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Pyridinium Boranephosphonate Modified DNA Oligonucleotides

Subhadeep Roy‡, Sibasish Paul‡, Mithun Royǂ, Rajen Kundu‡, Luca Monfregola‡ and Marvin H. Caruthers‡*

‡Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80303, United States

ǂ Department of Basic Sciences and Humanities, National Institute of Technology, Manipur, Langol, Imphal-795004 (Manipur), India

marvin.caruthers@colorado.edu

Page# Figure S1: 1H NMR spectrum of 3. S2 Figure S2: 13C NMR spectrum of 3. S3 Figure S3: HRMS trace of 3. S4 Figure S4: HRMS trace of 4. S5 Figure S5: 1H NMR of 6. S6 Figure S6: 13C NMR of 6. S7 Figure S7: HRMS trace of 6. S8 Figure S8: 1H NMR of 11 S9 Figure S9: 13C NMR of 11 S10 Figure S10: HRMS trace of 11 S11 Figure S11: 1H NMR spectrum of 13. S12 Figure S12: 13C NMR spectrum of 13 S13 Figure S13: HRMS trace of 13 S14 Figure S14: 31P NMR spectra of reaction mixtures with varying amount of pyridine S15 Figure S15: 31P NMR of solution from reaction of 1 with 2,6-dimethylpyridine S16 Figure S16: Comparison of 11B decoupled 1H NMR spectrum of 6 and 13. S17 Figure S17: Fluorescence microscopy image of Hela cells treated with 1 µM ODN 10 S18 Figure S18: Fluorescence microscopy image of Hela cells treated with 100 nM ODN 10 S19 Table S1: Mass spectrometry characterization data for ODNs used in cell uptake studies S20 Figure S19: UV-Vis spectral traces for reduction of metal ions by 5 and 6. S20

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Figure S1. 1H NMR spectrum of compound 3. Peaks in the aromatic region correspond to pyridine.

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Figure S2. 13C NMR spectrum of compound 3.

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Figure S3. HRMS spectrum of compound 3. The inset shows an expansion of the main peak.

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Figure S4. HRMS spectrum of compound 4. The inset shows an expansion of the main peak.

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Figure S5. 1H NMR of compound 6.

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Figure S6. 13C NMR of compound 6.

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Figure S7. HRMS spectrum of compound 6.

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Figure S8. 1H NMR of 11.

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Figure S9. 13C NMR spectrum of 11.

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Figure S10. HRMS spectrum of 11.

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Figure S11. 1H NMR of compound 13.

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Figure S12. 13C NMR of compound 13.

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Figure S13. HRMS spectrum of 13.

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Figure S14. 31P NMR spectra from reaction mixtures containing variable amounts of pyridine with respect to 5: (A) 1 equivalent (B) 4 equivalents, (C) 8 equivalents and (D) 16 equivalents. One equivalent of iodine with respect to 5 was used for each of these reactions.

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Figure S15. Reaction of 1 with 2,6-dimethylpyridine in the presence of iodine did not yield the expected product. A majority of the starting material remained after 48 h.

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Figure S16. Comparison of 11B decoupled 1H NMR of 6 (top) and 13 (bottom). Panel on the right shows a zoom-in of the region containing the resonance for the BH2 protons. The assignment of these peaks was based on comparison of the 11B decoupled and non-decoupled 1H NMR spectra.

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Figure S17. Fluorescence microscopy image (100 x magnification) of Hela cells treated with 1 µM ODN 10. The fluorescein signal is in green while that for the Hoechst 33258 dye is in blue.

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Figure S18. Fluorescence microscopy image (100 x magnification) of Hela cells treated with 100 nM ODN 10. The fluorescein signal is in green while that for the Hoechst 33258 dye is in blue.

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Sequence Theor. Mass. Obs. Mass

ODN 7 Fl- TpyTpTpTpTpTpTpTpTpTpTpTpTpTpTpTpTpTpTpTpyT – 3’ 7012.2 7012.2 ODN 8 Fl- TpyTpyTpTpTpTpTpTpTpTpTpTpTpTpTpTpTpTpTpyTpyT – 3’ 7163.6 7162.6 ODN 9 Fl- TpyTpyTpyTpTpTpTpTpTpTpTpTpTpTpTpTpTpTpyTpyTpyT – 3’ 7313.6 7312.4 ODN 10 Fl- TpyTpTpTpTpyTpTpTpTpyTpTpTpTpyTpTpTpTpyTpTpTpyT – 3’ 7313.6 7312.4 Table S1. LCMS data for ODNs used for cell uptake studies.

Figure S19. UV-visible spectral traces for the reduction of (a) HAuCl4, (b) K2PtCl4 at room temperature by 5 and (c) HAuCl4, (d) K2PtCl4 by 6. The reaction solutions contained 5 and 6 at 200 µM and the metals at 5 mM. Absorbance spectra were recorded from 0 to 120 min. and 0 to 240 min. for the reduction of HAuCl4

and K2PtCl4 respectively.

AuCl4-Vsd(TbpT) PtCl42-Vsd(TbpT)

AuCl4-Vsd(TpyT)PtCl42-Vsd(TpyT)

(a) (b)

(c) (d)

0-120min

0-120min

0-240min

0-120min