4IQS

RNA 8mer duplex modified with 4-Se-Uridine

Summary for 4IQS

• Entry DOI: 10.2210/pdb4iqs/pdb
• Descriptor: RNA (5'-R(*GP*UP*GP*(S5)P*AP*CP*AP*C)-3') (1 entity in total)
• Functional Keywords: selenium rna, rna
• Total number of polymer chains: 6
• Total formula weight: 15537.13

Authors

Sheng, J.,Gan, J.,Soares, A.,Huang, Z. (deposition date: 2013-01-13, release date: 2013-12-25, Last modification date: 2024-02-28)

Primary citation

Sheng, J.,Gan, J.,Soares, A.S.,Salon, J.,Huang, Z.
Structural insights of non-canonical U*U pair and Hoogsteen interaction probed with Se atom.
Nucleic Acids Res., 41:10476-10487, 2013

PubMed Abstract: Unlike DNA, in addition to the 2'-OH group, uracil nucleobase and its modifications play essential roles in structure and function diversities of non-coding RNAs. Non-canonical U•U base pair is ubiquitous in non-coding RNAs, which are highly diversified. However, it is not completely clear how uracil plays the diversifing roles. To investigate and compare the uracil in U-A and U•U base pairs, we have decided to probe them with a selenium atom by synthesizing the novel 4-Se-uridine ((Se)U) phosphoramidite and Se-nucleobase-modified RNAs ((Se)U-RNAs), where the exo-4-oxygen of uracil is replaced by selenium. Our crystal structure studies of U-A and U•U pairs reveal that the native and Se-derivatized structures are virtually identical, and both U-A and U•U pairs can accommodate large Se atoms. Our thermostability and crystal structure studies indicate that the weakened H-bonding in U-A pair may be compensated by the base stacking, and that the stacking of the trans-Hoogsteen U•U pairs may stabilize RNA duplex and its junction. Our result confirms that the hydrogen bond (O4(…)H-C5) of the Hoogsteen pair is weak. Using the Se atom probe, our Se-functionalization studies reveal more insights into the U•U interaction and U-participation in structure and function diversification of nucleic acids.

PubMed: 24013566
DOI: 10.1093/nar/gkt799

Experimental method

X-RAY DIFFRACTION (2.6 Å)