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Related Concept Videos

Labeling DNA Probes03:31

Labeling 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...
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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Fine-tuning the Size and Minimizing the Noise of Solid-state Nanopores
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Published on: October 31, 2013

DNA profiling using solid-state nanopores: detection of DNA-binding molecules.

Meni Wanunu1, Jason Sutin, Amit Meller

  • 1Department of Biomedical Engineering, Boston University, Boston Massachusetts 02215, USA.

Nano Letters
|July 10, 2009
PubMed
Summary

We developed a new nanopore method to measure small-molecule binding to single DNA molecules. This technique quantifies binding and offers a scalable platform for drug screening.

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Area of Science:

  • Nanotechnology
  • Molecular Biology
  • Biophysics

Background:

  • Evaluating small-molecule DNA interactions is crucial for drug development.
  • Existing methods often require large sample amounts and can be time-consuming.

Purpose of the Study:

  • To introduce a novel single-molecule nanopore method for assessing small-molecule binding to DNA.
  • To demonstrate the quantification of binding events and spatial sensitivity using this technique.

Main Methods:

  • Utilizing nanopores in ultrathin silicon membranes to analyze individual DNA molecules.
  • Measuring shifts in residual ion current caused by dye-intercalated DNA translocations.
  • Designing spatially distinct DNA segments to probe localized binding.

Main Results:

  • A measurable shift in ion current accurately quantifies the fraction of bound molecules.
  • The method successfully determined binding isotherms for four different dyes.
  • Results correlated well with bulk fluorescence measurements, confirming accuracy.

Conclusions:

  • The nanopore method provides a sensitive and direct way to study molecular binding to DNA at the single-molecule level.
  • This technique requires minimal DNA and is scalable for high-throughput applications.
  • It presents a promising platform for analytical drug screening and molecular diagnostics.