Related Experiment Video
Updated: Jul 17, 2026
08:56
Visual Detection of Multiple Nucleic Acids in a Capillary Array
Published on: November 15, 2017
Direct detection of double-stranded DNA: Molecular methods and applications for DNA diagnostics
Indraneel Ghosh1, Cliff I Stains, Aik T Ooi
1Department of Chemistry, University of Arizona, Tucson, Arizona 85721, USA. ghosh@email.arizona.edu
Molecular Biosystems
|January 12, 2007
Summary
New methods enable direct detection of double-stranded DNA (dsDNA) without denaturation. Engineered proteins offer precise dsDNA diagnostics for cell-based applications.
Area of Science:
- Molecular Biology
- Biotechnology
- Genomics
Background:
- Current DNA detection methods often require denaturation or hybridization of single-stranded DNA (ssDNA).
- Recent advancements allow for direct recognition of double-stranded DNA (dsDNA) through groove binding.
Purpose of the Study:
- To review progress in adapting molecules for direct dsDNA detection.
- To highlight the potential of engineered proteins for sensitive and specific dsDNA diagnostics.
Main Methods:
- Review of polyamides, triplex DNA, and engineered zinc finger DNA-binding proteins for dsDNA recognition.
- Focus on the sequence-enabled reassembly (SEER) method using custom zinc finger proteins.
Main Results:
- Polyamides, triplex DNA, and zinc finger proteins show promise for direct dsDNA detection.
- The SEER method offers potential for in-cell dsDNA detection.
Conclusions:
- Direct dsDNA detection bypasses traditional denaturation/hybridization steps.
- Engineered zinc finger proteins, via SEER, present a novel approach for cell-based diagnostics and therapeutics.
Related Concept Videos
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...
03:31Labeling 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...
02:34DNA 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...
01:24DNA 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...
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...
01:29Modern Molecular Taxonomy
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...