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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.
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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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Split Hybridization Probe Utilizing a DNA Fluorescent Light-up Aptamer as a Signal Reporter for Sequence-Specific

AnnaMarie Knowles1, Justine Monsalve1, Yulia Gerasimova2

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|July 28, 2025
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DNA-based fluorescent light-up aptamers (FLAPs) offer a label-free, low-cost method for detecting nucleic acid targets. This study details an algorithm for split light-up aptamer sensors (SLASs) enabling precise single-nucleotide substitution analysis.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Analytical Chemistry

Background:

  • Conventional nucleic acid detection often requires labeled probes, increasing costs and complexity.
  • Fluorescent light-up aptamers (FLAPs) offer a label-free alternative, utilizing dye ligands that fluoresce upon binding.
  • DAP-10-42 is the most efficient DNA FLAP reported, showing significant potential for biosensing.

Purpose of the Study:

  • To describe an algorithm for designing split light-up aptamer sensors (SLASs) based on the efficient DNA FLAP, DAP-10-42.
  • To enable sequence-specific nucleic acid detection with single-nucleotide resolution for applications like single-nucleotide substitution (SNS) analysis.
  • To highlight the advantages of SLASs for label-free, fluorescence-based detection in various biosensing contexts.

Main Methods:

  • Development of an algorithm to design split light-up aptamer sensors (SLASs).
  • Utilizing the DAP-10-42 DNA FLAP as the core component for sensor construction.
  • Equipping SLASs with sequences complementary to target nucleic acids for specific binding.

Main Results:

  • SLASs enable sequence-specific detection of nucleic acid targets.
  • The developed sensors achieve high selectivity, down to single-nucleotide resolution, for SNS analysis.
  • The fluorescence signal readout is label-free and compatible with standard fluorometers and visual observation.

Conclusions:

  • The SLAS approach provides a versatile and efficient platform for nucleic acid analysis.
  • SLASs offer a label-free, low-cost, and sensitive method for detecting nucleic acid targets, including single-nucleotide variations.
  • This technology holds promise for applications in disease diagnostics, environmental monitoring, and biomolecular research.