Oligonucleotides incorporating 7-(aminoalkynyl)-7-deaza-2'-deoxyguanosines: duplex stability and phosphodiester hydrolysis by exonucleases

Oligonucleotides containing 7-(omega-aminoalkyn-1-yl)-7-deaza-2'-deoxyguanosines (1a-c) were investigated regarding their thermal stability (T(m) values) as well as their phosphodiester hydrolysis catalyzed by exonucleases. Those derivatives are suitable for the labeling of nucleic acid constituents as well as for the postlabeling of DNA. For this, the phosphoramidites 7a,c (obtained from the nucleoside 1a,b), protected by an isobutyryl group at the 2-amino group and a phthaloyl residue at the side-chain amino function, were synthesized. Using compounds 7a,c together with the phosphoramidite of 1c in solid-phase synthesis, a series of self-complementary and non-self-complementary oligonucleotides were prepared and characterized by MALDI-TOF mass spectrometry. A comparison of the T(m) values of the modified oligomers shows that the thermal stability of the duplexes decreases with the length of the nucleobase 7-(omega-aminoalkyn-1-yl) side chain. Exonucleolytic cleavage of oligonucleotide single strands incorporating either the 7-(3-aminopropyn-1-yl)- or the 7-(4-aminobutyn-1-yl)-substituted nucleosides 1a or 1b, respectively, reveals that 3' --> 5' specific snake venom phosphodiesterase liberates 1a 5'-monophosphate but not the methylene-extended 1b 5'-monophosphate. On the contrary, the 5' --> 3' specific bovine spleen exonuclease is able to cleave off single 1a and 1b 3'-monophosphate residues; its action is, however, terminated in the case of oligonucleotides containing two consecutive 1a or 1b nucleotide units.