Fluorescence properties and base pair stability of oligonucleotides containing 8-aza-7-deaza-2'-deoxyisoinosine or 2'-deoxyisoinosine.
The fluorescence and the base pairing properties of 8-aza-7-deaza-2'-deoxyisoinosine (1) are described and compared with those of 2'-deoxyisoinosine (2). The corresponding phosphoramidites (11, 12) are synthesized using the diphenylcarbamoyl (DPC) residue for the 2-oxo group protection. The nucleosides 1 and 2 base pair with 2'-deoxy-5-methylisocytidine in DNA duplexes with antiparallel chain orientation and with 2'-deoxycytidine in a parallel DNA. These base pairs are less stable than the canonical dA-dT pair and that of 2'-deoxyinosine (4) with 2'-deoxycytidine. The fluorescence of the nucleosides 1 and 2 is quenched (approximately 95%) in duplex DNA. The residual fluorescence is used to determine the Tm-values, which are found to be the same as determined UV-spectrophotometrically.
Seela
F
F
Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie, Universität Osnabrück, Germany. Fraseela@rz.uni-osnabrueck.de
Becher
G
G
Chen
Y
Y
D020029:Base Pairing; D001483:Base Sequence; D002851:Chromatography, High Pressure Liquid; D007288:Inosine / Q000031:analogs & derivatives / Q000737:chemistry*; D009841:Oligonucleotides / Q000737:chemistry*; D013050:Spectrometry, Fluorescence; D013056:Spectrophotometry, Ultraviolet
C094914:2'-deoxyisoinosine; C423482:8-aza-7-deaza-2'-deoxyisoinosine; D009841:Oligonucleotides; D007288:Inosine