DSSR-PyMOL cartoon-block schematics: PDB entry 3ot0

PDB-id

3ot0; DSSR-derived features in text and JSON formats

Class

DNA

Method

X-ray (1.7 Å)

Summary

Crystal structure of a DNA containing the rigid nitroxide spin-labeled nucleotide c-spin

Reference

Edwards TE, Cekan P, Reginsson GW, Shelke SA, Ferre-D'Amare AR, Schiemann O, Sigurdsson ST (2011): "Crystal structure of a DNA containing the planar, phenoxazine-derived bi-functional spectroscopic probe C." Nucleic Acids Res., 10, 4419-4426. doi: 10.1093/nar/gkr015.

Abstract

Previously, we developed the deoxycytosine analog Ç (C-spin) as a bi-functional spectroscopic probe for the study of nucleic acid structure and dynamics using electron paramagnetic resonance (EPR) and fluorescence spectroscopy. To understand the effect of Ç on nucleic acid structure, we undertook a detailed crystallographic analysis. A 1.7 Å resolution crystal structure of Ç within a decamer duplex A-form DNA confirmed that Ç forms a non-perturbing base pair with deoxyguanosine, as designed. In the context of double-stranded DNA Ç adopted a planar conformation. In contrast, a crystal structure of the free spin-labeled base ç displayed a ∼ 20° bend at the oxazine linkage. Density function theory calculations revealed that the bent and planar conformations are close in energy and exhibit the same frequency for bending. These results indicate a small degree of flexibility around the oxazine linkage, which may be a consequence of the antiaromaticity of a 16-π electron ring system. Within DNA, the amplitude of the bending motion is restricted, presumably due to base-stacking interactions. This structural analysis shows that the Ç forms a planar, structurally non-perturbing base pair with G indicating it can be used with high confidence in EPR- or fluorescence-based structural and dynamics studies.