PDBsum entry 3n4n

DNA

PDB id: 3n4n

Contents

DNA/RNA

Waters ×49

PDB id:

3n4n

Name:

DNA

Title:

Insights into the stabilizing contributions of a bicyclic cytosine analogue: crystal structures of DNA duplexes containing 7,8- dihydropyrido[2,3-d]pyrimidin-2-one

Structure:

5'-d( Cp Gp Cp Gp Ap A)-3'. Chain: d. Engineered: yes. 5'-d(p Tp Tp (B7c)p Gp Cp G)-3'. Chain: e. Engineered: yes

Source:

Synthetic: yes. Synthetic: yes

Resolution:

1.92Å R-factor: 0.258 R-free: 0.263

Authors:

A.Takenaka,E.C.M.Juan,S.Shimizu

Key ref:

E.C.Magat Juan et al. (2010). Insights into the DNA stabilizing contributions of a bicyclic cytosine analogue: crystal structures of DNA duplexes containing 7,8-dihydropyrido [2,3-d]pyrimidin-2-one. Nucleic Acids Res, 38, 6737-6745. PubMed id: 20554855

Date:

22-May-10 Release date: 11-Aug-10

DNA/RNA chains

C-G-C-G-A-A 6 bases

T-T-B7C-G-C-G 6 bases

Nucleic Acids Res 38:6737-6745 (2010)

PubMed id: 20554855

Insights into the DNA stabilizing contributions of a bicyclic cytosine analogue: crystal structures of DNA duplexes containing 7,8-dihydropyrido [2,3-d]pyrimidin-2-one.

E.C.Magat Juan, S.Shimizu, X.Ma, T.Kurose, T.Haraguchi, F.Zhang, M.Tsunoda, A.Ohkubo, M.Sekine, T.Shibata, C.L.Millington, D.M.Williams, A.Takénaka.

ABSTRACT

The incorporation of the bicyclic cytosine analogue 7,8-dihydropyrido[2,3-d]pyrimidin-2-one (X) into DNA duplexes results in a significant enhancement of their stability (3-4 K per modification). To establish the effects of X on the local hydrogen-bonding and base stacking interactions and the overall DNA conformation, and to obtain insights into the correlation between the structure and stability of X-containing DNA duplexes, the crystal structures of [d(CGCGAATT-X-GCG)](2) and [d(CGCGAAT-X-CGCG)](2) have been determined at 1.9-2.9 A resolutions. In all of the structures, the analogue X base pairs with the purine bases on the opposite strands through Watson-Crick and/or wobble type hydrogen bonds. The additional ring of the X base is stacked on the thymine bases at the 5'-side and overall exhibits greatly enhanced stacking interactions suggesting that this is a major contribution to duplex stabilization.