Supporting Information

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1 Supporting Information Combinatorial synthesis of benzimidazolium dyes and its diversity directed application toward GTP-selective fluorescent chemosensors Shenliang Wang and Young-Tae Chang* Department of Chemistry, ew York University, ew York, ew York 13 General Information All chemicals and solvents were purchased from Sigma-Aldrich or Acros and used without further purification. 2-Chlorotrityl alcohol resin (1.37 mmol/g) were purchased from BeadTech Inc., Korea. All compounds were tested with LC-MSD (ChemStation 11, Agilent Technologies.) equipped with a Phenomenex Luna 3µ C18 column (2 4. mm). 1 H-MR and 13 C-MR spectra were obtained on a Bruker Avance MR spectrometer and were recorded at and 1 MHz respectively. Chemical shifts are reported relative to internal chloroform (1H δ 7.26 ppm, 13C δ 77. ppm) or dimethyl sulfoxide (1H δ 2.5 ppm, 13C δ ppm). All nucleosides and nucleotides were purchased from Sigma with the highest purity available with sodium as the counter cation. 5,6-dichloro-1,2-dimethyl-benzoimidazole (2) Triethyl orthoacetate (4.6 g, 1 eq) was added dropwisely to a refluxing mixture of 4,5-dichloro-1,2-phenylenediae (5 g, 1 eq) and a catalytic amount of p-toluenesulfonic acid in toluene ( ml). The mixture was refluxed for 3 hrs and 5.7 g black solid was collected after evaporation of the solvents under reduced pressure and used directly in the following step without further purification. ESI-MS (m/z) calcd (found): 2.(21.1) for [M + H] +. To the crude 5,6-dichloro-2-methyl-benzoimidazole (5.7 g, 1 eq) and grinded potassium hydroxide (4.8 g, 3 eq) in acetone (5 ml) was added iodomethane (5.2 g, 1.4 eq) dropwisely and the mixture was stirred overnight. The solvent was evaporated under reduced pressure and the residue was partitioned between dichloromethane (2 ml) and water (2 ml). The aqueous phase was washed 2 times with dichloromethane (2 ml) and the combined organic phase was dried over a 2 S 4 and evaporated to dryness. The crude product was recrystallized from ethyl acetate. 5.5 g product was collected as pale flakes with 9.6% yield for two steps. 1 H MR: (CD 3 ) 2.55 (s, 3H), 3.63 (s, 3H), 7.28 (s, 1H), 7.68 (s, 1H). 13 C MR: (CD 3 ): 13.82, 3.5, 11.2, 12., , , , , ESI-MS (m/z) calcd (found): 214.(215.1) for [M + H] +. - S1 -

2 Tf Ethyl 6-(trifluoromethylsulfonyloxy)hexanoate (4) To the suspension of poly(4-methylpyridine) (2.24 g, 2 eq) in newly dried dichloromethane (25 ml ) at C was added trifluoromethanesulfonic anhydride (5 g, 1 eq) dropwisely over 3 s. Ethyl 6-hydroxyhexanoate (2.76 g,.95 eq) was then added in dropwisely via a syringe. The mixture was stirred at C for 4 hrs and the polymer was filtered off by a frit. The solvent was evaporated under reduced pressure (without heating) and the crude product was subjected to a short silica gel pad with 1:4 (v/v) diethyl ether/hexane as the eluent solvent. The solvent was evaporated (without heating) and the product was used directly in the following step. (3.9 g, 75% yield based on ethyl 6-hydroxyhexanoate.) + 5,6-dichloro-1-(6-ethoxy-6-oxohexyl)-2,3-dimethyl-benzoimidazolium trifluoromethanesulfonate (5) To 2 (2 g, 1 eq) in 1 ml dichloromethane was added 4 (2.8 g, 1 eq) and stirred in dark for 24 hrs at room temperature. Solvent was evaporated under reduced pressure and the residue was recrystalized from MeH/diethyl ether to get the white powder as product(4.1 g, 87% yield.) 1 H MR: (DMS) 1.16 (t, 3H), 1.37 (m, 2H), 1.57 (m, 2H), 1.75 (m, 2H), 2.28 (t, 2H), 2.88 (s, 3H), 3.96 (s, 3H), 4.4 (q, 2H), 4.46 (t, 2H), 8.48 (s, 1H), 8.52 (s, 1H). 13 C MR: (DMS): 1.61, 13.98, 23.9, 25.4, 28.11, 31.98, 33.2, 45.9, 59.58, , , , , 13.6, 13.91, , ESI-MS (m/z) calcd (found): 357.1(357.3) for [M] +. - S2 -

3 + H 1-(5-carboxypentyl)- 5,6-dichloro- 2,3-dimethyl-benzoimidazolium bromide (6) 5 (4 g) was dissolved in 48% HBr aqueous solution (5 ml) and heated at 65 C for 2 hrs and then evaporated to dryness. The residue was recrystalized from acetone to yield 2.5 g white crystal, yield 77%. 1 H MR: (DMS) 1.36 (m, 2H), 1.54 (m, 2H), 1.74 (m, 2H), 2.21 (t, 2H), 2.87 (s, 3H), 3.95 (s, 3H), 4.46 (t, 2H), 8.49 (s, 1H), 8.54 (s, 1H). 13 C MR: (DMS): 1.75, 23.92, 25.14, 28.19, 32.8, 33.37, 45.13, , , , , 13.4, 13.91, , ESI-MS (m/z) calcd (found): 329.1(329.1) for [M] +. H H 2 Resin bound 2-ao-ethylae (8) To 2-chlorotrityl alcohol resin 7 (1 g, 1.37 mmol/g) pre-suspended in dichloromethane (1 ml) in a 2 ml vial for 1 was added thionyl chloride (1 ml, 1 eq), and the vial was shaken for 2 hrs at room temperature. The resin was filtered and washed with dichloromethane and acetonitrile alternatively for 5 times and dried in vacuum. The resin was then suspended in dichloromethane (1 ml) for 1 and was added ethylenediae ( µl, 4 eq) and shaken at room temperature for 3 hrs. The resin was filtered and washed with dichloromethane and methanol alternatively for 5 times and dried in vacuum. - S3 -

4 + H H Resin bound benzoimidazolium block (9) DIPEA ( µl, 3 eq), HATU (1.56 g, 3 eq) and 6 (1.64 g, 3 eq) in ml dichlormethane and 2 ml DMF were shaken at room temperature for 3 s. To this solution was added resin 8 (1 g, 1 eq) and shaken at room temperature overnight. The resin was filtered and washed with dichloromethane and methanol alternatively for 5 times and dried in vacuum. To an aliquot of the resin was added 1 µl 5% trifluoroacetic acid/dichloromethane cleavage cocktail solution and shook for 15 s. The solution was subjected to LC-MS. ESI-MS (m/z) calcd (found): 371.1(371.3) for [M] +. + R H H Resin bound benzimidazolium dyes (1) To resin 9 (1 mg, 1 eq) was added each aldehyde (chart S1) (1 eg) in 1-methyl-2-pyrrolidinone (3 µl) solution and pyrrolidine (2 µl). The reaction was shaken in dark and under a positive pressure of nitrogen for 24 hrs. The resin was filtered and washed with DMF (5 times), alternatively dichloromethane and methanol (5 times), dichloromethane (5 times) and dried in vacuum. - S4 -

5 Chart S1. Aldehyde building blocks for benzimidazolium dye library. R-CH, R= F 3 C CF 3 nbu H Bn 12 H H 13 H 14 Bn Bn Bn H Me H H 32 F S S H 48 H H H 49 Br 5 51 Me Me Me Me I 54 H I 55 Br Br 56 I 57 H H H 61 H C H 64 H H 68 2 F9 Br 7 H H H 73 2 Br H Br Br S H S CF 3 H I 83 H 84 Me H S Br S Bn 9 91 Me 92 CF 2 CF 2 H CF 3 H 96 eavage of benzimidazolium dyes from resin (11) Resin 1 (1 mg) was suspended in 5% trifluoroacetic acid/dichloromethane cleavage cocktail solution (.5 ml) and shook for 15. The resin was filtered off and washed with dichloromethane (1 ml) and methanol (1mL). The solutions were collected and evaporated to dryness to obtain the benzimidazolium dyes. - S5 -

6 Table S1. Benzimidazolium dye library member list Compound Purity (%) λ ex (nm) λ em (nm) Compound Purity (%) λ ex (nm) λ em (nm) Code Code G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G S6 -

7 G G G G G G G G G G G G G G G G G G G G : Products were collected without further purification. Purity of each product was calculated based on LC-MS 35nm trace area sizes. :All fluorescence excitation and emission data were recorded on a Gei XS fluorescent plate reader with 1mM compounds in methanol (1 µl) in Grainer 96 well black polypropylene plates. All λ em were measured at the corresponding λ ex, and vice versa. Primary screening procedure Benzimidazolium compounds were transferred to Grainer 384 well black polypropylene plates (final concentration as 2 µm) and tested against 1 µm AMP, ADP, ATP, UTP, CTP, GTP and blank control in 1 mm HEPES buffer (ph = 7.4) with 1% DMS. Fluorescence emission spectra were recorded on a Gei XS fluorescent plate reader with excitation at 35 nm (cutoff: 42 nm), nm (cutoff: 435 nm), 45 nm (cutoff: 495 nm). - S7 -

8 + H H H 2 G49 (GTP Green) Characterization 1 H MR (DMS): 1.18 (m, 2H), 1.38 (m, 2H), 1.71 (m, 2H), 1.95 (t, 2H), 2.46 (m, 2H), 3.2 (m, 2H), 4.2 (s 3H), 4.46 (t, 2H), 7.1 (d, 1H, J = 16 Hz), 7.31 (m, 2H), 7.55 (m, 4H), 7.64 (d, 2H), 7.74 (d, 1H, J = 16 Hz), 8.2 (d, 1H), 8.41 (s, 1H), 8.43 (s, 1H). 13 C MR (DMS): 24.41, 25.51, 28.45, 33.46, 35.5, 36.32, 45.53, 1.3, 19.34, , , , , , , 12.7, , 122.8, , , , , 129.2, , , 13.34, 13.72, 131., 137.1, 141., , , , ESI-MS (m/z) calcd (found): 574.2(574.4) for [M] +. Figure S1. LC-MS spectrum of G49. DAD1 A, Sig=45,16 Ref =of f (C:\G1.D) DAD1 B, Sig=,16 Ref =of f (C:\G1.D) DAD1 C, Sig=35,16 Ref =of f (C:\G1.D) DAD1 D, Sig=25,16 Ref =of f (C:\G1.D) MSD1 TIC, MS File (C:\G1.D) API-ES, Pos, Scan, Frag: *MSD1 SPC, time=1.663:2.33 of C:\G1.D API-ES, Pos, Scan, Frag: Max: m/z - S8 -

9 Figure S2. Excitation, emission, and absorbance spectra of G49 in MeH. Fluorescent Intensity Excitation Emission Wavelength(nm) Fluorescence excitation (emission: 52 nm, cutoff: 515 nm) and emission (excitation: 45 nm, cutoff: 495 nm) spectra of 1 mm G49 in methanol (1 µl) in a Grainer 96 well black polypropylene plate. 1.5 Absorbance Wavelength(nm) UV-Vis absorption spectrum of 1 mm G49 in methanol (1 µl) in a Falcon Microtest flat bottom 96 we polystyrene plate, recorded on a SpectraMax Plus plate reader. - S9 -

10 Figure S3. LC-MS spectrum of G32. ESI-MS (m/z) calcd (found): 592.2(592.1) for [M] +. + H F H H 2 1 DAD1 A, Sig=45,16 Ref =of f (C:\G2.D) DAD1 B, Sig=,16 Ref =of f (C:\G2.D) DAD1 C, Sig=35,16 Ref =of f (C:\G2.D) DAD1 D, Sig=25,16 Ref =of f (C:\G2.D) MSD1 TIC, MS File (C:\G2.D) API-ES, Pos, Scan, Frag: *MSD1 SPC, time=1.671:2. of C:\G2.D API-ES, Pos, Scan, Frag: Max: m/z - S1 -

11 Figure S4. LC-MS spectrum of Q49. ESI-MS (m/z) calcd (found): 53.3(53.2) for [M] +. + H H H 2 *DAD1 A, Sig=5,16 Ref =of f (E:\LC-MSS~1\Q-1\QE1.D) *DAD1 B, Sig=43,16 Ref =of f (E:\LC-MSS~1\Q-1\QE1.D) *DAD1 C, Sig=35,16 Ref =of f (E:\LC-MSS~1\Q-1\QE1.D) *DAD1 D, Sig=25,16 Ref =of f (E:\LC-MSS~1\Q-1\QE1.D) *MSD1 TIC, MS File (E:\LC-MSS~1\Q-1\QE1.D) *MSD1 SPC, time=1.6:1.643 of E:\LC-MSS~1\Q-1\QE1.D Max: m/z - S11 -

12 Figure S5. LC-MS spectrum of Q32. ESI-MS (m/z) calcd (found): 521.3(521.2) for [M] +. + H F H H 2 1 *DAD1 A, Sig=5,16 Ref =of f (E:\LC-MSS~1\Q-1\Q27.D) *DAD1 B, Sig=43,16 Ref =of f (E:\LC-MSS~1\Q-1\Q27.D) *DAD1 C, Sig=35,16 Ref =of f (E:\LC-MSS~1\Q-1\Q27.D) *DAD1 D, Sig=25,16 Ref =of f (E:\LC-MSS~1\Q-1\Q27.D) *MSD1 TIC, MS File (E:\LC-MSS~1\Q-1\Q27.D) *MSD1 SPC, time=1.624:1.643 of E:\LC-MSS~1\Q-1\Q27.D Max: m/z - S12 -

13 Figure S6. Fluorescence emission spectra of G49 with different concentrations of GTP. Fluorescent Intensity X 1-4 M GTP 1 X 1-4 M GTP 5 X 1-5 M GTP 2 X 1-5 M GTP 1.2 X 1-5 M GTP 1 X 1-5 M GTP Blank Control Wavelength(nm) Fluorescence emission spectra (excitation: 4 nm, cutoff: 495 nm) of 1 µm G49 with 5 µm, 1 µm, 5 µm, 2 µm, 12 µm, 1 µm GTP and blank control in 1 mm HEPES buffer (ph = 7.4) with 1% DMS. Figure S7. G49 titration experiment with GTP. Fluorescent Intensity Fold Change log[gtp] For each data point, 1 µm G49 was tested with indicated concentration of nucleotide in 1 mm HEPES buffer (ph=7.4) with 1% DMS. Excitation at 4 nm (cutoff: 515 nm) and emission read at 5 nm. From the titration experiment, GTP showed association constants 1 (K a ) to G49 as 3,3 M S13 -

14 Figure S8. G49 titration experiment with dgtp. Fluorescent Intensity Fold Change log[dgtp] For each data point, 1 µm G49 was tested with indicated concentration of nucleotide in 1 mm HEPES buffer (ph=7.4) with 1% DMS. Excitation at 4 nm (cutoff: 515 nm) and emission read at 5 nm. From the titration experiment, dgtp showed association constants 1 (K a ) to G49 as 25,1 M -1. Figure S9. G32 selectivity test. Fluorescent Intensity GTP ATP All others Wavelength/nm Fluorescence emission spectra (excitation: 4 nm, cutoff: 515 nm) of 1 µm G32 with 1 µm GTP(green), ATP(red), adenosine, AMP, ADP, uridine, UMP, UDP, UTP, cytosine, CMP, CDP, CTP, guanosine, GMP, GDP and blank control (all in black) in 1 mm HEPES buffer (ph = 7.4) with 1% DMS. - S14 -

15 Figure S1. G32 titration experiment with GTP. Fluoresent Intensity Fold Change log[gtp] For each data point, 1 µm G32 was tested with indicated concentration of nucleotide in 1 mm HEPES buffer (ph=7.4) with 1% DMS. Excitation at 4 nm (cutoff: 515 nm) and emission read at 5 nm. From the titration experiment, GTP showed association constants 1 (K a ) to G32 as 31,162 M -1. (1) (a) Conners, K. A. Binding Constants; Wiley: ew York, (b) onlinear fits were performed by Graphpad Prism 4 (GraphPad Software, Inc.) with variable slope sigmoidal dose-response equation: Y ( Top Bottom) Bottom +. log EC5 X 1+ 1 HillSlope = - S15 -