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Related Concept Videos

DNA Isolation01:24

DNA Isolation

DNA isolation protocols can be fast and straightforward or complex and time-consuming depending on the type and quality of DNA required for further processing. For example, plasmid DNA extraction is a bit more complicated than genomic DNA extraction because of the need for an appropriate lysis method to separate plasmid DNA from gDNA during isolation. However, for specific applications, such as long-range DNA sequencing that require a good yield of high- quality DNA samples, we need to follow...
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Labeling DNA Probes

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Southern Blot02:57

Southern 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...
DNA Microarrays02:34

DNA 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...

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Related Experiment Video

Updated: Jul 18, 2026

Proofreading and DNA Repair Assay Using Single Nucleotide Extension and MALDI-TOF Mass Spectrometry Analysis
11:08

Proofreading and DNA Repair Assay Using Single Nucleotide Extension and MALDI-TOF Mass Spectrometry Analysis

Published on: June 19, 2018

Using DNA-binding proteins as an analytical tool.

Maxim Berezovski1, Sergey N Krylov

  • 1Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada.

Journal of the American Chemical Society
|October 30, 2003
PubMed
Summary

DNA-binding proteins offer versatile tools for analyzing DNA, RNA, and proteins. Utilizing single-stranded DNA binding protein (SSB) in capillary electrophoresis enables efficient, gel-free separation and quantification of these molecules.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Analytical Chemistry

Background:

  • Traditional affinity analyses often require sieving matrices for electrophoretic separation.
  • Distinguishing between probes and probe-target complexes can be challenging in gel-free systems.

Purpose of the Study:

  • To develop a versatile and efficient method for analyzing DNA, RNA, and proteins using DNA-binding proteins.
  • To demonstrate gel-free separation and quantification of affinity probes and their targets in capillary electrophoresis.

Main Methods:

  • Utilized specific affinity probes (hybridization and aptamer probes), which are single-stranded DNA.
  • Employed single-stranded DNA binding protein (SSB) in capillary electrophoresis (CE) run buffer.
  • Leveraged SSB's differential binding to probes and probe-target complexes to induce mobility differences.

Main Results:

  • Achieved highly efficient, gel-free separation of DNA, RNA, and protein targets using SSB in CE.
  • Demonstrated that SSB concentration-dependently alters the electrophoretic mobilities of probes and their complexes.
  • Enabled affinity analyses for DNA, RNA, and proteins without the need for sieving matrices.

Conclusions:

  • DNA-binding proteins, exemplified by SSB, provide a powerful toolkit for versatile molecular analyses.
  • This gel-free CE method facilitates accurate quantification of DNA, RNA, and proteins.
  • Potential applications include genomic DNA identification and monitoring gene expression at mRNA and protein levels.