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Related Concept Videos

Labeling DNA Probes03:31

Labeling DNA Probes

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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...
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FISH - Fluorescent In-situ Hybridization02:07

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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,...
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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.
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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...
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Robust 3D DNA FISH Using Directly Labeled Probes
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Visualizing genomes with Oligopaint FISH probes.

Brian J Beliveau1, Nicholas Apostolopoulos, Chao-ting Wu

  • 1Department of Genetics, Harvard Medical School, Boston, Massachusetts.

Current Protocols in Molecular Biology
|February 11, 2014
PubMed
Summary
This summary is machine-generated.

Synthesize custom DNA Oligopaint probes for visualizing large genomic regions. This guide details probe synthesis and protocols for fluorescence in situ hybridization (FISH) and 3D-FISH applications.

Keywords:
FISHOligopaintcomplex DNA libraryoligonucleotide

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Area of Science:

  • Molecular Biology
  • Genomics
  • Biotechnology

Background:

  • Genomic region visualization is crucial for understanding genome organization and function.
  • Existing methods for large genomic region imaging can be complex or limited in scope.

Purpose of the Study:

  • To provide a detailed protocol for synthesizing Oligopaint probes.
  • To enable visualization of large genomic regions (tens of kilobases to megabases).
  • To offer methods for fluorescence in situ hybridization (FISH) and 3D-FISH.

Main Methods:

  • Synthesis of fluorescently labeled, single-stranded DNA oligonucleotides (Oligopaint probes).
  • Standard molecular biology techniques for probe creation.
  • Protocols for sample preparation for FISH and 3D-FISH.

Main Results:

  • Demonstrated successful synthesis of Oligopaint probes.
  • Established protocols for applying these probes in FISH and 3D-FISH experiments.
  • Enabled visualization of genomic regions across a wide size range.

Conclusions:

  • Oligopaint probes offer a versatile tool for genomic region visualization.
  • The provided protocols facilitate the use of Oligopaint probes in various cytogenetic applications.
  • This unit empowers researchers with accessible methods for advanced genomic imaging.