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Nucleic Acids Research, 2001, Vol. 29, No. 10 2163-2170
© 2001 Oxford University Press

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

Ali Sabahi, Jesse Guidry, Gopal B. Inamati1, Muthiah Manoharan1 and Pernilla Wittung-Stafshede*

Department of Chemistry, Tulane University, 6823 St Charles Avenue, New Orleans, LA 70118-5698, USA and 1Medicinal Chemistry, Isis Pharmaceuticals, Carlsbad, CA 92008, USA

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°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°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.

* To whom correspondence should be addressed. Tel: +1 504 862 8943; Fax: +1 504 865 5596; Email: pernilla{at}tulane.edu


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