Blue fluorescent deoxycytidine analogues: convergent synthesis, solid-state and electronic structure, and solvatochromism

Abstract

We report the synthesis and photospectroscopic characterisation of intrinsically fluorescent triazole-appended cytidines. Fluorescence was found to be highly dependent on solvent conditions. X-Ray crystallographic data show the proton of the exocyclic amine of the nucleobase and the triazole N(3) engaged in a H-bond.

Cleavage of Functionalized DNA Containing 5‐Modified Pyrimidines by Type II Restriction Endonucleases

“…The spectral data were in accordance with the literature. [24] Desilylation of dU TMSE and dC TMSE : A trimethylsilylethynyl nucleoside (0.67 mmol) and KF (390 mg, 6.7 mmol) were dissolved in a THF/MeOH mixture (1:1, 14 mL). The reaction mixture was stirred at room temperature for 2.5 h. Products were isolated from crude reaction mixture by silica gel column chromatography (gradient of CHCl 3 to 10 % MeOH), concentration, and drying under vacuum.…”

Synthesis and spectral characterization of environmentally responsive fluorescent deoxycytidine analogs

“…When 5-iododeoxycytidine 31,32 (8a) and 1-ethynylpyrene (4c) were subjected to the conditions of Sonogashira cross-coupling, the deoxycytidine analog 2b was obtained in 50% yield (Scheme 2). The 4-methoxyphenyl-modified deoxyuridine analog 2a was obtained in the same manner from deoxyuridine (9) and 4-methoxyphenylacetylene (4b) as described previously by our group 24 (Scheme 3).…”

Highly Fluorescent 5‐(5,6‐Dimethoxybenzothiazol‐2‐yl)‐2′‐Deoxyuridine 5′‐Triphosphate as an Efficient Substrate for DNA Polymerases

“…Chemical syntheses of short oligodeoxyribonucleotides (ODNs) containing fluorescent nucleobase analogues such as 2-aminopurine (2-AP), [2] 5-substituted pyrimidine analogues, [3] pyrrolo-dC, [4] pyrimidopyrimidoindole, [5] the blue fluorescent triazole deoxycytidine analogues, [6] triazole adenine (A T ), [7] and the base-discriminating fluorescent bases (BDF) at a specific site have been reported. [8] However, the enzymatic incorporation of these fluorescent nucleobase analogues into DNA has not been substantially studied, although the enzymatic method is useful for the synthesis of longer DNA probes for detecting biological processes and for DNA sequencing.…”

“…The coupling yields are similar to those of the natural DNA synthesis. These ODNs were used for enzymatic polymerization experiments, and the synthesized sequences of ODNs are shown in Figures 1, 2 [6][7][8][9][10][11][12][13], were able to incorporate two d bt UTP into a full-length elongated DNA (22-mer); here the exception was Pfu, which has strong 3'!5' exonuclease activity. Figure S1, lanes 4 and 5, respectively), afforded better results for the elongation reactions; this might be due to stabilization of the primer/template-polymerase-triphosphate complex, but at 45 or 35 8C ( Figure S1, lanes 6 and 7, respectively) the polymerase did not work well.…”