Furan decorated nucleoside analogues as fluorescent probes: synthesis, photophysical evaluation, and site-specific incorporation

Abstract

The synthesis and photophysical evaluation of modified nucleoside analogues in which a five-membered heterocycle (furan, thiophene, oxazole and thiazole) is attached to the 5 position of 2'-deoxyuridine are reported. The furan containing derivative is identified as the most promising responsive nucleoside of this family due to its emission quantum efficiency and degree of sensitivity to its microenvironment. The furan moiety was then attached to the 5 position of 2'-deoxycytidine as well as the 8 position of adenosine and guanosine. Photophysical evaluation of these four furan containing nucleoside analogues reveal distinct differences in the absorption, emission and quantum efficiency depending upon the class of nucleoside (pyrimidine or purine). Comparing the photophysical properties of all furan containing nucleosides, identifies the furan thymidine analogue, 5-(fur-2-yl)-2'-deoxyuridine, as the best candidate for use as a responsive fluorescent probe in nucleic acids. 5-(fur-2-yl)-2'-deoxyuridine was then converted to the corresponding phosphoramidite and site specifically incorporated into DNA oligonucleotides with greater than 88% coupling efficiency. Such furan-modified oligonucleotides form stable duplexes upon hybridization to their complementary DNA strands and display favorable fluorescent features.

Site‐Specific Control of N7–Metal Coordination in DNA by a Fluorescent Purine Derivative

“…[34][35][36]47] According to published procedures, [47] 8-phenyl-2'-deoxyguanosine (2) was obtained in 78 % isolated yield by Suzuki-Miyaura cross-coupling of 8-bomoguanosine and phenyl boronic acid. Unfortunately, other boronic substrates, including 2-aminopyridine-5-boronic acid pinacol ester, 2-nitro-5-pyridineboronic acid pinacol ester, and 4-pyridineboronic acid, all failed to give the desired products under the same reaction conditions.…”

“…[28][29][30] Metallo-nucleobase derivatives of purines are much less studied, with only a few reported examples of ferrocene, Ru II , and Os II complexes of C7-and C8-modified purines. [31][32][33] Due to biaryl-related fluorescence phenomena, [34] arylation of the 8 position of purines can provide highly emissive nucleobase derivatives [34][35][36][37][38][39][40][41][42][43] with the ability to mediate proper base-pairing interactions along both Watson-Crick and Hoogsteen faces. [40][41][42] Given the close proximity to N7, we speculated that the addition of 2-substituted heterocyclic groups to the C8 position of purine residues would furnish bidentate metal ligands capable of directing metal ions to specific N7 sites within folded DNA or RNA.…”

Flexible Nucleobase Analogues: Novel Tools for Exploring Nucleic Acids

“…Notably, the uridine moiety was still able to maintain normal base pairing as well as its Fig. 16 Rozners' G-U wobble base pairing absorption and emission properties and thus could prove useful in various biophysical applications (Greco and Tor 2007).…”

Glycosyltransferases and their Assays

“…Building on the work of Tor and Greco on fluorescent nucleotides, [93] autofluorescent derivatives of GDP-and UDPsugars were obtained by installing a small, fluorogenic substituent at the guanine or uracil nucleobase [94][95][96] (Scheme 6). The strong fluorescence emission of these base-modified sugar-nucleotides obviates the need for conjugation with an external fluorophore such as fluorescein.…”