Study of the Quality of Aminated Substrates Used for Hybridization Analysis

E. A. Shlyapnikova1 #, Yu. M. Shlyapnikov1, V. N. Afanas’ev1, G. V. Afanas’eva1, A. V. Gavryushkin1 and I. P. Beletskii1

#Phone: 8 (27) 73-91-08; fax: 8 (27) 33-05-53; e-mail:

1Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Institutskaya ul. 3, Pushchino, Moscow oblast, 142290, Russia

Received: March 20, 2006; in final form: May 11, 2006

Abstract.  A set of methods for analysis of the quality of aminated substrates that could be a basis for the large-scale manufacturing of biological microchips is suggested. The analysis includes the determination of the number of amino groups, their availability for the immobilization of phosphorylated oligonucleotides, and the characterization of surface properties of the substrates in respect to the nonspecific sorption of reagents during hybridization. A simple procedure was suggested for determination of the density/number of amino groups. It is based on the use of dimethoxytrityl chloride with the subsequent spectrophotometric determination of dimethoxytrityl cation. The availability of amino groups was estimated by covalent attachment of an oligonucleotide probe containing a fluorescently labeled group to the aminated surface and the subsequent comparison of the intensity of fluorescing zones formed on the chip. The sorption properties of the surface were investigated with the help of a model hybridization reaction. A comparative analysis of aminated glasses manufactured by various firms and in our laboratory showed that the glasses with the amino group density from 0.7 to 2.0 groups/nm2 prepared by our procedure have the best properties for the hybridization analysis.

Key words:  DNA chips, hybridization analysis, oligonucleotide immobilization

Russian Journal of Bioorganic Chemistry 2007, 33 (2): 243-250