Proceeding talk – Theme: Genome.
Abstract
In this study, we showed the crucial role of interplay between hybridization specificity and genome-wide cross-hybridization for efficient target prediction. We defined hybridization specificity as a ratio between oligo target-specific hybridization and oligo genome-wide cross-hybridization. An Affymetrix microarray database used in the study contains two different types of probes. The first type of oligo-probes does not have a specific target on the genome and their hybridization signals are derived from genome-wide cross-hybridization alone. The second probe type includes probes that have a specific target on the genomic DNA and their signals are derived from specific and cross- hybridization components combined together in a total signal. The comparison revealed that hybridization specificity was negatively affected by position-dependent nucleotide sequences and several thermodynamic parameters. Filtering out the probes with defined “negative” characteristics significantly increases hybridization specificity by dramatically decreasing genome-wide cross-hybridization. A new approach for efficient oligo- probe design is described.
Authors
Svetlana Shabalina, National Institutes of Health, United States
Olga Matveeva, Biopolymer Design LLC, Acton, United States
Yury Nechipurenko, Engelhardt Institute of Molecular Biology, Russian Federation
Nafisa Nazipova, Institute Mathematical Problems in Biology, Russian Federation
Aleksey Ogurtsov, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, United States
Evgeniy Riabenko, Moscow Institute of Physicas and Technology, Moscow, Russia, Russian Federation
Chikako Ragan, 5Queensland Brain Institute, The University of Queensland, Australia