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

Nucleic Acids Research
John W PhamE J Sontheimer

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.

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Citations

Aug 19, 2007·Nature Protocols·Thomas E Edwards, Snorri Th Sigurdsson
May 19, 2011·Bioanalysis·Ken Cook, Jim Thayer
Aug 12, 2009·Journal of Inorganic Biochemistry·Ulf-Peter ApfelWolfgang Weigand
Dec 7, 2007·Bioorganic & Medicinal Chemistry Letters·Sarita Sitaula, Scott M Reed
Feb 15, 2005·Analytical Biochemistry·J R ThayerChristopher Pohl
Apr 20, 2006·Bioorganic & Medicinal Chemistry Letters·Neerja KalraJesper Wengel
Oct 6, 2005·Bioorganic & Medicinal Chemistry·Qing DaiJoseph A Piccirilli

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