ArticleBiopolymers2007
Computation of nitroxide-nitroxide distances in spin-labeled DNA duplexes.
Article in Biopolymers, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- 2'-Alkynyl spin-labelling is a minimally perturbing tool for DNA structural analysis.Nucleic acids research · 2020Article
- Experimental Validation of the ALLNOX Program for Studying Protein-Nucleic Acid Complexes.The journal of physical chemistry. A · 2019Article
- Conformations of Human Telomeric G-Quadruplex Studied Using a Nucleotide-Independent Nitroxide Label.Biochemistry · 2016Article
- Anomalously Rapid Hydration Water Diffusion Dynamics Near DNA Surfaces.Journal of the American Chemical Society · 2015Article
- Pulse dipolar ESR of doubly labeled mini TAR DNA and its annealing to mini TAR RNA.Biophysical journal · 2015Article
- An Integrated Spin-Labeling/Computational-Modeling Approach for Mapping Global Structures of Nucleic Acids.Methods in enzymology · 2015Article
- Conformations of p53 response elements in solution deduced using site-directed spin labeling and Monte Carlo sampling.Nucleic acids research · 2014Article
- The internal dynamics of mini c TAR DNA probed by electron paramagnetic resonance of nitroxide spin-labels at the lower stem, the loop, and the bulge.Biochemistry · 2012Article
- Nitroxide sensing of a DNA microenvironment: mechanistic insights from EPR spectroscopy and molecular dynamics simulations.The journal of physical chemistry. B · 2012Article
- Global structure of a three-way junction in a phi29 packaging RNA dimer determined using site-directed spin labeling.Journal of the American Chemical Society · 2012Article
- Computer modeling of nitroxide spin labels on proteins.Biopolymers · 2012Article
- A nucleotide-independent nitroxide probe reports on site-specific stereomeric environment in DNA.Biophysical journal · 2010Article
- Site-specific DNA structural and dynamic features revealed by nucleotide-independent nitroxide probes.Biochemistry · 2009Article
- Diastereomer characterizations of nitroxide-labeled nucleic acids.Biochemical and biophysical research communications · 2008Article
- Site-directed spin labeling studies on nucleic acid structure and dynamics.Progress in nucleic acid research and molecular biology · 2008Review
- Nanometer distance measurements in RNA using site-directed spin labeling.Biophysical journal · 2007Article
- Measuring nanometer distances in nucleic acids using a sequence-independent nitroxide probe.Nature protocols · 2007Article
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5 authors.
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Abstract
Nanometer distances in nucleic acids can be measured by EPR using two 1-oxyl-2,2,5,5-tetramethylpyrroline radicals, with each label attached via a methylene group to a phosphorothioate-substituted backbone position as one of two phosphorothioate diastereomers (R(P) and S(P)). Correlating the internitroxide distance to the geometry of the parent molecule requires computational analysis of the label conformers. Here, we report sixteen 4-ns MD simulations on a DNA duplex d(CTACTGCTTTAG) .d(CTAAAGCAGTAG) with label pairs at C7/C19, T5/A17, and T2/T14, respectively. For each labeled duplex, four simulations were performed with S(P)/S(P), R(P)/R(P), S(P)/R(P), and R(P)/S(P) labels, with initial all trans label conformations. Another set of four simulations was performed for the 7/19-labeled duplex using a different label starting conformation. The average internitroxide distance r(MD) was within 0.2 A for the two sets of simulations for the 7/19-labeled duplex, indicating sufficient sampling of conformational space. For all three labeled duplexes studied, r(MD) agreed with experimental values, as well as with average distances obtained from an efficient conformer search algorithm (NASNOX). The simulations also showed that the labels have conformational preferences determined by the linker chemistry and label-DNA interactions. These results establish computational algorithms that allow use of the 1-oxyl-2,2,5,5-tetramethylpyrroline label for mapping global structures of nucleic acids.
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