ArticleNucleic acids research2019
Enzyme-free optical DNA mapping of the human genome using competitive binding.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 30 citations in OpenAlex.
- Chromosome-scale assembly of yeast genomes using enzyme-free, dense optical genome mapping.Nature communications · 2026Article
- Strain-Level Typing ofACS infectious diseases · 2025Article
- Article
- Write and Read: Harnessing Synthetic DNA Modifications for Nanopore Sequencing.bioRxiv : the preprint server for biology · 2025Article
- The Emergence of Nanofluidics for Single-Biomolecule Manipulation and Sensing.Analytical chemistry · 2025Review
- Artificial Intelligence-Enhanced Analysis of Genomic DNA Visualized with Nanoparticle-Tagged Peptides under Electron Microscopy.Small (Weinheim an der Bergstrasse, Germany) · 2025Article
- Article
- DOGMA: de novo assembly of densely labelled optical DNA maps using a matrix profile approach.PloS one · 2025Article
- Sequencing and Optical Genome Mapping for the Adventurous Chemist.Chemical & biomedical imaging · 2024Review
- Studying the Effects and Competitive Mechanisms of YOYO-1 on the Binding Characteristics of DOX and DNA Molecules Based on Surface-Enhanced Raman Spectroscopy and Molecular Docking Techniques.International journal of molecular sciences · 2024Article
- Design of optimal labeling patterns for optical genome mapping via information theory.Bioinformatics (Oxford, England) · 2023Article
- Single-molecule approaches for DNA damage detection and repair: A focus on Repair Assisted Damage Detection (RADD).DNA repair · 2023Review
- Strain-level bacterial typing directly from patient samples using optical DNA mapping.Communications medicine · 2023Article
- A Parallelized Nanofluidic Device for High-Throughput Optical DNA Mapping of Bacterial Plasmids.Micromachines · 2021Article
- Single-molecule optical genome mapping in nanochannels: multidisciplinarity at the nanoscale.Essays in biochemistry · 2021Article
- Combining dense and sparse labeling in optical DNA mapping.PloS one · 2021Article
- Detection of structural variations in densely-labelled optical DNA barcodes: A hidden Markov model approach.PloS one · 2021Article
- Quantifying DNA damage induced by ionizing radiation and hyperthermia using single DNA molecule imaging.Translational oncology · 2020Article
- Rapid Quantification of Oxidation and UV Induced DNA Damage by Repair Assisted Damage Detection-(Rapid RADD).Analytical chemistry · 2020Article
- Cultivation-Free Typing of Bacteria Using Optical DNA Mapping.ACS infectious diseases · 2020Article
Corrections and comments
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Authors and funding
9 authors at 4 institutions in 2 countries.
Funding
Abstract
Optical DNA mapping (ODM) allows visualization of long-range sequence information along single DNA molecules. The data can for example be used for detecting long range structural variations, for aiding DNA sequence assembly of complex genomes and for mapping epigenetic marks and DNA damage across the genome. ODM traditionally utilizes sequence specific marks based on nicking enzymes, combined with a DNA stain, YOYO-1, for detection of the DNA contour. Here we use a competitive binding approach, based on YOYO-1 and netropsin, which highlights the contour of the DNA molecules, while simultaneously creating a continuous sequence specific pattern, based on the AT/GC variation along the detected molecule. We demonstrate and validate competitive-binding-based ODM using bacterial artificial chromosomes (BACs) derived from the human genome and then turn to DNA extracted from white blood cells. We generalize our findings with in-silico simulations that show that we can map a vast majority of the human genome. Finally, we demonstrate the possibility of combining competitive binding with enzymatic labeling by mapping DNA damage sites induced by the cytotoxic drug etoposide to the human genome. Overall, we demonstrate that competitive-binding-based ODM has the potential to be used both as a standalone assay for studies of the human genome, as well as in combination with enzymatic approaches, some of which are already commercialized.
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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.