ArticleNucleic acids research2005
DNA bending by M.EcoKI methyltransferase is coupled to nucleotide flipping.
Article in Nucleic acids research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
19 citing papers in PubMed, 36 citations in OpenAlex.
- The Restriction Activity Investigation of Rv2528c, an Mrr-like Modification-Dependent Restriction Endonuclease fromMicroorganisms · 2024Article
- CRISPR-Cas9 bends and twists DNA to read its sequence.Nature structural & molecular biology · 2022Article
- Single-Molecule Imaging Reveals that Rad4 Employs a Dynamic DNA Damage Recognition Process.Molecular cell · 2016Article
- The evolutionary pathway from a biologically inactive polypeptide sequence to a folded, active structural mimic of DNA.Nucleic acids research · 2016Article
- ArdA proteins from different mobile genetic elements can bind to the EcoKI Type I DNA methyltransferase of E. coli K12.Biochimica et biophysica acta · 2014Article
- Type I restriction enzymes and their relatives.Nucleic acids research · 2014Review
- Restriction endonuclease TseI cleaves A:A and T:T mismatches in CAG and CTG repeats.Nucleic acids research · 2013Article
- Exploring the DNA mimicry of the Ocr protein of phage T7.Nucleic acids research · 2012Article
- Fluorescent DNA-based enzyme sensors.Chemical Society reviews · 2011Review
- 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
- Fusion of GFP to the M.EcoKI DNA methyltransferase produces a new probe of Type I DNA restriction and modification enzymes.Biochemical and biophysical research communications · 2010Article
- Dissection of the DNA mimicry of the bacteriophage T7 Ocr protein using chemical modification.Journal of molecular biology · 2009Article
- Atomic force microscopy of the EcoKI Type I DNA restriction enzyme bound to DNA shows enzyme dimerization and DNA looping.Nucleic acids research · 2009Article
- The structure of M.EcoKI Type I DNA methyltransferase with a DNA mimic antirestriction protein.Nucleic acids research · 2009Article
- Differential stabilization of reaction intermediates: specificity checkpoints for M.EcoRI revealed by transient fluorescence and fluorescence lifetime studies.Nucleic acids research · 2008Article
- A molecular dynamics study of slow base flipping in DNA using conformational flooding.Biophysical journal · 2007Article
- T4 DNA ligase is more than an effective trap of cyclized dsDNA.Nucleic acids research · 2007Article
- A rapid reaction analysis of uracil DNA glycosylase indicates an active mechanism of base flipping.Nucleic acids research · 2007Article
- Structural model for the multisubunit Type IC restriction-modification DNA methyltransferase M.EcoR124I in complex with DNA.Nucleic acids research · 2006Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
The maintenance methyltransferase M.EcoKI recognizes the bipartite DNA sequence 5'-AACNNNNNNGTGC-3', where N is any nucleotide. M.EcoKI preferentially methylates a sequence already containing a methylated adenine at or complementary to the underlined bases in the sequence. We find that the introduction of a single-stranded gap in the middle of the non-specific spacer, of up to 4 nt in length, does not reduce the binding affinity of M.EcoKI despite the removal of non-sequence-specific contacts between the protein and the DNA phosphate backbone. Surprisingly, binding affinity is enhanced in a manner predicted by simple polymer models of DNA flexibility. However, the activity of the enzyme declines to zero once the single-stranded region reaches 4 nt in length. This indicates that the recognition of methylation of the DNA is communicated between the two methylation targets not only through the protein structure but also through the DNA structure. Furthermore, methylation recognition requires base flipping in which the bases targeted for methylation are swung out of the DNA helix into the enzyme. By using 2-aminopurine fluorescence as the base flipping probe we find that, although flipping occurs for the intact duplex, no flipping is observed upon introduction of a gap. Our data and polymer model indicate that M.EcoKI bends the non-specific spacer and that the energy stored in a double-stranded bend is utilized to force or flip out the bases. This energy is not stored in gapped duplexes. In this way, M.EcoKI can determine the methylation status of two adenine bases separated by a considerable distance in double-stranded DNA and select the required enzymatic response.
Indexed as
Identifiers
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.