3IKI

5-SMe-dU containing DNA octamer

Summary for 3IKI

• Entry DOI: 10.2210/pdb3iki/pdb
• Descriptor: 5'-D(*GP*(UMS)P*GP*(US2)P*AP*CP*AP*C)-3', MAGNESIUM ION (3 entities in total)
• Functional Keywords: selenium, nucleic acid, 5-sme-deoxyuridine, 2'-seme-deoxyuridine, dna
• Total number of polymer chains: 1
• Total formula weight: 2561.95

Authors

Sheng, J.,Hassan, A.E.A.,Zhang, W.,Gan, J.,Huang, Z. (deposition date: 2009-08-05, release date: 2010-03-09, Last modification date: 2023-09-06)

Primary citation

Sheng, J.,Zhang, W.,Hassan, A.E.,Gan, J.,Soares, A.S.,Geng, S.,Ren, Y.,Huang, Z.
Hydrogen bond formation between the naturally modified nucleobase and phosphate backbone.
Nucleic Acids Res., 40:8111-8118, 2012

PubMed 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.

PubMed: 22641848
DOI: 10.1093/nar/gks426

Experimental method

X-RAY DIFFRACTION (1.38 Å)