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

• Published in: Nucleic acids research Vol. 29; no. 10; pp. 2163 - 2170
• Main Authors: Sabahi, A, Guidry, J, Inamati, G B, Manoharan, M, Wittung-Stafshede, P
• Format: Journal Article
• Language: English
• Published: England Oxford Publishing Limited (England) 15.05.2001; Oxford University Press
• Subjects: 2'-ribose; Base Pairing; Base Sequence; Circular Dichroism; DNA - chemistry; DNA - genetics; DNA - metabolism; Genetic Therapy; Kinetics; Nucleic Acid Denaturation; Nucleic Acid Hybridization; Oligonucleotides - chemistry; Oligonucleotides - genetics; Oligonucleotides - metabolism; Ribose - chemistry; Ribose - metabolism; RNA - chemistry; RNA - genetics; RNA - metabolism; Spectrometry, Fluorescence; Static Electricity; Temperature; Thermodynamics
• ISSN: 1362-4962; 0305-1048; 1362-4962
• DOI: 10.1093/nar/29.10.2163

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 oligonucleotides. Hybridization to the complementary non-modified DNA or RNA decamer was probed by fluorescence and circular-dichroism spectroscopy and compared to the same duplex formed between two non-modified strands. The thermal melting points of DNA-DNA duplexes were increased by 1.8, 2.2, 0.3 and 1.3 degrees C for each propyl, methoxyethyl, aminopropyl and fluoro modification, respectively. In the case of DNA-RNA duplexes, the melting points were increased by 3.1, 4.1 and 1.0 degrees C for each propyl, methoxyethyl and aminopropyl modification, respectively. The high stability of the duplexes formed with propyl-, methoxyethyl- and fluoro-modified oligonucleotides correlated with high preorganization in these single-strands. Despite higher thermodynamic duplex stability, hybridization kinetics to complementary DNA or RNA was slower for propyl- and methoxyethyl-modified oligonucleotides than for the non-modified control. In contrast, the positively-charged aminopropyl-modified oligonucleotide showed rapid binding to the complementary DNA or RNA.