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1 Electronic Supplementary Material (ESI) for Analyst. This journal is The Royal Society of Chemistry 2014 For submission to Analyst Identification and Discrimination of Binding Sites of an Organoruthenium Anticancer Complex to Single-Stranded Oligonucleotides by Tandem Mass Spectrometry Suyan Liu, Kui Wu,* Wei Zheng, Yao Zhao, Qun Luo, Shaoxiang Xiong, Fuyi Wang* Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Beijing Centre for Mass Spectrometry, Institute of Chemistry, Chinese Academy of Sciences, Beijing , PR China *Corresponding Authors: (FYW) and (KW) Electronic Supplementary Information

2 Table S1. Fragment ions detected by negative ESI-MS/MS for ruthenated ODN I. 1 = [( 6 -bip)ru(en)] 2+ (bip = biphenyl; en = ethylenediamine), I = 5 -CCCA 4 G 5 CCC-3. The results indicate that G 5 is the binding site of complex 1 on I. Fragment ions Observed (m/z) Calculated (m/z) [a 2 C 2 ] [a 3 C 3 ] [a 4 A 4 ] [a 4 A 4 ] [a 5 G 5 ] {[a 6 +1 ] C 6 en} {[a 7 +1 ] C 7 en} {[a 7 +1 ] C 7 bip} {[a 7 +1 ] C 7 bip en} {[I+1 ] C 8 en} {[ 4 +1 ] bip en} {[ 5 +1 ] en} {[ 6 +1 ] en} {[ 6 +1 ] bip en} {[ 7 +1 ] en} {[ 7 +1 ] bip en} [I+1 ] {[I+1 ] en} {[I+1 ] bip} {[I+1 ] bip en}

3 Table S2. Fragment ions detected by negative ESI-MS/MS for ruthenated ODN II. 1 = [( 6 -bip)ru(en)] 2+ ( bip = biphenyl; en = ethylenediamine), II = 5 -CCCG 4 A 5 CCC - 3. The results indicate that G 4 is the binding site of complex 1 on II. Fragment ions Observed (m/z) Calculated (m/z) [a 2 C 2 ] [a 3 C 3 ] [a 4 G 4 ] {[a 5 +1 ] A 5 bip en } {[a 6 +1 ] C 6 en} {[a 7 +1 ] C 7 en} {[a 7 +1 ] C 7 bip en } {[II+1 ] C 8 en} {[ 5 +1 ] en} {[ 6 +1 ] en} {[ 6 +1 ] bip en } {[ 7 +1 ] en} [II+1 ] {[II+1 ] en} {[II+1 ] bip} {[II+1 ] bip en}

4 Relative intensity [I] [I+1 ] m/z Figure S1. Mass spectrum for reaction mixtures of complex 1 and ODN I incubated at 310 K for 24 h ith the molar ratio of [1]/[I] = = ( 6 -bip)ru(en)] 2+ ; The calculated m/z for [I] 3 and [I+1 ] 3 ere and , respectively.

5 (a) (b) Figure S2. Isotopic models (red dots, for hich the values of x and y correspond to the m/z value and intensity of the respective isotopic ion peak, respectively) and mass spectra (lines) for 5 -exonuclease ladders: (a) [F 4 +1 ] 2 and (b) {[F 4 +1 ]+Na + } 2 produced by BSP digestion of the ruthenated ODN [I+1 ]. F 4 = 5 -A 4 G 5 CCC-3 ; 1 = [( 6 -bip)ru(en)] 2+.

6 (a) (b) Figure S3. Isotopic models (red dots, for hich the values of x and y correspond to the m/z value and intensity of the respective isotopic ion peak, respectively) and mass spectra (lines) for 3 -exonuclease ladders: (a) [F 5 +1 ] 2 and (b) {[F 5 +1 ]+Na + } 2 produced by SVP digestion of the ruthenated ODN [I+1 ]. F 5 = 5 -CCCA 4 G 5-3 ; 1 = [( 6 -bip)ru(en)] 2+.

7 Relative intensity [II] [II+1 ] m/z Figure S4. Mass spectrum for reaction mixtures of complex 1 and ODN II incubated at 310 K for 24 h ith the molar ratio of [1]/[II] = = ( 6 -bip)ru(en)] 2+ ; The calculated m/z for [II] 3 and [II+1 ] 3 ere and , respectively.

8 (a) (b) (c) (d) (e) (f) Figure S5. Isotopic models (red dots, for hich the values of x and y correspond to the m/z value and intensity of the respective isotopic ion peak, respectively) and mass spectra (lines) for 5 -exonuclease ladders: (a) [F 4 +1 ] 2, (b) {[F 4 +1 ]+Na + } 2 ; (c) [F 3 +1 ] 2 ; (d) {[F 3 +1 ]+Na + } 2 ; (e) {[F 3 +1 ]+2Na + } 2 and (f) {[F 3 +1 ]+3Na + } 2 produced by BSP digestion of the ruthenated ODN [II+1 ]. F 3 = 5 -C 3 G 4 A 5 CCC-3 ; F 4 = 5 -G 4 A 5 CCC-3 ; 1 = [( 6 -bip)ru(en)] 2+.

9 Figure S6. Isotopic models (red dots, for hich the values of x and y correspond to the m/z value and intensity of the respective isotopic ion peak, respectively) and mass spectra (lines) for 3 -exonuclease ladders [F 4 +1 ] 2 produced by SVP digestion of the ruthenated ODN [II+1 ]. F 4 = 5 -CCCG 4-3 ; 1 = [( 6 -bip)ru(en)] 2+.

10 (a) a 5 G 5 a 5 b 5 c 5 d 5 5 HO G 5 C 1 C 2 C 3 A 4 C 6 C 7 C 8 O O P O P O OH 3 OH 3 x 3 y 3 z 3 (b) (c) (d) (e) Figure S7. (a) Schematic diagram of MS/MS fragmentation of single-stranded ODN I; (b e) Isotopic models (red dots, for hich the values of x and y correspond to the m/z value and intensity of the respective isotopic ion peak, respectively) and mass spectra (lines) for CID fragment ions (b) 2 3, (c) {[ 4 +1 ] bip en} 2, (d) [a 5 G 5 ] 2 and (e) {[a 6 +1 ] C 6 en} 2 of the ruthenated ODN [I+1 ]. 1 = [( 6 - bip)ru(en)] 2+.

11 (a) a 5 A 5 a 5 b 5 c 5 d 5 C 1 C 2 C 3 G A 5 4 C 7 C 6 C 8 5 HO P O O O P O OH OH 3 3 x 3 y 3 z 3 (b) (c) (d) (e) A Figure S8. (a) Schematic diagram of MS/MS fragmentation of single-stranded ODN II; (b e) Isotopic models (red dots, for hich the values of x and y correspond to the m/z value and intensity of the respective isotopic ion peak, respectively) and mass spectra (lines) for CID fragment ions (b) 4 2, (c) {[ 5 +1 ] en} 2, (d) [a 4 G 4 ] 2 and (e) {[a 5 +1 ] A 5 en} 2 of the ruthenated ODN [II+1 ]. 1 = [( 6 -bip)ru(en)] 2+.