A Novel Cassette Method for Probe Evaluation in the Designed Biochips

Abstract

A critical step in biochip design is the selection of probes with identical hybridisation characteristics. In this article we describe a novel method for evaluating DNA hybridisation probes, allowing the fine-tuning of biochips, that uses cassettes with multiple probes. Each cassette contains probes in equimolar proportions so that their hybridisation performance can be assessed in a single reaction. The model used to demonstrate this method was a series of probes developed to detect TORCH pathogens. DNA probes were designed for Toxoplasma gondii, Chlamidia trachomatis, Rubella, Cytomegalovirus, and Herpes virus and these were used to construct the DNA cassettes. Five cassettes were constructed to detect TORCH pathogens using a variety of genes coding for membrane proteins, viral matrix protein, an early expressed viral protein, viral DNA polymerase and the repetitive gene B1 of Toxoplasma gondii. All of these probes, except that for the B1 gene, exhibited similar profiles under the same hybridisation conditions. The failure of the B1 gene probe to hybridise was not due to a position effect, and this indicated that the probe was unsuitable for inclusion in the biochip. The redesigned probe for the B1 gene exhibited identical hybridisation properties to the other probes, suitable for inclusion in a biochip.

Bioplastics against Microplastics: Screening of Environmental Bacteria for Bioplastics Production

“…In order to check and evaluate that the chosen probes have similar hybridization capacities, the cassette approach developed and published in Ref. [40] fluorescent signals in hybridization reactions. The result of the estimation of the hybridization capacity of the proposed probes showed that the probes exhibited comparable hybridization signals and were characterized by the mean signal-to-noise ratio S/N = 12 (data not shown).…”

“…The procedures for DNA preparation for hybridization that include DNA amplification, fragmentation, and fluorescent labeling are described in Ref. [40]. Two sludge and three compost environmental samples were analyzed for the bacterial assemblage, revealing PHAs producing capacity using a biochip method.…”