ArticleNucleic acids research2006
Site-specific labeling of supercoiled DNA.
Article in Nucleic acids research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
9 citing papers in PubMed, 19 citations in OpenAlex.
- Polymorphic potential of SRF binding site ofRSC advances · 2024Article
- Imaging of DNA and Protein-DNA Complexes with Atomic Force Microscopy.Critical reviews in eukaryotic gene expression · 2016Review
- Single molecular investigation of DNA looping and aggregation by restriction endonuclease BspMI.Scientific reports · 2014Article
- Visualization of DNA and protein-DNA complexes with atomic force microscopy.Methods in molecular biology (Clifton, N.J.) · 2014Article
- Mica functionalization for imaging of DNA and protein-DNA complexes with atomic force microscopy.Methods in molecular biology (Clifton, N.J.) · 2013Article
- Visual analysis of concerted cleavage by type IIF restriction enzyme SfiI in subsecond time region.Biophysical journal · 2011Article
- Efficient preparation of internally modified single-molecule constructs using nicking enzymes.Nucleic acids research · 2011Article
- AFM for analysis of structure and dynamics of DNA and protein-DNA complexes.Methods (San Diego, Calif.) · 2009Article
- Labeling of unique sequences in double-stranded DNA at sites of vicinal nicks generated by nicking endonucleases.Nucleic acids research · 2008Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
Visualization of site-specific labels in long linear or circular DNA allows unambiguous identification of various local DNA structures. Here we describe a novel and efficient approach to site-specific DNA labeling. The restriction enzyme SfiI binds to DNA but leaves it intact in the presence of calcium and therefore may serve as a protein label of 13 bp recognition sites. Since SfiI requires simultaneous interaction with two DNA recognition sites for stable binding, this requirement is satisfied by providing an isolated recognition site in the DNA target and an additional short DNA duplex also containing the recognition site. The SfiI/DNA complexes were visualized with AFM and the specificity of the labeling was confirmed by the length measurements. Using this approach, two sites in plasmid DNA were labeled in the presence of a large excess of the helper duplex to compete with the formation of looped structures of the intramolecular synaptic complex. We show that the labeling procedure does not interfere with the superhelical tension-driven formation of alternative DNA structures such as cruciforms. The complex is relatively stable at low and high pH (pH 5 and 9) making the developed approach attractive for use at conditions requiring the pH change.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.