title: Hybridization of 2'-ribose modified mixed-sequence oligonucleotides: thermodynamic and kinetic studies.
abstract: 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.
authors.affiliation: Department of Chemistry, Tulane University, 6823 St Charles Avenue, New Orleans, LA 70118-5698, USA.
authors.forename: A
authors.initials: A
authors.lastname: Sabahi
authors.forename: J
authors.initials: J
authors.lastname: Guidry
authors.forename: G B
authors.initials: GB
authors.lastname: Inamati
authors.forename: M
authors.initials: M
authors.lastname: Manoharan
authors.forename: P
authors.initials: P
authors.lastname: Wittung-Stafshede
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D015316:Genetic Therapy; D007700:Kinetics; D009691:Nucleic Acid Denaturation; D009693:Nucleic Acid Hybridization; D009841:Oligonucleotides / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D012313:RNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012266:Ribose / Q000737:chemistry / Q000378:metabolism*; D013050:Spectrometry, Fluorescence; D055672:Static Electricity; D013696:Temperature; D013816:Thermodynamics
chemical_list: D009841:Oligonucleotides; D012313:RNA; D012266:Ribose; D004247:DNA