PDBsum entry 1c4l

RNA

PDB id: 1c4l

Contents

DNA/RNA

PDB id:

1c4l

Name:

RNA

Title:

Solution structure of an RNA duplex including a c-u base-pair

Structure:

RNA (5'-r( Cp Gp Ap Cp Up Cp Ap Gp G)-3'). Chain: a. Engineered: yes. RNA (5'-r( Cp Cp Up Gp Cp Gp Up Cp G)-3'). Chain: b. Engineered: yes

Source:

Synthetic: yes. Other_details: this oligonucleotide was chemically synthesized (phosphoramidite method).. (Phosphoramidite method).

NMR struc:

1 models

Authors:

Y.Tanaka,C.Kojima,T.Yamazaki,T.S.Kodama,K.Yasuno,S.Miyashita,A.M.Ono, A.S.Ono,M.Kainosho,Y.Kyogoku

Key ref:

Y.Tanaka et al. (2000). Solution structure of an RNA duplex including a C-U base pair. Biochemistry, 39, 7074-7080. PubMed id: 10852704 DOI: 10.1021/bi000018m

Date:

30-Aug-99 Release date: 09-Aug-00

DNA/RNA chains

C-G-A-C-U-C-A-G-G 9 bases

C-C-U-G-C-G-U-C-G 9 bases

DOI no: 10.1021/bi000018m

Biochemistry 39:7074-7080 (2000)

PubMed id: 10852704

Solution structure of an RNA duplex including a C-U base pair.

Y.Tanaka, C.Kojima, T.Yamazaki, T.S.Kodama, K.Yasuno, S.Miyashita, A.Ono, A.Ono, M.Kainosho, Y.Kyogoku.

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.