Related Experiment Video
Updated: May 16, 2026
12:16
Robust 3D DNA FISH Using Directly Labeled Probes
Published on: August 15, 2013
Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes
Brian J Beliveau1, Eric F Joyce, Nicholas Apostolopoulos
1Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
Summary
Researchers developed a new oligonucleotide and PCR-based fluorescence in situ hybridization (FISH) method. This technique enables precise visualization of chromosome positioning and gene regions in various organisms and sample types.
Area of Science:
- Genomics
- Molecular Biology
- Cell Biology
Background:
- Nuclear architecture significantly influences gene expression and cellular processes.
- Existing technologies for chromosome positioning analysis include intermolecular interaction reconstruction and in situ visualization.
- There is a need for advanced methods to precisely map chromosome organization.
Purpose of the Study:
- To introduce a novel oligonucleotide- and PCR-based fluorescence in situ hybridization (FISH) strategy.
- To present a bioinformatic platform for extending this FISH technology to any sequenced genome.
- To provide researchers with enhanced capabilities for visualizing chromosome architecture.
Main Methods:
- Development of renewable, highly efficient oligonucleotide probes for robust chromosome labeling.
- Utilization of PCR-based amplification for enhanced signal detection.
- Integration with a bioinformatic platform for broad applicability across sequenced genomes.
- Application in cell culture, fixed tissues, and metaphase spreads.
Main Results:
- Demonstrated precise control over targeted DNA sequences for FISH probes.
- Achieved robust labeling of chromosomes in diverse biological samples.
- Enabled single and multicolor imaging of genomic regions from tens of kilobases to megabases.
- Validated the protocol's adaptability across different organisms with sequenced genomes.
Conclusions:
- The developed FISH strategy offers a versatile and efficient tool for chromosome analysis.
- This technology enhances the ability to visualize both interphase and metaphase chromosomes with high precision.
- The bioinformatic platform ensures broad accessibility and application in various research settings.
Related Concept Videos
03:31Labeling DNA Probes
DNA probes are fragments of DNA labeled with a reporter tag to enable their detection or purification. The resulting labeled DNA probes can then hybridize to target nucleic acid sequences through complementary base-pairing, and may be used to recover or identify these regions.
Radioisotopes, fluorophores, or small molecule binding partners like biotin or digoxigenin, are the most widely used reporter tags for labeling DNA probes. These labels can be attached to the probe DNA molecule via...
Radioisotopes, fluorophores, or small molecule binding partners like biotin or digoxigenin, are the most widely used reporter tags for labeling DNA probes. These labels can be attached to the probe DNA molecule via...
02:07FISH - Fluorescent In-situ Hybridization
Fluorescence in situ hybridization, or FISH, was developed in the early 1980s and has quickly become one of the most widely used techniques in cytogenetics. Labeled probes are used to bind complementary DNA or RNA sequences on a chromosome or in a region within a cell. Earlier, the probes could only be obtained by cloning or reverse transcription of a DNA template. Currently, the probe oligonucleotides can be synthesized synthetically. Additionally, with the advancement of optical techniques,...
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...
02:57Southern Blot
Agarose gel electrophoresis is very useful in separating DNA fragments by size. Running a DNA ladder containing fragments of the known length alongside the sample helps determine the approximate length of the sample DNA fragments. However, additional steps are needed to verify the sequence identity of the sample DNA fragments.
Denatured DNA fragments must be transferred onto a carrier membrane from the gel to make it accessible to a probe - a small ssDNA fragment complementary to the target DNA...
Denatured DNA fragments must be transferred onto a carrier membrane from the gel to make it accessible to a probe - a small ssDNA fragment complementary to the target DNA...
02:46Genetic Screens
Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which result in visible changes...
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which result in visible changes...