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principle of operation

The operation principle of all molecular microchips with immobilized probes consists in ability of biological macromolecules to molecular recognition (highly specific binding with the other molecules). For example, the formation of DNA duplexes obeys to Watson-Krick rule, A<->T и G<->C, while antibodies can form the stable specific immune complexes with particular parts of a protein (antigen) called antigen determinants or epitopes.
перфект - выполняются условия молекулярной комплементарности
The complementarity conditions are fulfilled and stable complex is formed.
Fluorescence intensity from the pads is measured with fluorescent microscope with CCD-camera. After that the data are processed with computer. A typical image of microchip is shown below (left figure). The intensity may also be visualized via three-dimensional representation (right figure).
флуоресцентное изображение микрочипа
Fluorescent image of microchip
увеличенный фрагмент флуоресцентного изображения чипа
Enlarged fragment of fluorescent image (marked red in figure above)
трехмерное изображение ячеек микрочипа
Three-dimensional representation for fluorescent image of microchip

If the correspondence between immobilized molecular probes and labeled analyzed molecules satisfies the exact complementarity conditions, then the resulting complexes will be most stable thermodynamically.
мисматч - не выполняются условия молекулярной комплементарности
The complementarity conditions are not fulfilled. The formed complexes are unstable.
As a result, the number of complete complexes will exceed that of with violation of complementarity condition. Therefore, the pads with complete complexes will produce stronger fluorescent signals than their incomplete counterparts. The complete and incomplete complexes corresponding to specific and non-specific binding are commonly called merely "perfects" and "mismatches".
трехмерное изображение ячеек микрочипа
Three-dimensional visualization for distribution of fluorescence intensity over the pads (fragment marked red on left figure).

Ideally, the formation of perfects and mismatches in the cells with particular probes should exactly correspond to the binary values 1 and 0 in the cells of electronic microchips. Thus, the cells with perfects and mismatches should be easily discerned by signal intensities. In a real situation the influence of non-specific binding may not be so small and the relevant differentiation of signals may be not so easy.
Профиль флуоресцентного изображения микрочипа вдоль некоторой линии
Profile of fluorescent signal along given lines.
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