Figures & data
Figure 1. (A) Chemical structures of ligand monomer for the introduction to PNA. (B) Sequences of target BFP gene and pcPNAs with or without the ligand (pSer, EDTA or bisP). K stands for lysine.
Scheme 1. Synthesis of EDTA monomer for the introduction to PNA. (A) (Boc)2O, K2CO3, H2O/1,4-dioxane = 1/1, 98%; (B) benzyl bromide, Et3N, THF, 89%; (C) TFA, CH2Cl2, 95%; (D) tbutyl bromoacetate, DIEA, DMF, 74%; (E) H2, 10% Pd/C, MeOH, 90%; (F) Z-Cl, DIEA, DMAP, CH2Cl2, quant; (G) TFA, CH2Cl2, quant; (H) 6, DIEA, HOBt, HBTU, DMF, 48% (I) H2, 10% Pd/C, MeOH, 82%.
Scheme 3. Benzyl-protected bisP monomer for the introduction to PNA. (A) allyl alcohol, TsOH, benzene, 13%; (B) dibenzyl phosphite, 37% formaldehyde aq, MeOH, 53%; (C) Pd(PPh3)4, pyrrolidine, CHCl3, 87%.
Scheme 2. Fmoc-EDTP monomer for the introduction to PNA. (A) (Boc)2O, K2CO3, H2O/1,4-dioxane = 1/1, 98%; (B) benzyl bromide, Et3N, THF, 89%; (C) TFA, CH2Cl2, 95%; (D) dimethyl phosphite, paraformaldehyde, THF, 43%; (E)H2, 10% Pd/C, MeOH, 90%; (F) Z-Cl, DIEA, DMAP, CH2Cl2, quant; (G) TFA, CH2Cl2, quant; (H) 13, DIEA, HOBt, HBTU, DMF, 48% (I) H2, 10% Pd/C, MeOH, 82%.
Figure 2. Gel shift assay for the confirmation of invasion complex composed of DNA and ligand-modified pcPNAs. Invasion conditions; [double-stranded DNA (119 bp)] = 50 nM, [each of pcPNAs] = 200 or 400 nM and [Hepes (pH 7.0)] = 5 mM at 50°C for 1 h.
![Figure 2. Gel shift assay for the confirmation of invasion complex composed of DNA and ligand-modified pcPNAs. Invasion conditions; [double-stranded DNA (119 bp)] = 50 nM, [each of pcPNAs] = 200 or 400 nM and [Hepes (pH 7.0)] = 5 mM at 50°C for 1 h.](/cms/asset/7bae30c4-31c8-4f4d-a8e9-50dfeb093de6/kdpx_a_10920727_f0005.gif)
Figure 3. (A) Site-selective scission of linearized BFP plasmid DNA by pcPNAs with or without EDTA for the confirmation of its metal-coordination behavior. Lane M, 1,000 bp ladder; Lanes 1 and 2, EDTA-pcPNA-1/EDTA-pcPNA-2; Lanes 3 and 4, pcPNA-1/pcPNA-2. Reaction conditions: [linearized BFP plamid DNA] = 4 nM, [each of pcPNAs] = 100 nM, [Hepes (pH 7.0)] = 5 mM, [NaCl] = 100 mM and [Ce(NO3)3] = 20 μM (Lanes 1 and 3) or 30 μM (Lanes 2 and 4) at 50°C for 17 h under air. (B) Comparison of the effect of ligands introduced to the terminal of pcPNAs on the site-selective DNA scission by using Ce(III) salt. Lanes 1, DNA only; Lane 2, DNA + Ce(III); Lanes 3, EDTA-pcPNA-1/EDTA-pcPNA-2; Lane 4, bisP-pcPNA-1/ bisP-pcPNA-2. Reaction conditions: [linearized BFP plamid DNA] = 4 nM, [each of pcPNAs] = 100 nM, [Hepes (pH 7.0)] = 5 mM, [NaCl] = 100 mM and [Ce(NO3)3] = 30 μM at 50°C for 17 h under air.
![Figure 3. (A) Site-selective scission of linearized BFP plasmid DNA by pcPNAs with or without EDTA for the confirmation of its metal-coordination behavior. Lane M, 1,000 bp ladder; Lanes 1 and 2, EDTA-pcPNA-1/EDTA-pcPNA-2; Lanes 3 and 4, pcPNA-1/pcPNA-2. Reaction conditions: [linearized BFP plamid DNA] = 4 nM, [each of pcPNAs] = 100 nM, [Hepes (pH 7.0)] = 5 mM, [NaCl] = 100 mM and [Ce(NO3)3] = 20 μM (Lanes 1 and 3) or 30 μM (Lanes 2 and 4) at 50°C for 17 h under air. (B) Comparison of the effect of ligands introduced to the terminal of pcPNAs on the site-selective DNA scission by using Ce(III) salt. Lanes 1, DNA only; Lane 2, DNA + Ce(III); Lanes 3, EDTA-pcPNA-1/EDTA-pcPNA-2; Lane 4, bisP-pcPNA-1/ bisP-pcPNA-2. Reaction conditions: [linearized BFP plamid DNA] = 4 nM, [each of pcPNAs] = 100 nM, [Hepes (pH 7.0)] = 5 mM, [NaCl] = 100 mM and [Ce(NO3)3] = 30 μM at 50°C for 17 h under air.](/cms/asset/3883261f-3e6b-42ba-9eab-e460499183d8/kdpx_a_10920727_f0006.gif)