title: Phenyl-imidazolo-cytidine analogues: structure-photophysical activity relationship and ability to detect single DNA mismatch.
abstract: To expand the arsenal of fluorescent cytidine analogues for the detection of genetic material, we synthesized para-substituted phenyl-imidazolo-cytidine ((Ph)ImC) analogues 5a-g and established a relationship between their structure and fluorescence properties. These analogues were more emissive than cytidine (λem 398-420 nm, Φ 0.009-0.687), and excellent correlation was found between Φ of 5a-g and σp(-) of the substituent on the phenyl-imidazolo moiety (R(2) = 0.94). Calculations suggested that the dominant tautomer of (Ph)ImC in methanol solution is identical to that of cytidine. DFT calculations of the stable tautomer of selected (Ph)ImC analogues suggested a relationship between the HOMO-LUMO gap and Φ and explained the loss of fluorescence in the nitro analogue. Incorporation of the CF3-(Ph)ImdC analogue into a DNA probe resulted in 6-fold fluorescence quenching of the former. A 17-fold reduction of fluorescence was observed for the G-matched duplex vs ODN(CF3-(Ph)ImdC), while for A-mismatched duplex, only a 2-fold decrease was observed. Furthermore, since the quantum yield of ODN(CF3-(Ph)ImdC):ODN(G) was reduced 17-fold vs that of a single strand, whereas that of ODN(CF3-(Ph)ImdC):ORN(G) was reduced only 3.8-fold, ODN(CF3-(Ph)ImdC) appears to be a DNA-selective probe. We conclude that the ODN(CF3-(Ph)ImdC) probe, exhibiting emission sensitivity upon single nucleotide replacement, may be potentially useful for DNA single nucleotide polymorphism (SNP) typing.
authors.affiliation: Department of Chemistry, Gonda-Goldschmied Medical Research Center and the Lise-Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University , Ramat-Gan 52900, Israel.
authors.forename: Marina
authors.initials: M
authors.lastname: Kovaliov
authors.forename: Michal
authors.initials: M
authors.lastname: Weitman
authors.forename: Dan Thomas
authors.initials: DT
authors.lastname: Major
authors.forename: Bilha
authors.initials: B
authors.lastname: Fischer
mesh_terms: D003562:Cytidine / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D015342:DNA Probes / Q000737:chemistry*; D005453:Fluorescence; D007093:Imidazoles / Q000737:chemistry*; D020641:Polymorphism, Single Nucleotide; D011789:Quantum Theory; D013050:Spectrometry, Fluorescence; D013329:Structure-Activity Relationship
chemical_list: D015342:DNA Probes; D007093:Imidazoles; D003562:Cytidine; D004247:DNA