ISDA

Entry Detail

PDB ID:

3N4N

Keywords:

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

Biological Source:

Source Organism:

PDB Version:

Deposition Date:

2010-05-22

Release Date:

2010-08-11

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.92 Å

R-Value Free:

0.26

R-Value Work:

0.25

Space Group:

P 32 1 2

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Macromolecular Entities

Polymer Type:polydeoxyribonucleotide
Description:5'-D(*CP*GP*CP*GP*AP*A)-3'
Chain IDs:A (auth: D)
Chain Length:6
Number of Molecules:1
Biological Source:

Polymer Type:polydeoxyribonucleotide
Description:5'-D(P*TP*TP*(B7C)P*GP*CP*G)-3'
Chain IDs:B (auth: E)
Chain Length:6
Number of Molecules:1
Biological Source:

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details	2D Image
B7C	B	DC	?

Primary Citation

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.

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.Show

Nucleic Acids Res. ? ? ? (2010)

PMID: 20554855 DOI: 10.1093/nar/gkq519

Abstact

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.

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