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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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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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Related Experiment Video

Updated: Apr 19, 2026

DNA-affinity-purified Chip DAP-chip Method to Determine Gene Targets for Bacterial Two component Regulatory Systems
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Structured oligonucleotides for target indexing to allow single-vessel PCR amplification and solid support microarray

Laurie D Girard1, Karel Boissinot, Régis Peytavi

  • 1Centre de recherche en infectiologie de l'Université Laval, Axe maladies infectieuses et immunitaires, Centre de recherche du CHU de Québec, Québec City, Québec, Canada. Michel.G.Bergeron@crchul.ulaval.ca.

The Analyst
|December 10, 2014
PubMed
Summary

We developed a new method, Structured Cleavage Induced Single-Stranded Oligonucleotide Hybridization Reaction (SCISSOHR), for molecular diagnostics. This technique combines PCR amplification and microarray hybridization in a single vessel, reducing costs and complexity for genetic target detection.

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Area of Science:

  • Molecular Diagnostics
  • Biotechnology
  • Genomics

Background:

  • Combining PCR amplification and microarray hybridization enhances sensitivity, specificity, and multiplexing for molecular diagnostics.
  • Current methods require separate buffers and chambers, increasing complexity, cost, and reagent usage.
  • Microarray hybridization efficiency can be sequence-dependent and unpredictable.

Purpose of the Study:

  • To develop a novel technology integrating nucleic acid amplification and microarray hybridization into a single reaction vessel.
  • To simplify lab-on-chip devices and reduce costs associated with molecular diagnostic assays.
  • To create a more efficient and predictable method for multiplexed genetic target detection.

Main Methods:

  • Developed Structured Cleavage Induced Single-Stranded Oligonucleotide Hybridization Reaction (SCISSOHR) probes.
  • SCISSOHR probes link target sequences to unique tag sequences via polymerase exonuclease activity.
  • Enabled single-vessel combination of PCR amplification and microarray hybridization using only PCR buffer.

Main Results:

  • SCISSOHR technology allows amplification and hybridization in a single vessel, using only PCR buffer.
  • Tags consist of a sequence-dependent segment and a unique sequence-independent segment for optimal hybridization.
  • Evaluated five PCR buffers for microarray hybridization performance.
  • Demonstrated a multiplexed assay for amplifying, detecting, and identifying three DNA targets.

Conclusions:

  • SCISSOHR technology simplifies lab-on-chip device design and reduces consumable costs.
  • Facilitates cost-effective automation of highly multiplexed assays for genetic target detection.
  • Offers a streamlined approach for molecular diagnostics with improved efficiency and predictability.