Synthesis and Applicability of Base‐Discriminating DNA‐Triplex‐Forming ¹⁹F NMR Probes

Abstract

Phosphoramidite building blocks of CF3‐modified N4(6‐amino‐2‐pyridinyl)deoxycytidines were synthesized, incorporated into triplex‐forming 2′‐deoxyoligonucleotide strands and the applicability of the probes to recognize nucleobase content in the pyrimidine‐rich strand of double‐helical DNA targets was evaluated. As expected, the obtained 19F NMR resonances were sensitive to the base content and unique 19F NMR spectral fingerprints could be obtained.

3-Fluoro-2-mercuri-6-methylaniline Nucleotide as a High-Affinity Nucleobase-Specific Hybridization Probe

“…Single stranded ON­(F) gave two signals at −122.18 ppm (minor) and at −123.05 ppm (major), which may be attributed to syn/anticonformers of the probe. Control measurements of ON­(F) in the presence of ON­(X) (1.0 and 2.0 equiv) resulted in two new signals with varying intensities and characteristic shifts depending on the complementary nucleobase (Figure S29); however, because of the modest affinity, it existed as a mixture of conformers in the double helices, and two resonance signals were observed …”

“…Control measurements of ON(F) in the presence of ON(X) (1.0 and 2.0 equiv) resulted in two new signals with varying intensities and characteristic shifts depending on the complementary nucleobase (Figure S29); however, because of the modest affinity, it existed as a mixture of conformers in the double helices, and two resonance signals were observed. 55 Mercuration of the probe caused a drastic ca. 20 ppm downfield shift, where ON(F−Hg) was observed as broad humps.…”

Synthesis of Trifluoromethylated Purine Ribonucleotides and Their Evaluation as 19F NMR Probes

“…1 were estimated spectrophotometrically by measurement of absorbance at 260 nm in 0.1 M phosphate buffer pH 6.0 (6, 28) or 7.0 (23,25,26,27). To calculate the exact concentrations, the following molar extinction coefficients [M −1 cm −1 ] were employed: ε = 11400 (6,13,20), ε = 15020 (23), ε = 27036 (25,26), ε = 22600 (27), and ε = 21132 (28).…”

2-Trifluoromethyl-6-mercurianiline Nucleotide, a Sensitive 19F NMR Probe for Hg(II)-mediated Base Pairing

“…In each case, the initial signal of ON(1) did not disappear entirely upon the addition of an equimolar amount of the complementary strand due to the low duplex stability. 61 These 19 F NMR data acted as a useful control that would expose plausible non-mercury-related signals in the experiments with ON(2) below.…”