Fig 1.
Schematic representation of PNA and DNA fragments.
(A) DNA fragment; (B) aeg-, γ- and α-ce-PNAs; (C) Starting thymine monomers 4 and 5 and their conformers, which coexist in solution due to the reduced rotation along the Ntert-C(O)-bond.
Fig 2.
Chromatographic profiles of the PNA monomers (enantiomers).
(A) Mixture of 4a and 4b (S- and R- enantiomers of the γ-monomer); (B) S-entantiomer of the γ-monomer, 4a (Conditions: Diasphere column 110-Chirasel-E-PA, 7 μm; elution system: MeOH/CH3COOH = 96/4 (v/v); flow rate: 1 mL/min; UV-detection at 254 nm; temperature: 20°C); (C) Mixture of 5a and 5b (R- and S-enantiomers of the α-monomer); (D) S-entantiomer of the α-monomer, 5a (Conditions: Diasphere column 110-Chirasel-E-PA, 7 μm; elution system: MeOH/CH3COOH/TEA = 100/0.1/0.1 (v/v/v); flow rate: 0.5 mL/min; UV-detection at 254 nm; temperature: 20°C); R = CH2CH2COOBn.
Fig 3.
Chromatographic profiles of the PNA monomer derivatives (diastereomers).
(A) Mixture of diastereomers 7a and 7b; (B) Diastereomer 7a (Conditions: Luna column, 5 μm, CN 100A, elution system: heptane/isopropanol (88/12), flow rate: 1 mL/min); (C) Mixture of diastereomers 8a and 8b; (D) Diastereomer 8a (Conditions: Separon SGX RP-S C18 column, 5 μm, 4x150 mm, elution system: acetonitrile/water (1/1), flow rate: 1 mL/min); R = -CH2CH2COOBn.
Fig 4.
UV-melting and CD spectra of PNA/DNA and DNA/DNA complexes.
(A) Thermal difference spectra of the complexes; (B) Thermal denaturation profiles of the complexes; (C) CD spectra of the single-stranded oligonucleotides and PNAs. The molar ellipticity was calculated per 1 nucleotide. (D) CD spectra of the complexes. Conditions: 10 mM Na2HPO4 (pH 7.4), 140 mM KCl, 5 mM MgCl2. The concentration of each PNA or oligonucleotide was 2.5 μM. The CD spectra were measured at 15°C.
Fig 5.
J-Plots and CD spectra of γ-ce-H-(T10)-Gly-NH2 (2)/dA10.
(A) Absorbance of the γ-ce-H-(T10)-Gly-OH (2)/dA10 mixtures with various PNA/DNA ratios at 260 nm; (B) Absorbance of the mixtures at 275 nm; (C) Molar ellipticity at 263 nm. Conditions: 10 mM Na2HPO4 (pH 7.4), 140 mM KCl, 5 mM MgCl2. The summed PNA and DNA concentration was 7 μM at each ratio; (D) CD spectra of the triplex. The molar ellipticity is given per 1 nucleotide in a strand. Conditions: 10 mM Na2HPO4 (pH 5 or 7.4), 140 mM KCl, 5 mM MgCl2. The triplex concentration was 1.8 μM.