Synthesis and physicochemical properties of new phosphoramide oligodeoxyribonucleotides. I. N-caffeine derivatives

Herein, we report the synthesis of new oligonucleotide derivatives containing an internucleotide N-caffeine phosphoramide (PN-caffeine) group. This modification was introduced via Staudinger's reaction with an appropriate caffeine azide during standard solid-phase oligonucleotide synthesis. Modified hexathymidylates and oligonucleotides with a heteronucleotide sequence were obtained with a yield of ∼90 %. Physicochemical properties of the new oligonucleotides were analyzed next. UV spectral determination of pK_a showed that the PN-caffeine group is neutral at pH < 5 and is negatively charged at pH > 8. The modified oligonucleotides emit weak fluorescence, and the same is true for different charge states of the PN-caffeine moiety and its positions in the DNA strand. A decrease in melting temperature of DNA/DNA and DNA/RNA duplexes was observed after the modification introduction into the DNA. Circular dichroism analysis indicated that the modification does not significantly disrupt either a DNA/DNA or DNA/RNA duplex at either low or high temperatures. This modification expands the existing classes of phosphoramide derivatives of nucleic acids and can be used for various biomedical applications.