8-Aza-2'-deoxyguanosine: base pairing, mismatch discrimination and nucleobase anion fluorescence sensing in single-stranded and duplex DNA.
Oligodeoxyribonucleotides containing 8-aza-2-deoxyguanosine 9 were synthesized and a new phosphoramidite 11, showing a high coupling yield in solid-phase synthesis, was prepared. Nucleoside 9 was found to be a perfect shape mimic of dG; it forms a strong base pair with dC and shows an excellent mismatch discrimination. Nucleoside 9 appears strongly fluorescent as the anion, and thus, it has unique reporter group properties as a replacement for dG. The pKa-value of 9 (8.4) is lower than that of dG (9.3) and increases from the single-stranded DNA (8.8) to duplex DNA (9.1). The fluorescence of the nucleoside 9 anion is decreased in ss-oligonucleotides and further reduced in duplex DNA. When mismatches of 9 are formed with the four DNA canonical bases, the fluorescence of mismatches is significantly higher than that of the perfectly paired duplex. The fluorescence of the nucleoside 9 anion correlates with the base pair stability.
Seela
Frank
F
Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany. Frank.Seela@uni-osnabrueck.de
Jiang
Dawei
D
Xu
Kuiying
K
D020137:Base Pair Mismatch / Q000187:drug effects*; D020029:Base Pairing / Q000187:drug effects*; D004247:DNA; D004277:DNA, Single-Stranded; D003849:Deoxyguanosine / Q000031:analogs & derivatives* / Q000494:pharmacology; D005456:Fluorescent Dyes; D009943:Organophosphorus Compounds
D004277:DNA, Single-Stranded; D005456:Fluorescent Dyes; D009943:Organophosphorus Compounds; C434331:phosphoramidite; D004247:DNA; D003849:Deoxyguanosine