Hybridization of 2 '-ribose modified mixed-sequence oligonucleotides: thermodynamic and kinetic studies

In this study, we characterize the thermodynamics of hybridization, binding kinetics and conformations of four ribose-modified (2'-fluoro, 2'-O-propyl , 2'-O-methoxyethyl and 2'-O-aminopropyl) decameric mixed-sequence oligonuc leotides, Hybridization to the complementary non-modified DNA or RNA decame r was probed by fluorescence and circulardichroism spectroscopy and compare d to the same duplex formed between two non-modified strands. The thermal m elting points of DNA-DNA duplexes were increased by 1.8, 2.2, 0.3 and 1.3 d egreesC for each propyl, methoxyethyl, aminopropyl and fluoro modification, respectively. In the case of DNA-RNA duplexes, the melting points were inc reased by 3.1, 4.1 and 1.0 degreesC for each propyl, methoxyethyl and amino propyl modification, respectively. The high stability of the duplexes forme d with propyl-, methoxyethyl- and fluoro-modified oligonucleotides correlat ed with high preorganization in these single-strands. Despite higher thermo dynamic duplex stability, hybridization kinetics to complementary DNA or RN A was slower for propyl- and methoxyethyl-modified oligonucleotides than fo r the nonmodified control. In contrast, the positively-charged aminopropyl- modified oligonucleotide showed rapid binding to the complementary DNA or R NA.