3ot0

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

spinqualitylabelsall models 3ot0, resolution 1.70Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 3ot0 is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.7004Å Ligands: EXC, OMU Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed Previously, we developed the deoxycytosine analog C (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 C on nucleic acid structure, we undertook a detailed crystallographic analysis. A 1.7 A resolution crystal structure of C within a decamer duplex A-form DNA confirmed that C forms a non-perturbing base pair with deoxyguanosine, as designed. In the context of double-stranded DNA C adopted a planar conformation. In contrast, a crystal structure of the free spin-labeled base c displayed a approximately 20 degrees 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-pi 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 C 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. Crystal structure of a DNA containing the planar, phenoxazine-derived bi-functional spectroscopic probe C.,Edwards TE, Cekan P, Reginsson GW, Shelke SA, Ferre-D'Amare AR, Schiemann O, Sigurdsson ST Nucleic Acids Res. 2011 May 1;39(10):4419-26. Epub 2011 Jan 19. PMID:21252294 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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