ArticleNature communications2025
Quantifying complexity in DNA structures with high resolution Atomic Force Microscopy.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 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
10 citing papers in PubMed.
- Cryo-EM structure of a 95-base-pair double-stranded DNA minicircle at 5.3 Å resolution.Nucleic acids research · 2026Article
- SEM mapping of sequence-specific protein-DNA interactions on long DNA molecules.Nucleic acids research · 2026Article
- Mapping the Conformational Landscape of DNA Minicircles Through Atomic Force Microscopy and Shape Space Analysis.Small (Weinheim an der Bergstrasse, Germany) · 2026Article
- A modular framework for automated segmentation and analysis of AFM imaging of chromatin organization.Nucleic acids research · 2026Article
- Assembling a True "Olympic Gel" From over 16 000 Combinatorial DNA Rings.Advanced materials (Deerfield Beach, Fla.) · 2026Article
- Pancancer Analysis and the Oncogenic Role ofInternational journal of molecular sciences · 2026Article
- G-quadruplexes self-assembled from nucleotide monomers as stable prepolymer scaffolds in aqueous environments.Scientific reports · 2026Article
- Metal- and polymer-assisted SEM imaging of protein-bound DNA molecules: a protocol.Biology methods & protocols · 2026Review
- Recent progress in probing small molecule interactions with DNA.Biophysical reviews · 2025Review
- Kinetoplast DNA: a polymer physicist's topological Olympic dream.Nucleic acids research · 2025Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
15 authors.
Funding
Abstract
DNA topology is essential for regulating cellular processes and maintaining genome stability, yet it is challenging to quantify due to the size and complexity of topologically constrained DNA molecules. By combining high-resolution Atomic Force Microscopy (AFM) with a new high-throughput automated pipeline, we can quantify the length, conformation, and topology of individual complex DNA molecules with sub-molecular resolution. Our pipeline uses deep-learning methods to trace the backbone of individual DNA molecules and identify crossing points, efficiently determining which segment passes over which. We use this pipeline to determine the structure of stalled replication intermediates from Xenopus egg extracts, including theta structures and late replication products, and the topology of plasmids, knots and catenanes from the E. coli Xer recombination system. We use coarse-grained simulations to quantify the effect of surface immobilisation on twist-writhe partitioning. Our pipeline opens avenues for understanding how fundamental biological processes are regulated by DNA topology.
Indexed as
Identifiers
What Socratic 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 Socratic graph.