Supporting Information for

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1 Electronic Supplementary Material (ESI) for Chemical Science. This journal is The Royal Society of Chemistry 218 Supporting Information for Detection of analytes in mitochondria without interference from other sites based on an innovative ratiometric fluorophore Tian-Bing Ren, ǂa Qian-Ling Zhang, ǂa Dongdong Su, b Xing-Xing Zhang, a Lin Yuan,* a Xiao- Bing Zhang a a State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 4182 (PR China). lyuan@hnu.edu.cn b College of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin 3384 (PR China). ǂ These authors contributed equally to this work. S1 / 23

2 Table of contents: 1 Materials and instruments...s3 2 Synthesis of compounds S4-5 3 Additional spectras.s Supplemental tables..s Fluorescence Microscopic Studies...S-18 6 NMR spectra and MS Spectra.S19-23 S2 / 23

3 1. Materials and instruments Materials and instruments. Unless otherwise stated, all reagents were purchased from commercial suppliers and used without further purification. Solvents were purified by standard methods prior to use. Twice-distilled water was used throughout all experiments. Low resolution mass spectra were performed using an LCQ Advantage ion trap mass spectrometer from Thermo Finnigan or Agilent 11 HPLC/MSD spectrometer. High-resolution electronspray (ESI-HRMS) mass spectra were recorded with a Bruker Q-TF Qualification Standard Kit. NMR spectra were recorded on Bruker-4, using TMS as the internal standard. UV Vis spectra were recorded on a UV-18 spectrophotometer (Shimadzu Corporation, Japan). nephoton photoluminescence spectra were recorded on a HITACHI F46 fluorescence spectrophotometer with a 1 cm standard quartz cell. Cell imaging was performed on Nikon A1plus confocal microscope. The ph measurements were carried out on a PHS-3C ph meter (INESA instrument). TLC analysis was performed on silica gel plates and column chromatography was conducted over silica gel (mesh 2 3) columns, obtained from the Yantai Jiangyou silica gel Development Company Limited. Calculation of fluorescence quantum yield. Fluorescence quantum yield was determined using optically matching solutions of cresol purple (Φ f =.54 in methanol), ICG (Φ f =.13 in DMS) 1 or rhodamine 6G ( f =.95 in EtH) 2 as the standard and the quantum yield was calculated using the following equation: Φ s = Φ r (A r F s /A s F r ) (n s2 /n r2 ) 2 where, s and r denote sample and reference, respectively. A is the absorbance. F is the relative integrated fluorescence intensity and n is the refractive index of the solvent. Calculation of pka Values. pka values of HDFL1 and HDFL2 dye at acidic to nearneutral ph regions were calculated by regression analysis of the fluorescence data to fit equation: ph pka = log (F max F)/(F F min ) Where F is the area under the corrected emission curve, F max and F min are maximum and minimum limiting values of F, respectively. Detection limit calculation. The detection limit was calculated based on the fluorescence titration. The detection limit is calculated using the following equation: 3σ/k where σ is the standard deviation of blank measurements, k is the slope between the emission ratios versus sample concentration. S3 / 23

4 2. Synthesis of compounds C H methylsulphonic acid 11 HDFL1 HDFL2 Scheme S1. The systhesis of HDFL1 and HDFL2. HDFL1. Beta-resorcylaldehyde (2. mmol, 276. mg) and dimedone (1. mmol, 14.1 mg) were dissolved in methylsulphonic acid (3. ml), then the reaction mixture was heated to 11 C and keep at this temperature for 2 hour. The obtained reaction solution was cooled to room temperature, and then poured onto crushed ice (1. g). Perchloric acid (7%, 2. ml) was then added, and the resulting precipitate was filtered off, washed with cold water (5. ml), and then the crude product was purified via chromatography (silica gel, CH 2 Cl 2 /CH 3 CH 2 H = 25:1) to get a red solid product. Yield 62. mg (18.%). 1 H NMR (4 MHz, MeD) δ 8.21 (s, 2H), 7.71 (s, 1H), 7.69 (s, 1H), 7.4 (d, J = 2.2 Hz, 1H), 7.2 (d, J = 2.2 Hz, 1H), 6.98 (2H), 6.47 (s, 1H), 1.72 (s, 6H). 13 C NMR (1 MHz, DMS) δ 167.4, 165.3, 4.5, 138., 13.9, 13.1, 117.9, 1.7, 12.4, 96.3, 56.5, HRMS (ESI): for C 22 H 17 4 : m/z = [M + H] +. HDFL2. Beta-Resorcylaldehyde (2. mmol, 276. mg) and diacetone (1. mmol, 1.2 mg) were dissolved in methylsulphonic acid (3. ml). The reaction mixture was heated to 11 C and keep at this temperature for 2 hour. The obtained reaction solution was cooled to room temperature, and then poured onto crushed ice (1. g). Perchloric acid (7%, 2. ml) was then added, and the resulting precipitate was filtered off and washed with cold water (5. ml), and then the crude product was purified via chromatography (silica gel, CH 2 Cl 2 /CH 3 CH 2 H = 25:1) to get solid product. Yield 55.2 mg (18.2%). 1 H NMR (4 MHz, MeD) δ 8.2 (2H), 7.8 (2H), 7.61 (2H), 7.3 (2H), 7. (1H), 6.98 (1H), 6.11 (1H). 13 C NMR (1 MHz, MeD) δ 166.2, 6.4, 141.9, 13.3, 118.1, 114.8, 12.3, HRMS (ESI): for C 19 H 13 4 : m/z = [M + H] +. HDFL-Cys. HDFL1 (1. mmol, 345. mg) and acryloyl chloride (1.5 mmol, 122. μl) were dissolved in anhydrous acetonitrile (5. ml), and the reaction mixture were stirred at room temperature for 5 hour, and then all solvent was evaporated. The crude product was purified via chromatography (silica gel, CH 2 Cl 2 ) to get HDFL-Cys (228.2 mg) with a yield of about 5.4%. 1 H NMR (4 MHz, CDCl 3 ) δ 8.59 (2H), 8. (2H), 7.53 (2H), 7.35 (2H), 6.69 (2H), 6.52 (1H), 6.35 (2H), 6.14 (2H), 1.87 (6H). 13 C NMR (1 MHz, CDCl 3 ) δ 17., 169.8, 163.3, 4.9, 2.6, 139.9, 134.5, 134.2, 131.4, 127.1, 121.8, 12.4, 11., 33.1, MS (ESI): for [C 28 H 21 6 ] + : m/z = [M] +. S4 / 23

5 H 2 N P + H HATU DIEPA N H P A B R1 Compound R1. A mixture of compound A (32 mg, 1 mmol), compound B (188 mg, 1 mmol), HATU (42 mg, 1.1 mmol) and catalytic amount of DIEPA was dissolved in DMF (5 ml) and stirred for 4 h at room temperature. After completion of reaction, the solution was poured into water. The resulting precipitate was filtered off and washed with plenty of water. After the sample dried, purification by flash column chromatography to obtain compound R1 as a white powder. We characterized its structure by mass spectral analysis. MS (ESI): calcd for [C 32 H 29 N 2 P] , found Additional spectras a) Absorption CH 3 CN DCM EtH PBS (2% EtH) b) Normalized Intensity CH 3 CN DCM EtH PBS (2% EtH) Figure S1. The absorption (a) and normalized fluorescence emission spectra (b) of HDFL1 (5 μm) in different solvent. a) Absorption CH 3 CN DCM EtH PBS (2% EtH) S5 / 23

6 b) Normalized Intensity CH 3 CN DCM EtH PBS (2% EtH) Figure S2. The absorption (a) and normalized fluorescence emission spectra (b) of HDFL2 (5 μm) in different solvent. H HDFL1 + H + - H + + H + - H + HDFL2 H + H + - H + + H + - H + Scheme S2. The dissociation and vibrational states of HDFL1-2 in polar solutions. H - H + + H + - H + + H + a) ph 11. b) ph S6 / 23

7 c) F pka = ph d) 3 F pka = ph Figure S3. Fluorescence emission spectra of HDFL1 (5 μm) in PBS buffer (containing 2% EtH) solution with ph changing from 3. to 11., (a) λ ex : 52 nm; (b) λ ex : 62 nm. Sigmoidal fitting of the ph-dependent fluorescence intensity at 592 nm (c) and 681 nm (d) of HDFL1. H - H + H - H + H a) 24 b) ph ph c) d) F pka = 5.54 F pka = ph ph Figure S4. Fluorescence emission spectra of HDFL2 (5 μm) in PBS buffer (containing 2% EtH) solution with ph changing from 3. to 11., (a) λ ex : 52 nm; (b) λ ex : 62 nm. Sigmoidal fitting of the ph-dependent fluorescence intensity at 599 nm (c) and 684 nm (d) of HDFL2. S7 / 23

8 Normalized Intensity Ex = 52 nm Ex = 62 nm ph ph Figure S5. The normalized emissiom intensity of HDFL2 (5 μm) in PBS buffer (containing 2% EtH) solution with ph changing from 3. to 11.. Absorptiom ph ph Figure S6. The absorption spectra of HDFL2 (5 μm) in PBS buffer (containing 2% EtH) solution with ph changing from 3. to Time, second Figure S7. Time-dependent fluorescence emission spectra of HDFL1 (5 μm) in 7.4 PBS (containing 2% EtH and 1 mm GSH) for -6 min. S8 / 23

9 Time, second Figure S8. Time-dependent fluorescence emission spectra of HDFL1 (5 μm) in 7.4 PBS (containing 2% EtH and.1 mm H 2 2 ) for -6 min Time, second Figure S9. Time-dependent fluorescence emission spectra of HDFL1 (5 μm) in 7.4 PBS (containing 2% EtH and.1 mm H 2 S) for -6 min Time, second Figure S1. Time-dependent fluorescence emission spectra of HDFL1 (5 μm) in 7.4 PBS (containing 2% EtH and.1 mm Cl) for -6 min S9 / Time, second

10 Figure S11. Time-dependent fluorescence emission spectra of HDFL1 (5 μm) in 7.4 PBS (containing 2% EtH and 25 μm N - ) for -6 min Time, second Figure S12. Time-dependent fluorescence emission spectra of HDFL2 (5 μm) in 7.4 PBS (containing 2% EtH and 1 mm GSH) for -6 min Time, second Figure S13. Time-dependent fluorescence emission spectra of HDFL2 (5 μm) in 7.4 PBS (containing 2% EtH and.1 mm H 2 2 ) for -6 min Time, second Figure S14. Time-dependent fluorescence emission spectra of HDFL2 (5 μm) in 7.4 PBS (containing 2% EtH and.1 mm H 2 S) for -6 min. S1 / 23

11 Time, second Figure S. Time-dependent fluorescence emission spectra of HDFL2 (5 μm) in 7.4 PBS (containing 2% EtH and.1 mm Cl) for -6 min Time, second Figure S16. Time-dependent fluorescence emission spectra of HDFL2 (5 μm) in 7.4 PBS (containing 2% EtH and 25 μm N - ) for -6 min. a) 14 b) Cys 75 M Fl. Intensity (a. u.) M Cys Figure S17. Fluorescence emission spectra fluorescent probe HDFL-Cys (5 μm) in the presence of various concentrations of Cys ( 75 μm ) in PBS (25 mm, ph = 7.4, 2% EtH), (a) λ ex : 52 nm; (b) λ ex : 62 nm. S11 / 23

12 F 675 /F Equation y = a + b* Adj. R-Squar Value Standard Erro B Intercept B Slope Y =.3795X R 2 = Concentration of Cys ( M) Figure S18. The linear correlation between fluorescence ratio change of HDFL-Cys (5 μm) and the concentrations of Cys. 4.5 Probe Blank Probe+ Cys F 675 nm /F 55 nm Time, second Figure S19. ph-dependent fluorescence intensity ratio changes of HDFL-Cys (5 µm) toward Cys (1 µm), in PBS buffer (25 mm, containing 2% EtH, ph = 3-1), λ ex : 52 nm and λ ex : 62 nm. S12 / 23

13 [M + H + ] 8 75 Relative Abundance Chemical Formula: C 28 H Exact Mass: m/z Chemical Formula: C 22 H 16 4 Exact Mass: HDFL-Cys Figure. S2. ESI-MS spectrum of compound HDFL-Cys in the presence of Cys in ph 7.4 PBS buffer (containing 2% EtH). 4. Supplemental tables HDFL1 HDFL2 Table S1. Photo-physical Properties of HDFL1 PBS (containing DCM CH 3 CN EtH 2% EtH) 592nm/ 574 nm/ 585 nm/ 624nm/ λ abs /λ em 68 nm 596 nm 62 nm 681 nm ε max /M -1 cm S13 / 23

14 Table S2. Photo-physical Properties of HDFL2. PBS (containing DCM CH 3 CN EtH 2% EtH) 6 nm/ 584nm/ 597 nm/ 649nm/ λ abs /λ em 616nm 63 nm 68 nm 684 nm ε max /M -1 cm Comp. Table S3. Photo-physical Properties of HDFL1-2. a Φ(1%) Φ(1%)( Φ(1%) Φ(1%) (DCM) CH 3 CN) (EtH) (PBS, 2% EtH) HDFL HDFL a All the measurements were carried out at 25 C. The relative fluorescence quantum yields in DCM, CH 3 CN and EtH were estimated using cresol purple ( f =.53 in CH 3 H) and in PBS (2% EtH) were estimated using ICG ( f =.13 in DMS) 1, as a fluorescence standard. Table S4. Photo-physical Properties of HDFL-Cys in PBS (containing 2% EtH). λ abs λ em ε max /M -1 cm -1 Φ(1%) HDFL-Cys 539 nm 551 nm a All the measurements were carried out at 25 C. The relative fluorescence quantum yield in PBS (2% EtH) were estimated using rhodamine 6G ( f =.95 in EtH) 2, as a fluorescence standard. N Table S5. Comparison of the response time of Cys probes Comp. Solution Response time Reference N HEPES, 1% 18 s Chem. Sci., 212, 3, EtH mm CTAB media HEPES buffer 9 s rg. Biomol. Chem., 212, 1, Et 3N HEPES, 5% DMS 144 s rg. Lett., 217, 19, EtHN NHEt N N PBS, 3% EtH 3 s Chem. Commun., 29, 39, N HEPES buffer 54 s Anal. Chem., 216, 88, PBS, 2% EtH 4 s This work S14 / 23

15 5. Fluorescence Microscopic Studies (C) Signal Loss % 2% 4% 6% 8% Cy5 HDFL1 1% Time, min Figure S21. Confocal fluorescence images of HepG2 cells co-stained with Cy5 (5 μm) (a) or HDFL1 (5 μm) (b) with continuous irradiation for 3 min using confocal microscope with the same parameters. (c) Quantification of the relative mean fluorescence levels of cells from the images of (a) and (b). Scale bar = 2 μm. For Cy5 and HDFL-Cys, λ ex = 64 nm, λ em = nm. Cell Viability Concentration of cys ( M) Figure S22. Cytotoxicity of HDFL-Cys (5 μm) for HeLa cells. Cells were incubated with HDFL-Cys at corresponding concentrations for 12 h. Cell viability was measured by MTT assay and the results are reported as percentage relative to untreated cells (mean ± SD). Figure S23. Confocal fluorescence images of HeLa cells co-stained with HDFL1 and tracker. (a-c) Cells pre-treated with HDFL1 (5 μm) for 3 min at 37 C and then treated with Mito-tracker red (1 μm) for 2 min; (d-f) Cells pre-treated with HDFL1 (5 μm) at 37 C for 3 min and then treated with Hoechst (1 μm) for 2 min. (a, d) images from HDFL1, λ ex = 64 nm, λ em = nm; (b) S / 23

16 Fluorescence images from Mito-tracker Red, λ ex = 561 nm, λ em = nm; (e) Fluorescence images from Hoechst 33342, λ ex = 45 nm, λ em = nm; (c) verlay of the green and red channels. (f) verlay of the blue and red channels. Scar bars= 1 μm. Figure S24. Confocal fluorescence images of HepG2 cells co-stained with HDFL-Cys or HDFL1. (ad) Cells pre-treated with HDFL1 (5 μm) for 3 min at 37 C and then treated with Mito-tracker Red (1 μm) at 37 C for 2 min; (e-h) Cells pre-treated with HDFL-Cys (5 μm) for 3 min and then treated with Mito-tracker Red (1 μm) at 37 C for 2 min. (a, e) Bright field; (b, f) Fluorescence images from Mito-tracker Red, λ ex = 561 nm, λ em = nm; (c) images from HDFL1, λ ex = 64 nm, λ em = nm; (g) Fluorescence images from HDFL-Cys, λ ex = 488 nm, λ em = 5-55 nm; (d) verlay of the orange and red channels; (f) verlay of the orange and green channels. Scar bars = 25 μm. Abs. (Normalized) Abs. FL FL Intensity (Normalized) P(Ph) 3 NH R1 Figure S25. The normalized absorption and normalized fluorescence emission spectra of R1 (5 μm) in PBS buffer (ph = 7.4, containing 2% EtH). S16 / 23

17 Figure S26. Confocal fluorescence images of Hela cells co-stained with HDFL-Cys or R1. (a-c) Cells pre-treated with R1 (5 μm) for 1 min at 37 C and then treated with Mito-tracker Red (1 μm) at 37 C for 1 min; (d-f) Cells pre-treated with R1 (5 μm) for 1 min and then treated with HDFL-Cys (5 μm) at 37 C for 1 min. (a, d) Fluorescence images from R1, λ ex = 45 nm, λ em = nm; (b images from Fluorescence images from Mito-tracker Red, λ ex = 561 nm, λ em = nm;; (e) Fluorescence images from HDFL-Cys, λ ex = 488 nm, λ em = 5-55 nm; (c) verlay of the blue and red channels; (f) verlay of the blue and green channels. Scar bars = 2 μm. Figure S27. Fluorescence images of HDFL-Cys responding to Cys in living HepG2 cells by confocal fluorescence imaging. (a) Control experiment without HDFL-Cys; (b) Cells only treated with HDFL- Cys (5 μm) for 3 min at 37 C. (c) Cells were pre-treated with NEM (5 μm) for 3 min, and then incubated with HDFL-Cys (5 μm) for another 3 min, (d) Cells were pre-treated with Cys (1 μm) for 3 min, and then incubated with HDFL-Cys (5 μm) for 3 min. The fluorescence images were captured from the green channel of 5-55 nm (second column) and red channel of nm (third column) with excitation at 488 nm and 64 nm. Fifth column: ratiometric images of the red channel to the green channel. Scale bar: 1 μm. S17 / 23

18 4 3 Ratio red/green 2 1 Cys+probe probe NEM+probe control Figure S28. Fluorescence intensity ratios (Ι red /Ι green ) in panels. Data are expressed as mean ± SD of three parallel experiments. Figure S29. Fluorescence images of HDFL-Cys responding to Cys in living HepG2 cells along with reaction time by confocal fluorescence imaging. (a) Brightfield image of cells pretreated with Mito-Tracker Red (1 μm) for 2 min and followed by the addition of HDFL- Cys (5 μm); (b) and (d) are the image of HDFL-Cys; (c) is the image of Mito-Tracker Red; (e) and (f) are the merged image of (b) and (c), (c) and (d), respectively. Fluorescence images were captured from the green channel of 5-55 nm (second column) and red channel of nm (fourth column) with excitation at 488 nm and 64 nm. Third column: the Mito- Tracker Red (1 μm) was captured from the orange channel of nm with excitation at 561 nm. Scale bar: 25 μm. S18 / 23

19 Ratio red/green Time, min Figure S3. Fluorescence intensity ratios (Ι red /Ι green ) in panels with reaction time. Data are expressed as mean ± SD of three parallel experiments. 6. MS Spectra and NMR spectra Intens. x MS,.1-.4min # Chemical Formula: C 22 H 16 4 Exact Mass: m/z Intens. x1 4 +MS,.1-.4min # Chemical Formula: C 19 H 12 4 Exact Mass: m/z S19 / 23

20 T: + c ESI Full ms [ 4.-6.] Relative Abundance Chemical Formula: C 28 H Exact Mass: Elemental Analysis: C, 74.16; H, 4.67;, m/z T: + c ESI Full ms [ 3.-7.] P(Ph) 3 8 Relative Abundance NH R1 Chemical Formula: C 32 H 29 N 2 P + Exact Mass: m/z S2 / 23

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23 (1) ushiki, D.; Kojima, H.; Terai, T.; Arita, M.; Hanaoka, K.; Urano, Y.; Nagano. T. J. Am. Chem. Soc., 21, 132, (2) Kubin, R. F.; Fletcher, A. N. J. Lumin. 1982, 27, S23 / 23