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

• Published in: Organic & biomolecular chemistry Vol. 9; no. 22; pp. 7763 - 7773
• Main Authors: Zilbershtein, Lital, Silberman, Alon, Fischer, Bilha
• Format: Journal Article
• Language: English
• Published: CAMBRIDGE Royal Soc Chemistry 26.10.2011
• Subjects: Base Pairing; Chemistry; Chemistry, Organic; DNA - analysis; DNA - chemistry; DNA - metabolism; Fluorescence; Fluorescent Dyes - analysis; Fluorescent Dyes - chemical synthesis; Fluorescent Dyes - metabolism; Magnetic Resonance Spectroscopy; Nucleic Acid Conformation; Oligonucleotides - chemistry; Oligonucleotides - metabolism; Phenols - chemistry; Physical Sciences; Purine Nucleosides - analysis; Purine Nucleosides - chemical synthesis; Purine Nucleosides - metabolism; Quantum Theory; RNA - analysis; RNA - chemistry; RNA - metabolism; Science & Technology; Spectrometry, Fluorescence; Staining and Labeling - methods; NUCLEOTIDES; DIRECT ARYLATION; RNA TRANSCRIPTS; MAGNETIC-RESONANCE; MOLECULAR BEACONS; CONFORMATIONAL-ANALYSIS; SUGAR RING; INTRAMOLECULAR CHARGE-TRANSFER; ELECTRONIC-STRUCTURE; NUCLEIC-ACIDS
• ISSN: 1477-0520; 1477-0539
• DOI: 10.1039/c1ob05681f

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, phi > 0.1, and short lambda(em) (<385 nm). Alkynyl conjugated analogues 22-25, exhibited low quantum yields, phi <0.075, and lambda(em) < 385 nm. The alkenyl conjugated analogues 15-21, exhibited lambda(em) 408-459 nm. While analogues 15,16, and 20 bearing an EDG on the aryl moiety, exhibited phi < 0.02, analogues 17, and 21 with EWG on the aryl moiety, exhibited extremely high quantum yields, phi approximate to 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.