Photolabile Peptide Nucleic Acid Monomers: Synthesis and Photodeprotection

Abstract

The photolabile 2-(2-nitrophenyl)propyloxy carbonyl (NPPOC) group has been introduced as an amino protecting group for peptide nucleic acids (PNA) to be used as building blocks in photolithographic solid-phase PNA synthesis. NPPOC-protected PNA derivatives undergo fast light-promoted deprotection with high per step coupling efficiency.

solid-phase synthesis - genomics - DNA - protecting groups - photolabile

References and Notes

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15

Spectroscopic Data for Selected Compounds. Compound 4: ¹H NMR (400 MHz, CDCl₃): δ = 7.66 (d, J = 8.0 Hz, 1 H, ArH), 7.51 (t, J = 7.4 Hz, 1 H, ArH), 7.41 (d, J = 7.6 Hz, 1 H, ArH), 7.30 (t, J = 7.8 Hz, 1 H, ArH), 6.14 (s, 1 H, NH), 4.05-4.25 (m, 2 H, CH₂), 3.59 (m, 1 H, CH), 3.42 (t, J = 5.2 Hz, 2 H, CH₂), 3.25 (br s, 1 H, NH₂), 3.10 (t, J = 5.6 Hz, 2 H, CH₂), 2.94 (br s, 1 H, NH₂), 1.26 (d, J = 6.8 Hz, 3 H, CH₃). MS (API-ES⁺): m/z = 268.1 [M + H⁺], 290.1 [M + Na⁺], 306.0 [M + K⁺].
Compound 5: ¹H NMR (400 MHz, CDCl₃): δ = 7.72 (d, J = 8.0 Hz, 1 H, ArH), 7.54 (t, J = 7.4 Hz, 1 H, ArH), 7.45 (d, J = 7.6 Hz, 1 H, ArH), 7.31 (t, J = 7.8 Hz, 1 H, ArH), 5.09 (s, 1 H, NH), 4.02-4.21 (m, 2 H, CH₂), 4.09 (q, J = 7.2 Hz, 2 H, CH₂), 3.70 (m, 1 H, CH), 3.38 (s, 2 H, CH₂), 3.20 (t, J = 5.2 Hz, 2 H, CH₂), 2.76 (t, J = 5.6 Hz, 2 H, CH₂), 2.21 (br s, 1 H, NH), 1.27 (d, J = 6.8 Hz, 3 H, CH₃), 1.21 (t, J = 7.0 Hz, 3 H, CH₃). MS (API-ES⁺): m/z = 354.1 [M + H⁺], 376.1 [M + Na⁺], 392.1 [M + K⁺].
Compound 6a: ¹H NMR (400 MHz, CDCl₃): δ = 8.52 and 8.50 (2 s, 1 H, NH), 7.67 (d, J = 8.0 Hz, 1 H, ArH), 7.52 (t, J = 7.4 Hz, 1 H, ArH), 7.43 (d, J = 7.6 Hz, 1 H, ArH), 7.30 (t, J = 7.8 Hz, 1 H, ArH), 7.01 and 6.98 (2 s, 1 H, CH), 5.63 and 5.05 (2 s, 1 H, NH), 4.38 and 4.32 (2 s, 2 H, CH₂), 4.03-4.20 (m, 2 H, CH₂), 4.08 (q, J = 7.2 Hz, 2 H, CH₂), 4.01 (s, 2 H, CH₂), 3.64 (m, 1 H, CH), 3.50 (t, J = 5.2 Hz, 2 H, CH₂), 3.32 (t, J = 5.6 Hz, 2 H, CH₂), 1.89 (s, 3 H, CH₃), 1.35 (d, J = 6.8 Hz, 3 H, CH₃), 1.25 (t, J = 7.0 Hz, 3 H, CH₃). MS (API-ES⁺): m/z = 520.1 [M + H⁺], 542.1 [M + Na⁺], 558.1 [M + K⁺].
Compound 7a: ¹H NMR (400 MHz, CDCl₃): δ = 9.81 and 9.79 (2 br s, 1 H, NH), 7.70 (d, J = 8.0 Hz, 1 H, ArH), 7.54 (t, J = 7.4 Hz, 1 H, ArH), 7.45 (d, J = 7.6 Hz, 1 H, ArH), 7.33 (t, J = 7.8 Hz, 1 H, ArH), 7.06 and 7.01 (2 s, 1 H, CH), 5.88 and 5.39 (2 s, 1 H, NH), 4.40 and 4.38 (2 s, 2 H, CH₂), 4.07-4.25 (m, 2 H, CH₂), 4.02 (s, 2 H, CH₂), 3.62 (m, 1 H, CH), 3.49 (t, J = 5.2 Hz, 2 H, CH₂), 3.35 (t, J = 5.6 Hz, 2 H, CH₂), 1.82 and 1.80 (2 s, 3 H, CH₃), 1.32 (d, J = 6.8 Hz, 3 H, CH₃). MS (API-ES⁺): m/z = 492.1 [M + H⁺], 514.1 [M + Na⁺], 530.0 [M + K⁺].

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17

In a typical procedure to attach photolabile PNA to an amino-glass slide, NPPOC-T was attached to the amino-glass slide mounted in a flow cell by activation of the carboxyl groups of NPPOC-T (14.7 mg, 0.03 mmol) in DMF (0.25 mL). After 20 min, excess NPPOC-T was flushed out with MeCN and specific areas (pixels) were irradiated at 365 nm in MeCN using DMD for varying period of time to remove the photolabile protecting groups at specific locations. The amino groups exposed by this treatment were visualized by being covalently coupled to a BODIPY dye (100 µg) in DMF (0.25 mL) for 10 min followed by scanning on a GenPix Scanner.

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