3OT0

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

Summary for 3OT0

• Entry DOI: 10.2210/pdb3ot0/pdb
• Related: 1DPL 1KGK
• Descriptor: Spin-labeled DNA (2 entities in total)
• Functional Keywords: nitroxide, spin-label, epr spectroscopy, fluorescence spectroscopy, modified nucleic acid, c-spin, deoxycytosine analog, phenoxazine, spectroscopic probe, peldor, 2'-o-methyl u, dna
• Total number of polymer chains: 2
• Total formula weight: 6526.47

Authors

Edwards, T.E. (deposition date: 2010-09-10, release date: 2011-01-19, Last modification date: 2023-09-06)

Primary citation

Edwards, T.E.,Cekan, P.,Reginsson, G.W.,Shelke, S.A.,Ferre-D'Amare, A.R.,Schiemann, O.,Sigurdsson, S.T.
Crystal structure of a DNA containing the planar, phenoxazine-derived bi-functional spectroscopic probe C.
Nucleic Acids Res., 10:4419-4426, 2011

PubMed 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.

PubMed: 21252294
DOI: 10.1093/nar/gkr015

Experimental method

X-RAY DIFFRACTION (1.7004 Å)