title: Thermodynamic and structural characterization of 2'-nitrogen-modified RNA duplexes.
abstract: 2'-aminonucleosides are commonly used as sites of post-synthetic chemical modification within nucleic acids. As part of a larger cross-linking strategy, we appended alkyl groups onto the N2' position of 2'-amino-modified RNAs via 2'-ureido and 2'-amido linkages. We have characterized the thermodynamics of 2'-amino, 2'-alkylamido and 2'-alkylureido-modified RNA duplexes and show that 2'-ureido-modified RNAs are significantly more stable than analogous 2'-amido-modified RNAs. Using NMR spectroscopy and NMR-based molecular modeling of 2'-modified RNA duplexes, we examined the effects that 2'-nitrogen modifications have on RNA helices. Our data suggest that the 2'-ureido group forms a specific intra-nucleoside interaction that cannot occur within 2'-amido-modified helices. These results indicate that 2'-ureido modifications are superior to analogous 2'-amido ones for applications that require stable base pairing.
authors.affiliation: Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, 2205 Tech Drive, Evanston, IL 60208-3500, USA.
authors.forename: John W
authors.initials: JW
authors.lastname: Pham
authors.forename: Ishwar
authors.initials: I
authors.lastname: Radhakrishnan
authors.forename: Erik J
authors.initials: EJ
authors.lastname: Sontheimer
mesh_terms: D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D009584:Nitrogen / Q000737:chemistry*; D020871:RNA Stability; D012330:RNA, Double-Stranded / Q000737:chemistry*; D013438:Sulfhydryl Compounds / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D012330:RNA, Double-Stranded; D013438:Sulfhydryl Compounds; D009584:Nitrogen