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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...
In-situ Hybridization02:31

In-situ Hybridization

In situ hybridization (ISH) is a technique used to detect and localize specific DNA or RNA molecules in cells, tissue, or tissue sections using a labeled probe. The technique was first used in 1969 for the investigation of nucleic acids. It is currently an essential tool in scientific research and clinical settings, especially for diagnostic purposes.
Types of probes and labels
A probe is a complementary strand of DNA or RNA that binds to corresponding nucleotide sequences in a cell. Many...

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DNAzyme 10-23 - Based Nanomachines for Nucleic Acid Recognition
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A rational approach in probe design for nucleic acid-based biosensing.

M L Ermini1, S Scarano, R Bini

  • 1Dipartimento di Chimica Ugo Schiff, Università degli Studi di Firenze, Via della Lastruccia 13, 50019, Sesto F.no (FI), Italy.

Biosensors & Bioelectronics
|July 2, 2011
PubMed
Summary

Computational methods enable rational design of nucleic acid probes for biosensors. This approach optimizes probe selection, improving sensor performance for accurate gene detection.

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Area of Science:

  • Biochemistry
  • Biotechnology
  • Analytical Chemistry

Background:

  • Nucleic acid-based sensing is crucial for basic and applied chemical research.
  • Successful sensor fabrication relies on effective probe design and surface immobilization.
  • The choice of bioprobes significantly impacts sensor analytical performance.

Purpose of the Study:

  • To demonstrate the impact of rational bioprobe selection on sensor performance.
  • To develop an optimized strategy for in silico probe design supported by experimental validation.
  • To validate computational probe design using Surface Plasmon Resonance imaging (SPRi).

Main Methods:

  • Utilized computational evaluations for designing optimal nucleic acid probes.
  • Employed Surface Plasmon Resonance imaging (SPRi) for optical transduction and real-time analysis.
  • Immobilized five selected probes on gold chip surfaces using thiol chemistry.
  • Conducted melting experiments to assess probe secondary structure strength and folding.

Main Results:

  • Computational evaluations successfully guided the design of effective probes for target sequences.
  • SPRi experiments validated the computational model, demonstrating real-time, label-free nucleic acid detection.
  • Experimental sensor behavior correlated with probe secondary structure strength and folding predictions.
  • The in silico probe design strategy proved reproducible and optimized sensor performance.

Conclusions:

  • Rational computational design of bioprobes is a highly promising approach for developing high-performance biosensors.
  • This strategy offers a useful tool for optimizing probe selection in nucleic acid-based sensing.
  • The integration of computational design with SPRi provides a robust platform for biosensor development.