ArticleNucleic acids research2009
Analyzing the forces binding a restriction endonuclease to DNA using a synthetic nanopore.
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 17 papers.
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Who cites it
17 citing papers in PubMed, 39 citations in OpenAlex.
- Aggregation and Oligomerization Characterization of ß-Lactoglobulin Protein Using a Solid-State Nanopore Sensor.Sensors (Basel, Switzerland) · 2023Article
- Electrical unfolding of cytochromeProceedings of the National Academy of Sciences of the United States of America · 2021Article
- Dynamics of a Molecular Plug Docked onto a Solid-State Nanopore.The journal of physical chemistry letters · 2018Article
- Single molecule high-throughput footprinting of small and large DNA ligands.Nature communications · 2017Article
- Graphene Nanopores for Protein Sequencing.Advanced functional materials · 2016Article
- Nanopore sensing of individual transcription factors bound to DNA.Scientific reports · 2015Article
- Nanopores suggest a negligible influence of CpG methylation on nucleosome packaging and stability.Nano letters · 2015Article
- Watching single proteins using engineered nanopores.Protein and peptide letters · 2014Review
- Fast, label-free force spectroscopy of histone-DNA interactions in individual nucleosomes using nanopores.Journal of the American Chemical Society · 2013Article
- Sampling a biomarker of the human immunodeficiency virus across a synthetic nanopore.ACS nano · 2013Article
- Modeling and simulation of ion channels.Chemical reviews · 2012Review
- Toward detection of DNA-bound proteins using solid-state nanopores: insights from computer simulations.Electrophoresis · 2012Article
- Recent advances in nanopore sequencing.Electrophoresis · 2012Review
- Nanopore detachment kinetics of poly(A) binding proteins from RNA molecules reveals the critical role of C-terminus interactions.Biophysical journal · 2012Article
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- Molecular diagnostics for personal medicine using a nanopore.Wiley interdisciplinary reviews. Nanomedicine and nanobiotechnologyReview
Corrections and comments
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
Abstract
Restriction endonucleases are used prevalently in recombinant DNA technology because they bind so stably to a specific target sequence and, in the presence of cofactors, cleave double-helical DNA specifically at a target sequence at a high rate. Using synthetic nanopores along with molecular dynamics (MD), we have analyzed with atomic resolution how a prototypical restriction endonuclease, EcoRI, binds to the DNA target sequence--GAATTC--in the absence of a Mg(2+) ion cofactor. We have previously shown that there is a voltage threshold for permeation of DNA bound to restriction enzymes through a nanopore that is associated with a nanonewton force required to rupture the complex. By introducing mutations in the DNA, we now show that this threshold depends on the recognition sequence and scales linearly with the dissociation energy, independent of the pore geometry. To predict the effect of mutation in a base pair on the free energy of dissociation, MD is used to qualitatively rank the stability of bonds in the EcoRI-DNA complex. We find that the second base in the target sequence exhibits the strongest binding to the protein, followed by the third and first bases, with even the flanking sequence affecting the binding, corroborating our experiments.
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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.