Thermodynamic and structural characterization of 2′ -nitrogen-modified RNA duplexes

John W. Pham, Ishwar Radhakrishnan, Erik J. Sontheimer*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

15 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)3446-3455
Number of pages10
JournalNucleic acids research
Issue number11
StatePublished - 2004

ASJC Scopus subject areas

  • Genetics


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