ArticleMethods (San Diego, Calif.)2009
AFM for analysis of structure and dynamics of DNA and protein-DNA complexes.
Article in Methods (San Diego, Calif.), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 77 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
77 citing papers in PubMed, 175 citations in OpenAlex.
- Advances in scanning probe microscopy for biological systems.Biophysics reports · 2026Article
- The effects of DMSO on DNA conformations and mechanics.Biophysical journal · 2025Article
- Recent progress in probing small molecule interactions with DNA.Biophysical reviews · 2025Review
- Hormone response elements for the thyroid receptor-α include specific distal 5'-flanking DNA.Science advances · 2024Article
- Fructose-1-kinase has pleiotropic roles inbioRxiv : the preprint server for biology · 2023Article
- Protamine folds DNA into flowers and loop stacks.Biophysical journal · 2023Article
- Review
- Features of DNA-Montmorillonite Binding Visualized by Atomic Force Microscopy.International journal of molecular sciences · 2023Article
- Toehold-Mediated Shape Transition of Nucleic Acid Nanoparticles.ACS applied materials & interfaces · 2023Article
- PARP3 Affects Nucleosome Compaction Regulation.International journal of molecular sciences · 2023Article
- 3D Generation of Multipurpose Atomic Force Microscopy Tips.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2022Article
- Atomic Force Microscopy of DNA and DNA-Protein Interactions.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Site-Search Process for Synaptic Protein-DNA Complexes.International journal of molecular sciences · 2021Article
- Key Physicochemical Determinants in the Antimicrobial Peptide RiLK1 Promote Amphipathic Structures.International journal of molecular sciences · 2021Article
- Two C-terminal sequence variations determine differential neurotoxicity between human and mouse α-synuclein.Molecular neurodegeneration · 2020Article
- Single-molecule level structural dynamics of DNA unwinding by human mitochondrial Twinkle helicase.The Journal of biological chemistry · 2020Article
- Article
- DNA accessibility of chromatosomes quantified by automated image analysis of AFM data.Scientific reports · 2019Article
- Single-Molecule 3D Images of "Hole-Hole" IgG1 Homodimers by Individual-Particle Electron Tomography.Scientific reports · 2019Article
- Specific delivery of delta-5-desaturase siRNA via RNA nanoparticles supplemented with dihomo-γ-linolenic acid for colon cancer suppression.Redox biology · 2019Article
17 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
This paper describes protocols for studies of structure and dynamics of DNA and protein-DNA complexes with atomic force microscopy (AFM) utilizing the surface chemistry approach. The necessary specifics for the preparation of functionalized surfaces and AFM probes with the use of silanes and silatranes, including the protocols for synthesis of silatranes are provided. The methodology of studies of local and global conformations DNA with the major focus on the time-lapse imaging of DNA in aqueous solutions is illustrated by the study of dynamics of Holliday junctions including branch migration. The analysis of nucleosome dynamics is selected as an example to illustrate the application of the time-lapse AFM to studies of dynamics of protein-DNA complexes. The force spectroscopy is the modality of AFM with a great importance to various fields of biomedical studies. The AFM force spectroscopy approach for studies of specific protein-DNA complexes is illustrated by the data on analysis of dynamics of synaptic SfiI-DNA complexes. When necessary, additional specifics are added to the corresponding example.
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.