ArticleProceedings of the National Academy of Sciences of the United States of America2013
DNA conformations in mismatch repair probed in solution by X-ray scattering from gold nanocrystals.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
- Redundant mispair excision mechanisms in eukaryotic DNA mismatch repair.Nucleus (Austin, Tex.) · 2026Review
- Determination of absolute intramolecular distances in proteins using anomalous X-ray scattering interferometry.Nanoscale · 2025Article
- Mapping the Morphology of DNA on Carbon Nanotubes in Solution Using X-ray Scattering Interferometry.Journal of the American Chemical Society · 2024Article
- Recent advances in RNA structurome.Science China. Life sciences · 2022Review
- Universally Accessible Structural Data on Macromolecular Conformation, Assembly, and Dynamics by Small Angle X-Ray Scattering for DNA Repair Insights.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Monitoring Nuclease Activity by X-Ray Scattering Interferometry Using Gold Nanoparticle-Conjugated DNA.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Strand discrimination in DNA mismatch repair.DNA repair · 2021Review
- X-ray scattering reveals disordered linkers and dynamic interfaces in complexes and mechanisms for DNA double-strand break repair impacting cell and cancer biology.Protein science : a publication of the Protein Society · 2021Review
- Visualizing functional dynamicity in the DNA-dependent protein kinase holoenzyme DNA-PK complex by integrating SAXS with cryo-EM.Progress in biophysics and molecular biology · 2021Article
- Importance of base-pair opening for mismatch recognition.Nucleic acids research · 2020Article
- Site-specific covalent labeling of large RNAs with nanoparticles empowered by expanded genetic alphabet transcription.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- MutS sliding clamps on an uncertain track to DNA mismatch repair.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- The structural ensemble of a Holliday junction determined by X-ray scattering interference.Nucleic acids research · 2020Article
- Recurrent mismatch binding by MutS mobile clamps on DNA localizes repair complexes nearby.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Cancer mutational burden is shaped by G4 DNA, replication stress and mitochondrial dysfunction.Progress in biophysics and molecular biology · 2019Article
- Evolving SAXS versatility: solution X-ray scattering for macromolecular architecture, functional landscapes, and integrative structural biology.Current opinion in structural biology · 2019Review
- The properties of Msh2-Msh6 ATP binding mutants suggest a signal amplification mechanism in DNA mismatch repair.The Journal of biological chemistry · 2018Article
- Coordinated protein and DNA conformational changes govern mismatch repair initiation by MutS.Nucleic acids research · 2018Article
- Recording and Analyzing Nucleic Acid Distance Distributions with X-Ray Scattering Interferometry (XSI).Current protocols in nucleic acid chemistry · 2018Article
- Gold nanocrystal labels provide a sequence-to-3D structure map in SAXS reconstructions.Science advances · 2018Article
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Authors and funding
11 authors.
Funding
Abstract
DNA metabolism and processing frequently require transient or metastable DNA conformations that are biologically important but challenging to characterize. We use gold nanocrystal labels combined with small angle X-ray scattering to develop, test, and apply a method to follow DNA conformations acting in the Escherichia coli mismatch repair (MMR) system in solution. We developed a neutral PEG linker that allowed gold-labeled DNAs to be flash-cooled and stored without degradation in sample quality. The 1,000-fold increased gold nanocrystal scattering vs. DNA enabled investigations at much lower concentrations than otherwise possible to avoid concentration-dependent tetramerization of the MMR initiation enzyme MutS. We analyzed the correlation scattering functions for the nanocrystals to provide higher resolution interparticle distributions not convoluted by the intraparticle distribution. We determined that mispair-containing DNAs were bent more by MutS than complementary sequence DNA (csDNA), did not promote tetramer formation, and allowed MutS conversion to a sliding clamp conformation that eliminated the DNA bends. Addition of second protein responder MutL did not stabilize the MutS-bent forms of DNA. Thus, DNA distortion is only involved at the earliest mispair recognition steps of MMR: MutL does not trap bent DNA conformations, suggesting migrating MutL or MutS/MutL complexes as a conserved feature of MMR. The results promote a mechanism of mismatch DNA bending followed by straightening in initial MutS and MutL responses in MMR. We demonstrate that small angle X-ray scattering with gold labels is an enabling method to examine protein-induced DNA distortions key to the DNA repair, replication, transcription, and packaging.
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