8-(p-CF3-cinnamyl)-modified purine nucleosides as promising fluorescent probes

Abstract

Natural nucleotides are not useful as fluorescent probes because of their low quantum yields. Therefore, a common methodology for the detection of RNA and DNA is the application of extrinsic fluorescent dyes coupled to bases in oligonucleotides. To overcome the many limitations from which fluorescent nucleotide-dye conjugates suffer, we have developed novel purine nucleosides with intrinsic fluorescence to be incorporated into oligonucleotide probes. For this purpose we synthesized adenosine and guanosine fluorescent analogues 7-25, conjugated at the C8 position with aryl/heteroaryl moieties either directly, or via alkenyl/alkynyl linkers. Directly conjugated analogues 7-14, exhibited high quantum yields, φ >0.1, and short λ(em) (<385 nm). Alkynyl conjugated analogues 22-25, exhibited low quantum yields, φ <0.075, and λ(em)<385 nm. The alkenyl conjugated analogues 15-21, exhibited λ(em) 408-459 nm. While analogues 15,16, and 20 bearing an EDG on the aryl moiety, exhibited φ <0.02, analogues 17, and 21 with EWG on the aryl moiety, exhibited extremely high quantum yields, φ ≈ 0.8, suggesting better intramolecular charge transfer. We determined the conformation of selected adenosine analogues. Directly conjugated analogue 8 and alkynyl conjugated analogue 22, adapted the syn conformation, whereas alkenyl conjugated analogue 15 adapted the anti conformation. Based on the long emission wavelengths, high quantum yields, anti conformation and base-paring compatibility, we suggest analogues 17 and 21 for further development as fluorescent probes for the sensitive detection of genetic material.

New class of 8-aryl-7-deazaguanine cell permeable fluorescent probes

“…9 Therefore, we hypothesized that 7-deazaguanine analogs would exhibit similar fluorescence emission. 10-14 Data presented here far exceeded our expectations. Specific experimental procedures for the synthesis of 8aryl 7DGs were not published.…”

Synthesis and Photophysical Properties of Conjugates of Green Fluorescent Protein (GFP) Chromophore and 2'-Deoxy-Uridine Developed as Labelled Building Blocks for Oligonucleotide Probes

“…Specifically, we coupled a 6-atom spacer at the dU C5-position by Suzuki reaction of 5-iodo-2'-deoxyuridine with (E)-6-chloro-1-hexenylboronic acid pinacol ester to get 15 at 83% yield [17], followed by S N 2 reaction with sodium azide to obtain 16. The latter, without purification, was reacted with triphenylphosphine to give 17 at 79% yield [18]. Compound 17 was treated with HBI analogue, 11, in ethanol at 70 °C for 5 days to get 16 at 82% yield.…”

Synthesis and photophysical characterisation of new fluorescent triazole adenine analogues

“…However, the design and characterisation of new FBAs remains important to the field due to the large potential for brighter and more photostable isomorphic probes. Although most FBAs show a decrease in fluorescence upon incorporation into nucleic acid systems, 7,11,12,20,22,26,31,34 increasing quantum efficiencies have been reported for some analogues. 50 Therefore it will be interesting to investigate the potential of 12a or 12b inside DNA as it is likely that the C7-triazole modification will be well accommodated in the major groove, potentially accompanied by interesting and applicable fluorescence properties.…”

“…7,21 Purine analogues are commonly modified on the C8 position of natural adenine/guanine. [22][23][24][25][26][27][28][29][30][31] Interest in these compounds stems from their utility as fluorescent markers, biomolecular probes, supramolecular building blocks, conformational probes and the use they have in therapeutics. Even though small modifications are reported to insignificantly perturb the DNA duplex, 25,31 bulky C8-substituents have shown to be destabilizing 22,23,29,30 and can shift the conformation around the glycosidic bond from anti to syn.…”