ArticleNucleic acids research2011
Crystal structure of a DNA containing the planar, phenoxazine-derived bi-functional spectroscopic probe C.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Paramagnetic Chemical Probes for Studying Biological Macromolecules.Chemical reviews · 2022Review
- Orientation and dynamics of CuPhysical chemistry chemical physics : PCCP · 2020Article
- Cu2+-based distance measurements by pulsed EPR provide distance constraints for DNA backbone conformations in solution.Nucleic acids research · 2020Article
- 2'-Alkynyl spin-labelling is a minimally perturbing tool for DNA structural analysis.Nucleic acids research · 2020Article
- Structure guided fluorescence labeling reveals a two-step binding mechanism of neomycin to its RNA aptamer.Nucleic acids research · 2019Article
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Authors and funding
7 authors.
Funding
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.
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