ArticleNucleic acids research2009
Atomic force microscopy of the EcoKI Type I DNA restriction enzyme bound to DNA shows enzyme dimerization and DNA looping.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- RecA-dependent or independent recombination of plasmid DNA generates a conflict with the host EcoKI immunity by launching restriction alleviation.Nucleic acids research · 2024Article
- Structural insights into assembly, operation and inhibition of a type I restriction-modification system.Nature microbiology · 2020Article
- Phage T7 DNA mimic protein Ocr is a potent inhibitor of BREX defence.Nucleic acids research · 2020Article
- A model for the evolution of prokaryotic DNA restriction-modification systems based upon the structural malleability of Type I restriction-modification enzymes.Nucleic acids research · 2018Article
- Single-molecule studies of high-mobility group B architectural DNA bending proteins.Biophysical reviews · 2017Review
- Structural model of FeoB, the iron transporter from Pseudomonas aeruginosa, predicts a cysteine lined, GTP-gated pore.Bioscience reports · 2016Article
- Direct evidence for functional TRPV1/TRPA1 heteromers.Pflugers Archiv : European journal of physiology · 2014Article
- DNA bridging and looping by HMO1 provides a mechanism for stabilizing nucleosome-free chromatin.Nucleic acids research · 2014Article
- Single molecular investigation of DNA looping and aggregation by restriction endonuclease BspMI.Scientific reports · 2014Article
- Crystal structure and molecular imaging of the Nav channel β3 subunit indicates a trimeric assembly.The Journal of biological chemistry · 2014Article
- Type I restriction enzymes and their relatives.Nucleic acids research · 2014Review
- Assembly of high molecular weight complexes of lipin on a supported lipid bilayer observed by atomic force microscopy.Biochemistry · 2013Article
- α-Amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) and N-methyl-D-aspartate (NMDA) receptors adopt different subunit arrangements.The Journal of biological chemistry · 2013Article
- Oligomerization and DNA binding of Ler, a master regulator of pathogenicity of enterohemorrhagic and enteropathogenic Escherichia coli.Nucleic acids research · 2012Article
- The sigma-1 receptor binds to the Nav1.5 voltage-gated Na+ channel with 4-fold symmetry.The Journal of biological chemistry · 2012Article
- Single-stranded loops as end-label polarity markers for double-stranded linear DNA templates in atomic force microscopy.Nucleic acids research · 2012Article
- Using DNA as a fiducial marker to study SMC complex interactions with the atomic force microscope.Biophysical journal · 2012Article
- Structure and operation of the DNA-translocating type I DNA restriction enzymes.Genes & development · 2012Article
- Atomic force microscopy reveals the architecture of the epithelial sodium channel (ENaC).The Journal of biological chemistry · 2011Article
- An investigation of the structural requirements for ATP hydrolysis and DNA cleavage by the EcoKI Type I DNA restriction and modification enzyme.Nucleic acids research · 2011Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Atomic force microscopy (AFM) allows the study of single protein-DNA interactions such as those observed with the Type I Restriction-Modification systems. The mechanisms employed by these systems are complicated and understanding them has proved problematic. It has been known for years that these enzymes translocate DNA during the restriction reaction, but more recent AFM work suggested that the archetypal EcoKI protein went through an additional dimerization stage before the onset of translocation. The results presented here extend earlier findings confirming the dimerization. Dimerization is particularly common if the DNA molecule contains two EcoKI recognition sites. DNA loops with dimers at their apex form if the DNA is sufficiently long, and also form in the presence of ATPgammaS, a non-hydrolysable analogue of the ATP required for translocation, indicating that the looping is on the reaction pathway of the enzyme. Visualization of specific DNA loops in the protein-DNA constructs was achieved by improved sample preparation and analysis techniques. The reported dimerization and looping mechanism is unlikely to be exclusive to EcoKI, and offers greater insight into the detailed functioning of this and other higher order assemblies of proteins operating by bringing distant sites on DNA into close proximity via DNA looping.
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