1C4L

SOLUTION STRUCTURE OF AN RNA DUPLEX INCLUDING A C-U BASE-PAIR

Summary for 1C4L

• Entry DOI: 10.2210/pdb1c4l/pdb
• Descriptor: RNA (5'-R(*CP*GP*AP*CP*UP*CP*AP*GP*G)-3'), RNA (5'-R(*CP*CP*UP*GP*CP*GP*UP*CP*G)-3') (2 entities in total)
• Functional Keywords: c-u base pair, rna
• Total number of polymer chains: 2
• Total formula weight: 5694.50

Authors

Tanaka, Y.,Kojima, C.,Yamazaki, T.,Kodama, T.S.,Yasuno, K.,Miyashita, S.,Ono, A.M.,Ono, A.S.,Kainosho, M.,Kyogoku, Y. (deposition date: 1999-08-30, release date: 2000-08-09, Last modification date: 2023-12-27)

Primary citation

Tanaka, Y.,Kojima, C.,Yamazaki, T.,Kodama, T.S.,Yasuno, K.,Miyashita, S.,Ono, A.,Ono, A.,Kainosho, M.,Kyogoku, Y.
Solution structure of an RNA duplex including a C-U base pair.
Biochemistry, 39:7074-7080, 2000

PubMed Abstract: The formation of the C-U base pair in a duplex was observed in solution by means of the temperature profile of (15)N chemical shifts, and the precise geometry of the C-U base pair was also determined by NOE-based structure calculation. From the solution structure of the RNA oligomer, r[CGACUCAGG].r[CCUGCGUCG], it was found that a single C-U mismatch preferred being stacked in the duplex rather than being flipped-out even in solution. Moreover, it adopts an irregular geometry, where the amino nitrogen (N4) of the cytidine and keto-oxygen (O4) of the uridine are within hydrogen-bonding distance, as seen in crystals. To further prove the presence of a hydrogen bond in the C-U pair, we employed a point-labeled cytidine at the exocyclic amino nitrogen of the cytidine in the C-U pair. The temperature profile of its (15)N chemical shift showed a sigmoidal transition curve, indicating the presence of a hydrogen bond in the C-U pair in the duplex.

PubMed: 10852704
DOI: 10.1021/bi000018m

Experimental method

SOLUTION NMR