53. Sequence Analysis and Thermodynamic Studies of Short DNA Duplexes on Oligonucleotide Generic Microchip 

A. Fotin, D. Proudnikov, E. Timofeev, G. Yershov, Eu. Kirillov, A. Drobyshev, E. Khomyakova, A. Zasedatelev, and A. Mirzabekov 
Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 117984 Moscow, Russia; Argonne National Laboratory, Argonne, IL 60439, USA; and Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia 
timofeye@everest.bim.anl.gov 

Generic microchip -- an oligonucleotide microchip containing a complete set of hexanucleotide probes -- has been manufactured and applied for sequence analysis and thermodynamic studies. Isothermal hybridizations as well as thermal denaturation experiments allowed performing sequencing of model synthetic oligomers up to 70 bases long. Melting experiments on the chip using fluorescent microscope have demonstrated reliable discrimination between perfect and mismatched duplexes. This technique was succesively applied for identification of mutations. Studies of thermodynamics of DNA duplex and triplex formation and the effect of modified bases and minor groove binding ligands on duplex stability have been carried out on the generic microchip.