ArticleBiochemistry2009
Site-specific DNA structural and dynamic features revealed by nucleotide-independent nitroxide probes.
Article in Biochemistry, 2009. 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.
- 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
- CRISPR-Cas9 Mediated DNA Unwinding Detected Using Site-Directed Spin Labeling.ACS chemical biology · 2017Article
- Doubly Spin-Labeled RNA as an EPR Reporter for Studying Multicomponent Supramolecular Assemblies.Biophysical journal · 2015Article
- Anomalously Rapid Hydration Water Diffusion Dynamics Near DNA Surfaces.Journal of the American Chemical Society · 2015Article
- A nucleotide-independent cyclic nitroxide label for monitoring segmental motions in nucleic acids.BMC biophysics · 2015Article
- An Integrated Spin-Labeling/Computational-Modeling Approach for Mapping Global Structures of Nucleic Acids.Methods in enzymology · 2015Article
- Experimental mapping of DNA duplex shape enabled by global lineshape analyses of a nucleotide-independent nitroxide probe.Nucleic acids research · 2014Article
- Characterizing the dynamics of the leader-linker interaction in the glycine riboswitch with site-directed spin labeling.Biochemistry · 2014Article
- Conformations of p53 response elements in solution deduced using site-directed spin labeling and Monte Carlo sampling.Nucleic acids research · 2014Article
- Nonlinear scaling of surface water diffusion with bulk water viscosity of crowded solutions.Journal of the American Chemical Society · 2013Article
- 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
- A nucleotide-independent nitroxide probe reports on site-specific stereomeric environment in DNA.Biophysical journal · 2010Article
- RNA dynamics: perspectives from spin labels.Wiley interdisciplinary reviews. RNAReview
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
In site-directed spin labeling, a covalently attached nitroxide probe containing a chemically inert unpaired electron is utilized to obtain information on the local environment of the parent macromolecule. Studies presented here examine the feasibility of probing local DNA structural and dynamic features using a class of nitroxide probes that are linked to chemically substituted phosphorothioate positions at the DNA backbone. Two members of this family, designated as R5 and R5a, were attached to eight different sites of a dodecameric DNA duplex without severely perturbing the native B-form conformation. Measured X-band electron paramagnetic resonance (EPR) spectra, which report on nitroxide rotational motions, were found to vary depending on the location of the label (e.g., duplex center vs termini) and the surrounding DNA sequence. This indicates that R5 and R5a can provide information on the DNA local environment at the level of an individual nucleotide. As these probes can be attached to arbitrary nucleotides within a nucleic acid sequence, they may provide a means to "scan" a given DNA molecule in order to interrogate its local structural and dynamic features.
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