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- Title
Hydrogen bond formation between the naturally modified nucleobase and phosphate backbone.
- Authors
Sheng, Jia; Zhang, Wen; Hassan, Abdalla E A; Gan, Jianhua; Soares, Alexei S; Geng, Song; Ren, Yi; Huang, Zhen
- Abstract
Natural RNAs, especially tRNAs, are extensively modified to tailor structure and function diversities. Uracil is the most modified nucleobase among all natural nucleobases. Interestingly, >76% of uracil modifications are located on its 5-position. We have investigated the natural 5-methoxy (5-O-CH(3)) modification of uracil in the context of A-form oligonucleotide duplex. Our X-ray crystal structure indicates first a H-bond formation between the uracil 5-O-CH(3) and its 5'-phosphate. This novel H-bond is not observed when the oxygen of 5-O-CH(3) is replaced with a larger atom (selenium or sulfur). The 5-O-CH(3) modification does not cause significant structure and stability alterations. Moreover, our computational study is consistent with the experimental observation. The investigation on the uracil 5-position demonstrates the importance of this RNA modification at the atomic level. Our finding suggests a general interaction between the nucleobase and backbone and reveals a plausible function of the tRNA 5-O-CH(3) modification, which might potentially rigidify the local conformation and facilitates translation.
- Publication
Nucleic acids research, 2012, Vol 40, Issue 16, p8111
- ISSN
1362-4962
- Publication type
Journal Article
- DOI
10.1093/nar/gks426