A generalized probe selection method for DNA chips

Abstract

The flaws in the present probe selection methods restrained the development of the DNA chip technology and its applications. The presented generalized probe selection method for the DNA chips elaborates the length of the probe, the melting temperatures, the specificity of the probe, and the position where the probe may bind to the targets.

HPV 9G DNA Chip: 100% Clinical Sensitivity and Specificity

“…Generalized probe selection method. Probes were selected according to our recent report on the generalized probe selection method (15). In brief, the probes were designed to hybridize with the MY11/GP6 ϩ primer set-mediated PCR products of the HPV genotypes.…”

“…The HPV 9G DNA chip was prepared according to our previous report (17) using the probes obtained by our recently reported generalized probe selection method for DNA chips (15). The immobilization solutions containing the probes (probe 1 to probe 23) corresponding to the 19 HPV genotypesthe 14 high-risk groups (HPV-16, HPV-18, HPV-31, HPV-33, HPV-35, HPV-39, HPV-45, HPV-51, HPV-52, HPV-56, HPV-58, HPV-59, HPV-66, and HPV-68) and the 5 low-risk groups (HPV-6, HPV-11, HPV-34, HPV-40, and HPV-42), along with the hybridization control (HC), positive control (PC), and PCR control (PCR) probes (Table 1), were spotted on the AMCA (aminocalix [4]arene) slide using a microarrayer.…”

Biological applications of functionalized calixarenes

“…47 The HPV 9G DNA chip test established its efficiency in terms of a signal-to-background ratio (SBR) of 200, which is 50 times superior to commercial HPV DNA chips, and 100% target-specific hybridization at 25 1C. The clinical sensitivities of HPV genotyping by the HPV 9G DNA chip test and a commercial HPV DNA chip test were 100% and 88%, respectively.…”

MTB-DR-RIF 9G test: Detection and discrimination of tuberculosis and multi-drug resistant tuberculosis strains

“…All probes were designed according to the recently reported generalized probe selection method ( [26]). The MTB-DR-RIF 9G membranes consist of 7 lines corresponding to seven probes.…”