Open AccessSpecificity of randomly generated genomic DNA fragment probes on a DNA array
Author(s) -
Tobino Tomohiro,
Kurisu Futoshi,
Kasuga Ikuro,
Furumai Hiroaki
Publication year - 2012
Publication title -
fems microbiology letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.899
H-Index - 151
eISSN - 1574-6968
pISSN - 0378-1097
DOI - 10.1111/j.1574-6968.2011.02486.x
Subject(s) - dna , biology , genomic dna , hybridization probe , genome , computational biology , genetics , dna nanoball sequencing , nucleic acid thermodynamics , dna sequencing , molecular probe , dna–dna hybridization , genomic library , microbiology and biotechnology , gene , base sequence
The use of randomly generated DNA fragment sequences as probes on DNA arrays offers a unique potential for exploring unsequenced microorganisms. In this study, the detection specificity was evaluated with respect to probe‐target sequence similarity using genomic DNA s of four P seudomonas strains. Genome fragments averaging 2000 bp were found to be specific enough to discriminate 85–90% similarity under highly stringent hybridization conditions. Such stringent conditions compromised signal intensities; however, specific signals remained detectable at the highest stringency (at 75 °C hybridization) with negligible false negatives. These results suggest that, without any probe design or selection, genomic fragments can provide a reasonable specificity for microbial diagnostics or species delineation by DNA – DNA similarities.