ArticleNucleic acids research2003
Polylysine-coated mica can be used to observe systematic changes in the supercoiled DNA conformation by scanning force microscopy in solution.
Article in Nucleic acids research, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 100 citations in OpenAlex.
- The effects of DMSO on DNA conformations and mechanics.Biophysical journal · 2025Article
- Multiplexed stamp-transfer AFM deposition improves resolution of protein-DNA conformational states.Biophysical journal · 2025Article
- Using the Radial Distribution Function to Analyze Atomic Force Microscopy Images of Colloidal Systems.International journal of molecular sciences · 2024Article
- Supercoiling-dependent DNA binding: quantitative modeling and applications to bulk and single-molecule experiments.Nucleic acids research · 2024Article
- High-yield ligation-free assembly of DNA constructs with nucleosome positioning sequence repeats for single-molecule manipulation assays.The Journal of biological chemistry · 2023Article
- A High-throughput Pipeline to Determine DNA and Nucleosome Conformations by AFM Imaging.Bio-protocol · 2021Article
- Atomic force microscopy-A tool for structural and translational DNA research.APL bioengineering · 2021Review
- PEGylated surfaces for the study of DNA-protein interactions by atomic force microscopy.Nanoscale · 2019Article
- DNA accessibility of chromatosomes quantified by automated image analysis of AFM data.Scientific reports · 2019Article
- Effects of charge-modifying mutations in histone H2A α3-domain on nucleosome stability assessed by single-pair FRET and MD simulations.Scientific reports · 2017Article
- Atomic force microscopy of chromatin arrays reveal non-monotonic salt dependence of array compaction in solution.PloS one · 2017Article
- A biomimetic DNA-based channel for the ligand-controlled transport of charged molecular cargo across a biological membrane.Nature nanotechnology · 2016Article
- Protein/DNA interactions in complex DNA topologies: expect the unexpected.Biophysical reviews · 2016Review
- Imaging of DNA and Protein-DNA Complexes with Atomic Force Microscopy.Critical reviews in eukaryotic gene expression · 2016Review
- Protein/DNA interactions in complex DNA topologies: expect the unexpected.Biophysical reviews · 2016Review
- Segrosome assembly at the pliable parH centromere.Nucleic acids research · 2011Article
- Separating DNA with different topologies by atomic force microscopy in comparison with gel electrophoresis.The journal of physical chemistry. B · 2010Article
- Filamentous biopolymers on surfaces: atomic force microscopy images compared with Brownian dynamics simulation of filament deposition.PloS one · 2009Article
- DNA deformations near charged surfaces: electron and atomic force microscopy views.Biophysical journal · 2009Article
- UVA generates pyrimidine dimers in DNA directly.Biophysical journal · 2009Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The conformations of supercoiled (sc) DNA and linear DNA bound to polylysine (PL)-coated mica were investigated by scanning force microscopy (SFM) in solution. From the polymer statistical analysis of linear DNA, we could distinguish between re-arrangements or trapping of the DNA on the surface. Conditions of re-arrangements to an almost equilibrated state can be achieved at appropriate PL surface concentrations. We could show that the ability of re-arrangements depends on the salt concentration of the adsorption/imaging buffer. Comparing the statistical analysis of the linear DNA with SFM images of scDNA suggested that irregular scDNA conformations are formed under conditions of trapping, whereas plectonemic structures are favoured under conditions of surface re-arrangements. Salt-dependent changes in the scDNA conformation over the range of 10-100 mM NaCl, as characterised by the parameters writhe and the superhelix radius r, are observable only under conditions that enable surface re-arrangements. The measured values of writhe suggest that the scDNA loses approximately one-half of the supercoils during the binding to the surface. At the same time r increases systematically with decreasing writhe, thus the scDNA topology remains determined by the constraints on supercoiling during the binding to PL-coated mica.
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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.