Spatial Thermal or Ionic Strength Gradients over DNA Microarray give Specific and Flexible DNA Microarrays Assays

Martin Dufva, Professor, University of Denmark

Launch presentation

About the speaker

Martin Dufva received his M.Sc. in 1998 and his PhD in 2001 both from the Göteborg University (Sweden). Martin Dufva currently holds an associate professor position at the Department of Micro and Nanotechnology at the Technical University of Denmark. Leading the Fluidic Array System and Technology (FAST) group, his research is orientated towards molecular biology on chip, with the microarray of various forms as core technology. Martin Dufva has published about 30 scientific papers in various fields of microarray technology and cell culture chip technology.

Abstract

Much of the problems of DNA array technology such as cross hybridizations and poor detection limits can be traced to poor combination of probes and assay condition. Microarray performance is hampered by imperfect in silico methods to choose probes and that all probes on the microarray are exposed to the same assay conditions. Here we present three fluidics devices for rapid identification of suitable combination of probes and assay conditions. The devices divide a microarrays slide into 8-10 separate zones. The experimental condition, e.i. stringency, can be chosen for each zone. Such devices were used to create spatial gradient of temperature or ionic strength buffers over hybridized slides. The devices were useful for assay development as demonstrated by a systematic and large scale multi-parametric analysis of probe length, linker length and stringency for specificity and function in genetic assays. The devices allowed for using probes with different melting temperature in the same assay and this added flexibility improved the reproducibility and robustness of genotyping of mutation in the beta-globin and PAH genes. In conclusion, these devices are powerful generic tools for finding combination of probe and assay conditions for obtaining DNA microarrays assays with high specificity and selectivity.

Launch presentation