Peptide Nucleic Acid with Double Face: Homothymine–Homocytosine Bimodal Cα-PNA (bm-Cα-PNA) Forms a Double Duplex of the bm-PNA₂:DNA Triplex

Abstract

Cα-bimodal peptide nucleic acids (bm-Cα-PNA) are PNAs with two faces and are designed homologues of PNAs in which each aminoethylglycine (aeg) repeating unit in the standard PNA backbone hosts a second nucleobase at Cα through a spacer chain with a triazole linker. Such bm-Cα-PNA with mixed sequences can form double duplexes by simultaneous binding to two complementary DNAs, one to the base sequence on t-amide side and the other to the bases on the Cα side chain. The synthesis of bm-Cα-PNA with homothymine (T 7 ) on the t-amide face and homocytosine (C 5 ) on the Cα side chain through the triazole linker was achieved by solid phase synthesis with the global click reaction. In the presence of complementary DNAs dA 8 and dG 6 at neutral pH, bm-Cα-PNA 1 forms a higher order pentameric double duplex of a triplex composed of two bm-Cα-PNA-C 5 :dG 5 duplexes built on a core (bm-Cα-PNA-T 7 ) 2 :dA 8 triplex. Circular dichroism studies showed that assembly can be achieved by either triplex first and duplex later or vice versa. Isothermal titration calorimetry data indicated that the assembly is driven by favorable enthalpy. These results validate concurrent multiple complex formation by bimodal PNAs with additional nucleobases at Cα or Cγ on the aeg-PNA backbone and open up ways to design programmed supramolecular assemblies.

Double‐Headed Nucleotides with Non‐Native Nucleobases: Synthesis and Duplex Studies

“…Column chromatography was performed with Silica Gel 60 (particle size 0.040-0.063 μm, Merck). 1 H NMR, 13 C NMR, 19 F NMR and 31…”

“…In recent years, several double-headed nucleoside designs have been presented in the literature. [7][8][9][10][11][12][13] Our previous work has shown that depending on the site of attachment, the additional nucleobase can be positioned in the minor groove, [14][15][16][17] the major groove, [18][19][20] or the center of a DNA duplex. [21][22][23] In the latter case, given that the additional nucleobase is linked through a methylene to the 2'-position of 2'-deoxyuridine or arabinouridine (Figure 1, U X ), the doubleheaded nucleotide has been shown to behave as a condensed dinucleotide.…”

“….81 (br s, 1H, NH), 10.69 (br s, 1H, NH), 7.49 (d, J = 8.1 Hz, 1H, H6), 7.37 (d, J = 2.5 Hz, 1H, H7''), 6.92 (d, J = 2.5 Hz, 1H, H8''), 6.84 (br s, 1H, 2'OH), 5.88 (s, 1H, H1'), 5.73 (d, J = 8.1 Hz, 1H, H5), 4.33 (d, J = 9.3 Hz, 1H, H3'), 4.26 (s, 2H, H6'), 4.11 (dd, J = 13.0, 2.3, 1H, H5 a '), 4.01 (dd, J = 13.0, 2.3 Hz, 1H, H5 b '), 3.72 (m, 1H, H4'), 1.14-1.00 (m, 28H, TIPDS); 13 C NMR (101 MHz, CDCl 3 ) δ 164.0 (C4), 155.4 (C2''), 151.4, 151.3 (C2, C4''), 145.0 (C6''), 141.7 (C6), 120.7 (C8''), 108.7 (C7''), 102.0 (C5), 85.0 (C1'), 80.1 (C2'), 79.5 (C4'), 77.2 (C3'), 60.2 (C5'), 51.9 (C6'), 17.4, 17.3, 17.3 1-((2'-C-(5-Aza-7-deazaxanthin-9-yl)methyl)-β-Darabinofuranosyl)uracil (10): Nucleoside 9 (0.40 g, 0.61 mmol) was dissolved in anhydrous THF (15 mL), and Et 3 N • 3HF (0.30 mL, 1.84 mmol) was added. The mixture was stirred for 20 h at rt.…”

“….97 (m, 2H, H6'), 3.93-3.86 (m, 2H, H3', H4'), 3.71-3.59 (m, 2H, H5'); 13 C NMR (101 MHz, DMSO-d 6 ) δ 163.1 (C4), 154.5 (C2''), 150.8 (C2), 150.6 (C4''), 145.7 (C6''), 142.0 (C6), 120.8 (C8''), 106.8 (C7''), 100.6 (C5), 85.0 (C1'), 84.4 (C4'), 80.9 (C2'), 75.3 (C3'), 60.7 (C5'), 45.9 (C6'); HRMS-ESI m/z 431.0902 [M + Na] + ; calcd (C 15 H 16 N 6 O 8 Na + ) 431.0922.…”

Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications

“…Others have also investigated positively charged α-and γ-modifications of the PNA backbone, and most of them showed promising hybridization properties and improved cellular uptake [82][83][84][85][86]. Very recent work has used α-and γ-positions of the PNA backbone to attach additional nucleobases, which enable these "double face" PNAs to form higher order double and triple helical structures [87,88].…”