Collect. Czech. Chem. Commun. 2009, 74, 935-955
Published online 2009-06-01 11:40:28

Synthesis and hybridization of oligonucleotides modified at AMP sites with adenine pyrrolidine phosphonate nucleotides

Dominik Rejman*, Petr Kočalka, Radek Pohl, Zdeněk Točík and Ivan Rosenberg*

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 166 10 Prague 6, Czech Republic


Three structurally diverse types of the protected pyrrolidine nucleoside phosphonates were prepared as the monomers for the introduction of pyrrolidine nucleotide units into modified oligonucleotides on the solid phase. Two different chemistries were used for incorporation of modified and natural units: the phosphotriester method for the former, i.e., monomers containing N-phosphonoalkyl and N-phosphonoacyl moieties attached to the pyrrolidine ring nitrogen atom, and phosphoramidite chemistry for the latter. Since the synthesized pyrrolidine nucleoside phosphonic acids are close mimics of the 3′-deoxynucleoside 5′-phosphates, the incorporation of one modified unit into oligonucleotides gives rise to one 2′,5′ internucleotide linkage. A series of nonamers containing two or three modified units, as well as the fully modified adenine 15-mer, were synthesized in reverse order, i.e., from the 5′ to the 3′ end of the strand. The measurement of thermal characteristics of the complexes of modified nonamers with the complementary strand revealed a destabilizing effect of the introduced modification. The modified adenine homooligonucleotide, was found to form the most stable complex with oligothymidylate of all the tested modified oligonucleotides in terms of ΔTm per modification.

Keywords: Oligonucleotides; Pyrrolidines; Phosphonates; Nucleotides; Nucleosides.

References: 38 live references.