Synthesis, structural studies and stability of the model, cysteine containing DNA-protein cross-links

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1 Electronic Supplementary Material (ESI) for New Journal of Chemistry. This journal is The Royal Society of Chemistry and the Centre National de la Recherche Scientifique 2017 ELECTRONIC SUPPLEMENTARY INFORMATION Synthesis, structural studies and stability of the model, cysteine containing DNA-protein cross-links Kinga Salus, Marcin Hoffmann, Tomasz Siodła, Bożena Wyrzykiewicz, Donata Pluskota-Karwatka* Adam Mickiewicz University in Poznań, Faculty of Chemistry, Umultowska 89b, Poznań, Poland 1. Chromatograms of reaction mixtures and of solutions subjected to stability studies 2 2. NMR data of M 1 MGx-Ade-NAC 5 3. Mass spectra of studied compounds 6 4. VT 1 H NMR spectra of M 1 MGx-A-NAC Temperature calibration data Quantum-chemical calculation results for M 1 MGx-A-NAC Transition state structures of M 1 MGx-Ade-NAC NMR spectra 23 NMR spectra of M 1 Gx-A-NAC (D 2 O) 24 NMR spectra of M 1 MGx-Ade-NAC (D 2 O) 30 NMR spectra of M 1 MGx-A-NAC (D 2 O) 35 1

2 Chromatograms of reaction mixtures and of solutions subjected to stability studies Absorbance M 1 MGx-A M 1 MGx-A-NAC [min] Fig. S1. C18 analytical column LC-DAD chromatogram (recorded at 254 nm) of the reaction mixture of M 1 MGx-A with NAC in 0.1 M PB held at 37 C for 24 h. Absorbance M 1 MGx-A M 1 MGx-A-NH 2 M 1 MGx-A-NAC [min] Fig. S2. C18 analytical column LC-DAD chromatogram (recorded at 254 nm) of the M 1 MGx-A-NAC solution in 0.1 M PB held at 37 C for 9 days. 2

3 Absorbance M 1 MGx-Ade M 1 MGx-Ade-NH 2 M 1 MGx-Ade-NAC [min] Fig. S3. C18 analytical column LC-DAD chromatogram (recorded at 254 nm) of the M 1 MGx-Ade-NAC solution in 0.1 M PB held at 37 C for 12 days. Absorbance M 1 Gx-A-( N α -AcLys) 2 M 1 Gx-A- N α -AcLys M 1 Gx-A-NAC [min] Fig. S4. C18 analytical column LC-DAD chromatogram (recorded at 254 nm) of the M 1 Gx-A-NAC mixture with N α - acetyllysine in 0.1 M PB solution held at 37 C for 15 min. 3

4 Absorbance M 1 Gx-A M 1 Gx-A-NAC [min] Fig. S5. C18 analytical column LC-DAD chromatogram (recorded at 254 nm) of the reaction mixture of M 1 Gx-A with NAC and N α -acetyllysine in 0.1 M PB held at 37 C for 3 h. Absorbance M 1 Gx-A M 1 Gx-A- N α -AcLys M 1 Gx-A-NAC [min] Fig. S6. C18 analytical column LC-DAD chromatogram (recorded at 254 nm) of the reaction mixture of M 1 Gx-A with NAC and N α AcLys in 0.1 M PB held at 37 C for 26 h. 4

5 NMR data of M 1 MGx-Ade-NAC Table S1. NMR data of M 1 MGx-Ade-NAC (D 2 O, standard NMR TSP-d 4 ) δ(h) [ppm] Multiplicity J H.H [Hz] δ(c) [ppm] HMBC CHO 9.56 s C7, C8, C1, C2 C C C7, CHO, Cβ CH s (split) C7, C8, C1, C2, CHO H-C s C3a, C9a, C9b C3a H-C s (split) C3a, C7, C9a C C C9a C9b CH 3 (Ac) 2.05 s (split) C=O (Ac) C=O (Ac) H-Cα 4.56 td 4.25; Cβ, C=O (Ac) Ha-Cβ 3.39 dd (split) 8.36; Cα, C2, COOH Hb-Cβ 3.64 dd (split) 4.30; Cα, C2, COOH COOH

6 Mass spectra of studied compounds * * * Fig. S7. Positive ions MS spectrum of M 1 Gx-A-NAC Fig. S8. Positive ions MS/MS spectrum of M 1 Gx-A-NAC; collision energy 30 ev (M-H) (M-H) (M-H) Fig. S9. Negative ions MS spectrum of M 1 Gx-A-NAC 6

7 * * * Fig. S10. Positive ions MS spectrum of M 1 MGx-Ade-NAC Fig. S11. Positive ions MS/MS spectrum of M 1 MGx-Ade-NAC; collision energy 10 ev * (M-H) (M-H) (M-H) (M-H) Fig. S12. Negative ions MS spectrum of M 1 MGx-Ade-NAC 7

8 Fig. S13. Negative ions MS/MS spectrum of M 1 MGx-Ade-NAC; collision energy 10 ev * * * Fig. S14. Positive ions MS spectrum of M 1 MGx-dA-NAC Fig. S15. Positive ions MS/MS spectrum of M 1 MGx-dA-NAC; collision energy 15 ev 8

9 (M-H) (M-H) (M-H) Fig. S16. Negative ions MS spectrum of M 1 MGx-dA-NAC Fig. S17. Negative ions MS spectrum of M 1 MGx-dA-NAC; collision energy 10 ev * * * Fig. S18. Positive ions MS spectrum of M 1 MGx-A-NAC 9

10 Intensywność Fig. S19. Positive ions MS/MS spectrum of M 1 MGx-A-NAC; collision energy 10 ev * Fig. S20. Positive ions MS spectrum of M 1 Gx-A Fig. S21. Positive ions MS/MS spectrum of M 1 Gx-A; collision energy 10 ev 10

11 Fig. S22. Positive ions MS spectrum of M 1 Gx-A-NH Fig. S23. Positive ions MS/MS spectrum of M 1 Gx-A-NH 2 ; collision energy 10 ev * * Fig. S24. Positive ions MS spectrum of M 1 MGx-Ade 11

12 Intensywność Fig. S25. Positive ions MS/MS spectrum of M 1 MGx-Ade; collision energy 30 ev * * (M+Na)+ * (M+K) Fig. S26. Positive ions MS spectrum of M 1 MGx-Ade-NH Fig. S27. Positive ions MS/MS spectrum of M 1 MGx-Ade-NH 2 ; collision energy 30 ev 12

13 * * Fig. S28. Positive ions MS spectrum of M 1 MGx-A Fig. S29. Positive ions MS/MS spectrum of M 1 MGx-A; collision energy 15 ev * * Fig. S30. Positive ions MS spectrum of M 1 MGx-A-NH 2 13

14 Fig. S31. Positive ions MS/MS spectrum of M 1 MGx-A-NH 2 ; collision energy 10 ev * * Fig. S32. Positive ions MS spectrum of M 1 Gx-A-N α AcLys * Fig. S33. Positive ions MS/MS spectrum of M 1 Gx-A-N α AcLys; collision energy 20 ev 14

15 * * Fig. S34. Positive ions MS spectrum of M 1 Gx-A-(N α AcLys) Fig. S35. Positive ions MS/MS spectrum of M 1 Gx-A-(N α AcLys) 2 ; collision energy 20 ev * Fig. S36. Positive ions MS spectrum of M 1 MGx-A-N α AcLys

16 Fig. S37. Positive ions MS/MS spectrum of M 1 MGx-A-N α AcLys; collision energy 10 ev Fig. S38. Positive ions MS spectrum of M 1 MGx-A-(N α AcLys) Fig. S39. Positive ions MS spectrum of M 1 MGx-A-(N α AcLys) 2 ; collision energy 10 ev 16

17 VT 1 H NMR spectra of M 1 MGx-A-NAC 376 K 373 K 365 K 364 K 342 K 297 K Fig. S40. Fragments of 1 H NMR spectra of M 1 MGx-A-NAC (D 2 O) recorded at 297 K, 342 K, 364, 365 K and 376. The split acetyl proton signals at 1.96 coalesced to singlet at Tc = 376 K, methyl protons signals at 2.23 ppm coalesced at lower temperature, but artefacts may be misleading. High temperature caused partial degradation of M 1 MGx-A-NAC leading to the formation of products which gave rise to additional signals in 1 H NMR spectra of the studied compound. This process interfered with the variable-temperature studies. 17

18 Temperature calibration data Table S2. Temperature values calculated based on 1 H NMR chemical shift values of hydroxyl and methylene protons of ethylene glycol Thermostat temperature (T t ) δ ( OH) [ppm] δ (-CH 2 ) [ppm] Δδ [ppm] T calc * *Temperature values calculated based on T calc = * Δδ 1,70 1,60 y = x R² = ,50 δ[ppm] 1,40 1,30 1,20 1, Thermostat temperature, T t [K] Chart S1. The relationship between 1 H NMR chemical shift difference values ( δ) of ethylene glycol protons and temperature values showed by thermostat (T t ) 18

19 350 Actual temperature, T [K] y = x R² = Thermostat temperature, T t [K] Chart S2. Calibration curve showing the relationship between thermostat temperature values (T t ) and calculated temperature (T calc ). Equation T = * T t allows to determine the actual temperature in thermostat. 19

20 Quantum-chemical calculation results for M 1 MGx-A-NAC Relative energy [kcal/mol] Dihedral angle N6-C7-C1"-C2" value s-cis s-trans Chart S3. The relative energy of s-cis and s-trans conformers of M 1 MGx-A-NAC dependent on the N6-C7-C1 -C2 dihedral angle value calculated at M06/6-31G(d) level of theory in vacuo Fig. S41. Energy minima structures of M 1 MGx-A-NAC: s-cis/m -50 (A) and s-cis/p (B); arrows show correlations observed in NOESY spectrum of M 1 MGx-A-NAC (D 2 O) 20

21 Table S3. Comparison of the relative energies ( E) and Gibbs free energies ( G) of M 1 MGx-A-NAC s-cis and s-trans conformers calculated at M06/6-31G(d) level of theory in vacuo, and using PCM for water Dihedral angle* In vacuo E [kcal/mol] G [kcal/mol] Dihedral angle* PCM (water) E [kcal/mol] G [kcal/mol] s-cis/m º º 0 0 s-cis/m º º s-cis/p 130.0º º s-cis/ts_0 4.5º º s-cis/ts _ º º s-trans/m º º s-trans/p 130.5º º s-trans/ts_0-9.3º º s-trans/ts _ º º * N6-C7-C1 -C2 dihedral angle value Table S4. The relative energy values ( E) of s-cis and s-trans conformers of M 1 MGx-A-NAC calculated using M06/6-31++G(d,p), B3LYP/6-31++G(d,p), ωb97x-d/6-31g(d) and MP2/6-31G(d) in vacuo. For comparison the E values calculated at initial M06/6-31G(d) level were given. Dihedral angle* M06/ 6-31G(d) M06/ G(d,p) B3LYP/ G(d,p) ωb97x-d/ 6-31G(d) MP2/ 6-31G(d) s-cis/m º s-cis/p 130.0º s-cis/ts_0 4.5º s-cis/ts _ º s-trans/m º s-trans/p 130.5º s-trans/ts_0-9.3º s-trans/ts _ º * N6-C7-C1 -C2 dihedral angle value 21

22 Transition state structures of M 1 MGx-Ade-NAC s-cis/ts_00 s-cis/ts_180 s-trans/ts 0 s-trans/ts_180 M/TS_-900 P/TS_90 M/TS_90 P/TS -90 Fig. S42. Transition state structures of M 1 MGx-Ade-NAC calculated at M06/6-31G(d) level of theory in vacuo 22

23 NMR spectra 23

24 Fig. S43. 1 H NMR spectrum of M 1 Gx-A-NAC (D 2 O) B (dd) 4.57 J(4.33, 7.79) C (dd) 4.30 J(4.12, 7.34) E (dd) 3.88 J(4.30, 12.72) D (dd) 3.95 J(3.04, 12.73) F (dd) 3.61 J(4.33, 14.19) G (dd) 3.42 J(7.83, 14.18)

25 Fig. S C NMR spectrum of M 1 Gx-A-NAC (D 2 O)

26 {4.57,3.43} {3.61,3.44} {4.58,3.62} {3.43,3.62} {4.30,3.86} {4.88,4.49} {6.22,4.88} {4.50,4.88} {4.49,4.34} {3.95,4.30} {3.61,4.58} {3.44,4.57} {4.31,4.48} {4.88,6.22} Fig. S45. COSY spectrum of M 1 Gx-A-NAC (D 2 O) 26

27 {2.02,24.59} {3.61,40.35} {3.42,40.34} {4.57,57.32} {3.94,63.96} {4.88,76.57} {3.88,63.95} 70 {6.22,91.52} {4.30,88.10} {8.64,139.41} {7.70,136.45} {8.49,143.83} 150 {8.66,169.53} {9.52,194.23} Fig. S46. HSQC spectrum of M 1 Gx-A-NAC (D 2 O) 27

28 Fig. S47. HMBC spectrum of M 1 Gx-A-NAC (D 2 O) 28

29 M1GxA_NAC_1 KS_M1MGx_NAC_1 spin off temp. 298K 1 2 {8.66,3.60} {8.64,3.40} {8.66,3.41} {3.62,3.42} {8.49,3.90} {4.88,3.87} {8.66,4.56} {8.49,4.49} {6.22,4.46} {8.65,4.91} {8.49,4.87} {6.21,4.91} {4.88,4.51} {3.89,4.30} {6.22,4.29} {3.94,4.29} {3.42,3.61} {3.43,4.57} {3.60,4.56} {8.49,6.21} 6 {2.05,7.64} 7 {6.21,8.49} {9.53,8.66} {3.60,8.65} {3.44,8.65} {8.66,9.52} Fig. S48. NOESY spectrum of M 1 Gx-A-NAC (D 2 O) 29

30 C (d) 2.31 J(4.94) B (d) 2.05 J(8.16) D (d) 8.52 J(13.10) A (td) 4.56 J(4.25, 8.02) F (ddd) 3.64 J(4.30, 9.37, 13.79) E (ddd) 3.39 J(8.36, 10.40, 14.24) C (d) 2.31 J(4.94) B (d) 2.05 J(8.16) Fig. S49. 1 H NMR spectrum of M 1 MGx-Ade-NAC (D 2 O) 30

31 Fig. S C NMR spectrum of M 1 MGx-Ade-NAC (D 2 O)

32 2 {4.55,3.40} {4.56,3.64} {3.62,3.43} 3 {3.40,3.61} {3.64,4.57} {3.39,4.56} Fig. S51. COSY spectrum of M 1 MGx-Ade-NAC (D 2 O) 32

33 {4.56,57.31} {2.27,15.07} {3.62,40.13} {3.37,40.03} {2.03,24.88} {8.52,138.11} {8.29,143.45} {9.56,194.13} {8.72,171.44} Fig. S52. HSQC spectrum of M 1 MGx-Ade-NAC (D 2 O) 33

34 {8.72,39.96} {4.57,39.70} {3.37,57.36} {3.63,57.31} {9.56,114.83} {8.29,118.50} {9.53,127.07} {8.51,115.43} {8.52,145.44} {8.28,145.82} {9.56,144.87} {8.29,142.49} {9.56,171.64} {8.72,194.26} 100 {2.30,114.85} 110 {2.30,127.37} {2.30,145.00} {3.63,171.34} {3.38,171.49}{2.30,171.53} {3.63,178.04} {3.39,177.94} 170 {2.04,176.25} 180 {4.55,178.35} {2.30,193.72} Fig. S53. HMBC spectrum of M 1 MGx-Ade-NAC (D 2 O) 34

35 G (dd) 4.87 J(5.14, 10.20) F (ddd) 4.58 J(4.34, 8.36, 9.88) E (m) 4.50 D (dd) 4.30 J(3.67, 7.51) C (ddd) B (m) J(3.73, 12.77, 17.04) A (ddd) J(8.32, 14.22, 15.59) B (d) 2.33 J(6.98) 3000 A (d) J(9.66) Fig. S54. 1 H NMR spectrum of M 1 MGx-A-NAC (D 2 O) 35

36 Fig. S C NMR spectrum of M 1 MGx-A-NAC (D 2 O)

37 {4.58,3.43} {4.59,3.64} {4.31,3.88} 3.5 {6.20,4.88} {4.49,4.33} {4.88,4.51} {4.50,4.87} {3.95,4.30} {3.90,4.31} {3.41,4.59} {4.31,4.48} {3.66,4.59} {4.88,6.20} Fig. S56. COSY spectrum of M 1 MGx-A-NAC (D 2 O) 37

38 0 {2.30,15.82} {4.58,58.00} {4.50,73.65} {3.40,40.62} {2.07,25.02} {3.65,40.70} {3.88,64.52} {3.95,64.57} {6.20,92.12} {4.88,77.01} {4.30,88.57} {8.54,139.07} {8.49,144.47} {8.74,171.88} {9.54,194.80} Fig. S57. HSQC spectrum of M 1 MGx-A-NAC (D 2 O) 38

39 20 {8.74,40.28} {8.49,91.51} {6.19,76.73} {6.20,88.67} {4.58,40.38} {3.66,57.60} {3.41,57.55} {4.31,72.97} {4.50,64.28} {4.88,91.55} {4.50,91.68} {9.57,115.27} {8.55,114.08} {9.55,126.95} {8.48,124.63} {4.30,91.98} {2.33,115.17} {3.39,127.55} {2.33,127.51} {9.57,145.03} {8.49,141.89}{6.20,141.49} {6.20,144.80} {3.66,127.28} {2.33,145.01} {8.54,142.32} {9.57,171.89} {3.41,171.66}{2.32,171.63} {3.66,178.61} {8.74,194.30} {4.58,176.95} {3.40,180.91}{2.33,194.34} {2.08,175.58} Fig. S58. HMBC spectrum of M 1 MGx-A-NAC (D 2 O) 39

40 {9.58,2.12} {8.74,2.07} 2 {9.58,2.31} {8.74,2.33} {8.74,3.40} 3 {4.58,3.43} {3.67,3.38} {8.74,3.65} {4.50,3.89} {8.48,4.50} {8.49,3.90} {8.49,4.87} {8.74,4.58} {6.19,4.31} {3.42,3.66} {4.31,3.94} {2.32,3.65} {3.42,4.57} {4.88,4.51} {3.97,3.88} {3.94,4.30} {6.20,4.87} 4 {3.66,4.58} 5 {4.50,4.87} {8.49,6.19} {4.31,6.20} {4.87,6.20} 6 7 {6.20,8.48} {4.88,8.48} {9.57,8.74} {4.50,8.49} 8 {3.66,8.74} {4.58,8.74} {8.74,9.57} 9 {3.40,8.74} Fig. S59. NOESY spectrum of M1MGx-A-NAC (D2O)

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Manuscript submitted to the Journal of the American Society for Mass Spectrometry, September 2011.

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