3N4O

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

Summary for 3N4O

• Entry DOI: 10.2210/pdb3n4o/pdb
• Related: 3GJJ 3N4N
• Descriptor: 5'-D(*CP*GP*CP*GP*AP*AP*TP*(B7C)P*CP*GP*CP*G)-3', 2'-(4-HYDROXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE (3 entities in total)
• Functional Keywords: bicyclic cytosine, dna
• Total number of polymer chains: 2
• Total formula weight: 7797.36

Authors

Takenaka, A.,Juan, E.C.M.,Shimizu, S. (deposition date: 2010-05-22, release date: 2010-08-11, Last modification date: 2023-11-01)

Primary citation

Juan, E.C.M.,Shimizu, S.,Ma, X.,Kurose, T.,Haraguchi, T.,Zhang, F.,Tsunoda, M.,Ohkubo, A.,Sekine, M.,Shibata, T.,Millington, C.L.,Williams, D.M.,Takenaka, A.
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., 2010

PubMed 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 Å 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.

PubMed: 20554855
DOI: 10.1093/nar/gkq519

Experimental method

X-RAY DIFFRACTION (2.9 Å)