ArticleNucleic acids research2014
Conformations of p53 response elements in solution deduced using site-directed spin labeling and Monte Carlo sampling.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 25 citations in OpenAlex.
- Caught in the Middle: A Rigid DNA Label That Provides an Incisive Picture of DNA Conformational Flexibility in Protein-DNA Complexes.Journal of the American Chemical Society · 2025Article
- Paramagnetic Chemical Probes for Studying Biological Macromolecules.Chemical reviews · 2022Review
- The complex architecture of p53 binding sites.Nucleic acids research · 2021Article
- Experimental Validation of the ALLNOX Program for Studying Protein-Nucleic Acid Complexes.The journal of physical chemistry. A · 2019Article
- Experimental maps of DNA structure at nucleotide resolution distinguish intrinsic from protein-induced DNA deformations.Nucleic acids research · 2018Article
- Systematic prediction of DNA shape changes due to CpG methylation explains epigenetic effects on protein-DNA binding.Epigenetics & chromatin · 2018Article
- Structure of the Forkhead Domain of FOXA2 Bound to a Complete DNA Consensus Site.Biochemistry · 2017Article
- DNAproDB: an interactive tool for structural analysis of DNA-protein complexes.Nucleic acids research · 2017Article
- A Nitroxide-Tagged Platinum(II) Complex Enables the Identification of DNA G-Quadruplex Binding Mode.Chemistry (Weinheim an der Bergstrasse, Germany) · 2016Article
- Conformations of Human Telomeric G-Quadruplex Studied Using a Nucleotide-Independent Nitroxide Label.Biochemistry · 2016Article
- Doubly Spin-Labeled RNA as an EPR Reporter for Studying Multicomponent Supramolecular Assemblies.Biophysical journal · 2015Article
- Evolving insights on how cytosine methylation affects protein-DNA binding.Briefings in functional genomics · 2015Review
- An Integrated Spin-Labeling/Computational-Modeling Approach for Mapping Global Structures of Nucleic Acids.Methods in enzymology · 2015Article
- GBshape: a genome browser database for DNA shape annotations.Nucleic acids research · 2015Article
- Experimental mapping of DNA duplex shape enabled by global lineshape analyses of a nucleotide-independent nitroxide probe.Nucleic acids research · 2014Article
- Absence of a simple code: how transcription factors read the genome.Trends in biochemical sciences · 2014Review
Corrections and comments
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Authors and funding
10 authors at 1 institution in 1 country.
Funding
Abstract
The tumor suppressor protein p53 regulates numerous signaling pathways by specifically recognizing diverse p53 response elements (REs). Understanding the mechanisms of p53-DNA interaction requires structural information on p53 REs. However, such information is limited as a 3D structure of any RE in the unbound form is not available yet. Here, site-directed spin labeling was used to probe the solution structures of REs involved in p53 regulation of the p21 and Bax genes. Multiple nanometer distances in the p21-RE and BAX-RE, measured using a nucleotide-independent nitroxide probe and double-electron-electron-resonance spectroscopy, were used to derive molecular models of unbound REs from pools of all-atom structures generated by Monte-Carlo simulations, thus enabling analyses to reveal sequence-dependent DNA shape features of unbound REs in solution. The data revealed distinct RE conformational changes on binding to the p53 core domain, and support the hypothesis that sequence-dependent properties encoded in REs are exploited by p53 to achieve the energetically most favorable mode of deformation, consequently enhancing binding specificity. This work reveals mechanisms of p53-DNA recognition, and establishes a new experimental/computational approach for studying DNA shape in solution that has far-reaching implications for studying protein-DNA interactions.
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