Related Experiment Video
Updated: Jul 10, 2026
09:14
DamID-seq: Genome-wide Mapping of Protein-DNA Interactions by High Throughput Sequencing of Adenine-methylated DNA Fragments
Published on: January 27, 2016
SEM mapping of sequence-specific protein-DNA interactions on long DNA molecules
Chanyoung Noh1, Sangwon Lee1, Yoonjung Kang1
1Department of Chemistry, Sogang University, Seoul 04107, Korea.
Nucleic Acids Research
|July 9, 2026
Summary
Scanning electron microscopy (SEM) now visualizes protein-DNA interactions on individual molecules with high resolution. This method overcomes limitations of previous imaging techniques, enabling precise mapping of binding sites on extended DNA strands.
Area of Science:
- Molecular Biology
- Microscopy
- Genomics
Background:
- Single-molecule imaging of DNA-protein interactions is crucial for understanding molecular mechanisms.
- Existing methods like fluorescence imaging face trade-offs in resolution, field of view, and throughput.
- There is a need for advanced techniques to visualize binding events on extended DNA molecules with high precision.
Purpose of the Study:
- To develop and validate a scanning electron microscopy (SEM)-based approach for direct visualization of protein-binding positions on individual DNA molecules.
- To overcome the spatial resolution, field of view, and throughput limitations of current single-molecule imaging techniques.
- To enable quantitative mapping of sequence-specific DNA-protein interactions along extended DNA molecules.
Main Methods:
- Established a scanning electron microscopy (SEM) approach combining contrast enhancement and sequence-defined labeling.
- Imaged extended DNA molecules, including biotinylated λ DNA with streptavidin-fluorescent protein labels, and plasmid DNA with dCas9.
- Utilized machine learning for detecting dCas9 binding on human genomic DNA.
Main Results:
- SEM successfully visualized protein-bound regions along the contour of extended DNA molecules.
- Achieved significantly improved positional accuracy (116 ± 63 bp for dCas9) compared to fluorescence imaging (~3-fold improvement).
- Demonstrated capability for large-area surveys across multiple magnifications, a feat not possible with TEM or AFM.
Conclusions:
- Scanning electron microscopy (SEM) provides a scalable platform for high-resolution, quantitative mapping of DNA-protein interactions at the single-molecule level.
- This technique overcomes key limitations of existing methods, offering enhanced spatial resolution and broader imaging capabilities.
- SEM enables simultaneous structural visualization and precise localization of sequence-specific binding events on individual DNA molecules.
Related Concept Videos
01:03Single-Strand DNA Binding Proteins
For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...
02:34DNA Microarrays
Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
01:57Sanger Sequencing
DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
03:21RNA-seq
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
02:26Protein Networks
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...