Mathematical modeling of functionalized-microsphere based assays for rapid DNA detection

From sample preparation to results

Tobias M. Louw, Oscar G. Gomez-Duarte, Anuradha Subramanian, Hendrik J Viljoen

Research output: Contribution to journalArticle

Abstract

Functionalized microspheres are frequently used in the detection of biomolecules. A fundamental understanding of the mechanisms involved in enzymatic assays is required to estimate a method's utility. The mathematical methodology is illustrated through a theoretical analysis to assess the performance of a diagnostic method based on the horseradish peroxidase catalyzed reaction to detect pathogens in clinical specimens. The first part of the analysis focuses on the collection of target DNA molecules onto a functionalized fiber in a lysis micro-reactor (LMR). Expressions are derived for hybridization rates that include convective transport. In the next step the fiber is contacted with functionalized chitosan microspheres containing horse radish peroxidase. Chitosan microspheres are conjugated to the fiber with the target DNA acting as a unique tether. The final step is the release of chitosan microspheres in a chromogenic substrate and monitoring absorption changes. The analysis provides estimates of the method sensitivity and processing time and we show that DNA with a concentration as low as 10-4 copies per milliliter can be detected in less than 30min. The modeling methodology presented can readily be extended to similar enzymatic, microsphere-based assays for quantitative purposes and feasibility studies.

Original languageEnglish (US)
Pages (from-to)50-60
Number of pages11
JournalBiochemical Engineering Journal
Volume88
DOIs
StatePublished - Jul 15 2014

Fingerprint

Microspheres
Assays
DNA
Chitosan
Fibers
Chromogenics
Chromogenic Compounds
Raphanus
Enzyme Assays
Feasibility Studies
Biomolecules
Pathogens
Horseradish Peroxidase
Peroxidase
Molecules
Monitoring
Substrates
Processing

Keywords

  • Biomedical
  • Diagnostics
  • Diffusion-reaction
  • Dynamic modeling
  • Enzyme biocatalysis

ASJC Scopus subject areas

  • Biotechnology
  • Bioengineering
  • Environmental Engineering
  • Biomedical Engineering

Cite this

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abstract = "Functionalized microspheres are frequently used in the detection of biomolecules. A fundamental understanding of the mechanisms involved in enzymatic assays is required to estimate a method's utility. The mathematical methodology is illustrated through a theoretical analysis to assess the performance of a diagnostic method based on the horseradish peroxidase catalyzed reaction to detect pathogens in clinical specimens. The first part of the analysis focuses on the collection of target DNA molecules onto a functionalized fiber in a lysis micro-reactor (LMR). Expressions are derived for hybridization rates that include convective transport. In the next step the fiber is contacted with functionalized chitosan microspheres containing horse radish peroxidase. Chitosan microspheres are conjugated to the fiber with the target DNA acting as a unique tether. The final step is the release of chitosan microspheres in a chromogenic substrate and monitoring absorption changes. The analysis provides estimates of the method sensitivity and processing time and we show that DNA with a concentration as low as 10-4 copies per milliliter can be detected in less than 30min. The modeling methodology presented can readily be extended to similar enzymatic, microsphere-based assays for quantitative purposes and feasibility studies.",
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