Carboranyl Oligonucleotides: 4. Synthesis and Physicochemical Studies of Oligonucleotides Containing 2′- O -( o -Carboran-1-yl)Methyl Group

Abstract

Boronated oligonucleotides are potential candidates for antisense oligonucleotide technology (AOT), boron neutron capture therapy (BNCT), and as tools in molecular biology. A method was developed for the solid phase synthesis of oligonucleotides containing 2′-O-(o-carboran-1-yl-methyl) (2′-CBM) group. Synthesis was performed using a standard β-cyanoethyl cycle and automated DNA synthesizer. Manual steps were performed for the insertion of a modified monomer bearing the 2′-CBM group. Several tetradecanucleotides complementary to DNA-HCMV, and bearing 2′-CBM modification near the 3′-end or 5′-end or in the middle of the oligonucleotide chain were synthesized. The resulting oligomers were characterized by polyacrylamide gel electrophoresis (PAGE), reverse phase high-performance liquid chromatography (RP-HPLC), matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) and ultraviolet spectroscopy (UV), circular dichroism (CD), and melting temperature (T_m) measurements. T_m of duplexes formed between 2′-CBM-modified tetradecanucleotides and complementary DNA and RNA template were compared with those formed by the unmodified oligonucleotide and complementary sequence. The stability of 2′-CBM oligonucleotides in the presence of phosphodiesterase I from Crotalus atrox venom and in human serum was studied. Oligonucleotides bearing the 2′-CBM group are characterized by increased resistance to enzymatic digestion, increased lipophilicity, and the ability to form stable duplexes with complementary templates.