title: Synthesis and site-specific incorporation of a simple fluorescent pyrimidine.
abstract: We describe procedures for the synthesis of a fluorescent pyrimidine analog and its site-specific incorporation into a DNA oligomer. The 5'-protected and 3'-activated nucleoside 4 is synthesized in three steps with an overall yield of 40%. Site-specific incorporation into a DNA oligomer occurs with greater than 88% coupling efficiency. This isosteric fluorescent DNA analog can be used to monitor denaturation of DNA duplexes via fluorescence and can positively detect the presence of abasic sites in DNA duplexes. The total time for synthesis of the phosphoramidite 4 is about 75 h, whereas the total time for site-specific incorporation of nucleoside 2 into an oligonucleotide and purification of the corresponding oligonucleotide is about 114 hours.
authors.affiliation: Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, MC 0358, La Jolla, California 92093, USA. ngreco@ucsd.edu
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: Greco
authors.forename: Yitzhak
authors.initials: Y
authors.lastname: Tor
mesh_terms: D005453:Fluorescence; D005821:Genetic Techniques; D015394:Molecular Structure; D009841:Oligonucleotides / Q000737:chemistry*; D009943:Organophosphorus Compounds / Q000138:chemical synthesis*; D011741:Pyrimidine Nucleosides / Q000138:chemical synthesis* / Q000737:chemistry*
chemical_list: D009841:Oligonucleotides; D009943:Organophosphorus Compounds; D011741:Pyrimidine Nucleosides; C434331:phosphoramidite