title: 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.
authors.affiliation: School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, United Kingdom.
authors.forename: Vitaly
authors.initials: V
authors.lastname: Zinkevich
authors.affiliation: Andronikashvili Institute of Physics, I. Javakhishvili Tbilisi State University, Tbilisi, Georgia.
authors.forename: Nelly
authors.initials: N
authors.lastname: Sapojnikova
authors.affiliation: School of Biological Sciences, University of Portsmouth, Portsmouth, United Kingdom.
authors.forename: Julian
authors.initials: J
authors.lastname: Mitchell
authors.affiliation: Andronikashvili Institute of Physics, I. Javakhishvili Tbilisi State University, Tbilisi, Georgia.
authors.forename: Tamar
authors.initials: T
authors.lastname: Kartvelishvili
authors.affiliation: Andronikashvili Institute of Physics, I. Javakhishvili Tbilisi State University, Tbilisi, Georgia.
authors.forename: Nino
authors.initials: N
authors.lastname: Asatiani
authors.affiliation: School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, United Kingdom.
authors.forename: Samia
authors.initials: S
authors.lastname: Alkhalil
authors.affiliation: School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, United Kingdom.
authors.forename: Irina
authors.initials: I
authors.lastname: Bogdarina
authors.affiliation: Saudi Aramco's Research and Development Center, Dharan, Saudi Arabia.
authors.forename: Abdulmohsen A
authors.initials: AA
authors.lastname: Al-Humam
mesh_terms: D002692:Chlamydia trachomatis / Q000235:genetics; D003587:Cytomegalovirus / Q000235:genetics; D015342:DNA Probes; D018258:Herpesvirus 2, Human / Q000235:genetics; D006801:Humans; D009693:Nucleic Acid Hybridization / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012412:Rubella virus / Q000235:genetics; D014122:Toxoplasma / Q000235:genetics
chemical_list: D015342:DNA Probes