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.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 3446-3455 |
| Number of pages | 10 |
| Journal | Nucleic acids research |
| Volume | 32 |
| Issue number | 11 |
| DOIs | |
| State | Published - 2004 |
Funding
We thank Joshua Veatch and Roger Wu for their assistance with organic synthesis, Kai Huang and Ben Ramirez for their help in setting up NMR experiments, and Scott Silverman and Philip Bevilacqua for their helpful suggestions on melting analysis. NMR spectra of RNA samples were recorded in the WCAS Structural Biology NMR facility. Small molecule NMR and MALDI-TOF MS were performed in the Analytical Services Lab. Melting analysis was done in the Keck Biophysics Facility at Northwestern University. J.W.P. is a Presidential Fellow of Northwestern University and was supported by an NIH Biophysics Training Grant. This work was supported by a National Science Foundation CAREER Award to E.J.S.
ASJC Scopus subject areas
- Genetics