Novel Nucleoside Analogues with Fluorophores Replacing the DNA Base

Abstract

We describe the preparation and fluorescence properties of a set of new nucleosides in which a known hydrocarbon or oligothiophene fluorophore replaces the DNA base at C(1) of the deoxyribose moiety (see 3a -f). These compounds are potentially useful as probes in the study of the structure and dynamics of nucleic acids and their complexes with proteins. In addition, they may find use as fluorescent labels for nucleic-acid-based biomedical diagnostics methods. The fluorophores conjugated to deoxyribose at C(1) in the α-D-form include terphenyl, stilbene, terthiophene, benzoterthiophene, and pyrene. Also included is a non-fluorescent spacer in which cyclohexene replaces the DNA base. The nucleosides are derived from brominated fluorophore precursors and Hoffer's 2-deoxy-3,5-di-O-(p-toluoyl)-D-ribofuranosyl chloride. The emission maxima of the free nucleosides range from 345 to 536 nm. Also described are the 5′-(dimethoxytrityl) 3′-O-phosphoramidite derivatives 5a -f, suitable for incorporation into oligonucleotides by automated synthesizers.We have taken a related approach to developing new fluorescent labels for DNA [10]. Rather than modifying an existing DNA base, however, we have simply replaced it by another flat aromatic structure, i.e.

Photophysical Characterization of Fluorescent DNA Base Analogue, tC

“…pyrene and phenanthrene, in the place of the base. [28][29][30][31] These fluorescent base analogues obviously lack the hydrogen bonding specificity, but can sterically mimic a base pair, causing only relatively modest perturbations to the natural DNA helix, when incorporated against an abasic site.…”

Replacing the Nucleobases in DNA with Designer Molecules

“…Examples include stilbene, terphenyl, pyrene, phenanthrene, terthiophene, and benzoterthiophene. 10,28 Some of these have high quantum yields and absorbances, and by making a series of such molecules, we hope to make available a wide range of fluorescence properties, including variable excitation and emission maxima. This has become an active area for investigation recently, and other laboratories have reported base replacement by a coumarin dye, 26 by a tethered stilbene, 54 and by pteridine dyes.…”

Strain Promoted Click Chemistry of 8-Azidopurine and 5-Azidopyrimidine Nucleosides and Nucleotides with Cyclooctynes and Applications to Living Cell Imaging

“…193 These compounds were used as probes to study the complexation of nucleic acids with proteins and because of their fluorescent color tunability can potentially be used as biomedical diagnostic tools; they, however, do not form canonical base pairs. [194][195][196] Figure 13.…”