Hybridization kinetics of double-stranded DNA probes for rapid molecular analysis

Vinay Gidwani, Reza Riahi, Donna Zhang, Pak Kin Wong

Research output: Contribution to journalArticle

15 Citations (Scopus)

Abstract

This study reports the hybridization kinetics of double-stranded DNA probes for rapid molecular analysis. Molecular binding schemes based on double-stranded DNA probes have been developed for quantitative detection of various biomolecules, such as nucleic acids and DNA binding proteins recently. The thermodynamic competition between the target and the competitor in binding to the probe provides a highly specific mechanism for molecular detection. The kinetics of the double-stranded DNA probe, on the other hand, represent another key aspect toward its general applicability for a wide set of biomedical applications. Herein we report a systematic investigation of the kinetics of double-stranded DNA probes. The signal-to-background ratio and assay time of the double-stranded DNA probes are optimized at a high ionic strength (over 100 mM NaCl). Both the donor probe and the quencher probe sequences are shown to be important in the hybridization kinetics. A long sticky end of the probe is able to dramatically accelerate the kinetics of the assay. To provide a quantitative description of the kinetics, a two-stage binding model is developed to describe the major features of the kinetics of the assay. The sensitivity of the kinetic model and the dominant affinity constants are studied. The study provides a general guideline for the design of the probes for reducing the total assay time. With an appropriate design of the probes, the assay can be finished within minutes at room temperature.

Original languageEnglish (US)
Pages (from-to)1675-1681
Number of pages7
JournalAnalyst
Volume134
Issue number8
DOIs
StatePublished - 2009

Fingerprint

molecular analysis
DNA Probes
DNA
probe
kinetics
Kinetics
Assays
assay
DNA-Binding Proteins
Biomolecules
Ionic strength
Thermodynamics
Osmolar Concentration
Nucleic Acids
Nucleic acids
nucleic acid
Guidelines
Temperature
thermodynamics

ASJC Scopus subject areas

  • Analytical Chemistry
  • Spectroscopy
  • Electrochemistry
  • Biochemistry
  • Environmental Chemistry

Cite this

Hybridization kinetics of double-stranded DNA probes for rapid molecular analysis. / Gidwani, Vinay; Riahi, Reza; Zhang, Donna; Wong, Pak Kin.

In: Analyst, Vol. 134, No. 8, 2009, p. 1675-1681.

Research output: Contribution to journalArticle

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