Crystal structure of a DNA containing the planar, phenoxazine-derived bi-functional spectroscopic probe C.
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.
Emerald BioStructures, Bainbridge Island, WA 98110, USA.
Thomas E
TE
Edwards
Pavol
P
Cekan
Gunnar W
GW
Reginsson
Sandip A
SA
Shelke
Adrian R
AR
Ferré-D'Amaré
Olav
O
Schiemann
Snorri Th
ST
Sigurdsson
D018360:Crystallography, X-Ray; D003497:Cyclic N-Oxides / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D004578:Electron Spin Resonance Spectroscopy; D008958:Models, Molecular; D010078:Oxazines / Q000737:chemistry*; D013050:Spectrometry, Fluorescence; D013113:Spin Labels
D003497:Cyclic N-Oxides; D010078:Oxazines; D013113:Spin Labels; D004247:DNA
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