hz, H, H),. (dd,

4 J =. Hz, J =. Hz, H, H ) ppm; C (D /DCl, MHz) δ 0. (C), 8.7 (C), 7.8 (C), 7.0 (C), 8.0 (C), 0. (C-NH ) ppm, in agreement with lit. a data; H NMR (DMS-d, 98K, 00 MHz) δ 8. (br s, disappears with D, NH ),. (br m, diminishes with D, H, H, H),.08 (d, J =. Hz, H, H),. (br t, J = 8 Hz, H, H),.8 (t, J = 9. Hz, H, H),. (t, J = 9. Hz, H, H),. (dd, J =.7 Hz, J = 9.7 Hz, H, H),.9 (d, J =.9 Hz, H, H),.0 (m, H, H ) ppm. Heptakis(-amino--deoxy)-β-cyclodextrin (b). It was prepared according to ref. 8 in % yield (free base); mp =9 ºC (dec) H NMR (D / DCl, 98K, 00 MHz) δ. (d, J =.0 Hz, 7H, H),. (m, 7H, H),.9 (t, J = 9.7 Hz, 7H, H),. (dd, J = 9.7 Hz, J =.0 Hz, 7H, H),. (t, J = 9. Hz, 7H, H),.0 (dd, J =. Hz, J =. Hz, 7H, H),. (dd, J =. Hz, J =.7 Hz, 7H, H ) ppm; C (D /DCl, MHz) δ 00.9 (C), 8. (C), 7. (C), 7. (C), 7.9 (C), 9. (C-NH ) ppm, in agreement with lit. a data. H NMR (DMSd, 98K, 00 MHz) δ 8. (br s, NH ),.9 (d, J =.0 Hz, H, H),.8 (br s, H, H).0 (br s, H, H),.0 (t, J = 8, Hz, H, H),. (t, J = 9. Hz, H, H),.9 (t, J = 8.8 Hz, H, H),. (br s, H, H),.0 (H hidden under HD peak),.0 (m, H, H ) ppm. ctakis(-amino--deoxy)-γ-cyclodextrin (c). It was prepared according to ref. 8 in 7% yield (free base); mp = 9-97 ºC (dec) H NMR (D / DCl, 98K, 00 MHz) δ.0 (d, J =. Hz, 8H, H),. (m, 8H, H),.9 (t, J = 9.7 Hz, 8H, H),. (dd, J = 9.7 Hz, J =. Hz, 8H, H),. (t, J = 9. Hz, 8H, H),. (dd, J =. Hz, J =. Hz, 8H, H),. (dd, J =. Hz, J = 8. Hz, 8H, H ) ppm; C (D /DCl, MHz) δ (C), 80. (C), 7. (C), 7.00 (C), 7.0 (C), 9. (C-NH ) ppm, in agreement with lit. a data.

5 Supporting Figure. Bottom: H ΝΜR spectrum of hexakis(-amino--deoxy)-αcyclodextrin hydrochloride (a) in D at ph ~ (DCl), corresponding to a symmetrical α- cyclodextrin derivative i.e. fully aminated in the primary side and protonated. Top: H ΝΜR spectrum of a in D at ph 7 showing complete breaking of the symmetry. The C spectrum was the same in both cases.

6 NH D H H 7 H H H H H H DMF ppm (f) NH D H H 8 H H H H H H ppm (f) Supporting Figure. Top: H ΝΜR spectrum of heptakis(-amino--deoxy)-β-cyclodextrin hydrochloride (b) in D. Bottom: H ΝΜR spectrum of octakis(-amino--deoxy)-γcyclodextrin hydrochloride (c).

7 NH C NH HN H H Supporting figure. Left: Partial H- H correlation, and Right: Partial H- C correlation ΝΜR spectrum of hexakis(-guanidino--deoxy)-α-cyclodextrin hydrochloride (a), in D. 7

8 Supporting figure. ESI mass spectrum of hexakis(-guanidino--deoxy)-α-cyclodextrin hydrochloride (a), in positive mode. 8

9 NH C NH HN H H 7 Supporting figure. Left: Partial H- H correlation NMR spectrum in DMS-d, and Right: Partial H- C correlation ΝΜR spectrum in D of heptakis(-guanidino--deoxy)-βcyclodextrin hydrochloride (b). 9

10 Supporting figure. ESI mass spectrum of heptakis(-guanidino--deoxy)-β-cyclodextrin hydrochloride (b), in positive (top) and negative (bottom) mode. 0

11 NH C NH HN H H 8 Supporting figure 7 Left: Partial H- H correlation NMR spectrum, and Right: Partial H- C correlation NMR spectrum in D of octakis(-guanidino--deoxy)-γ-cyclodextrin hydrochloride (c).

12 NH C NH HN H H 8 Supporting figure 8. Left: Partial H- H correlation NMR spectrum, and Right: Partial H- C correlation ΝΜR spectrum of octakis(-guanidino--deoxy)-β-cyclodextrin hydrochloride (c) in DMS- d.

13 . Table : Volumes used for agarose gel electrophoresis. Lane Compound V (µl) Lane Compound V (µl) 7 8 λhindiii Calf Thymus DNA guanidine.hcl + DNA αcd + DNA a + DNA a + DNA a + DNA βcd + DNA Calf Thymus DNA b + DNA b + DNA b + DNA γcd + DNA c + DNA c + DNA c + DNA