The Efficacy of Hybridization Analysis of DNA Labeled with Red and Near-Infrared Cyanine Dyes

Abstract

We present a study of the sensitivity of a hybridization microarray analysis of DNA labeled with 2'‑deoxyuridine-5'-triphosphate derivatives that contain the Cy5 and Cy7 cyanine fluorophore dyes. Two Cy5-dUTP and two Cy7-dUTP derivatives that can be effectively incorporated into a newly synthesized DNA strand during PCR were chosen for this study. PCR products fluorescently labeled with different dyes were hybridized with a matrix of oligonucleotide probes immobilized in the microchip hydrogel cells. Fluorescent signals were recorded on a digital fluorescence microscope in the red (for Cy5-dUTP) and near-infrared (for Cy7-dUTP) range. Using the serial dilution method, the minimum DNA concentration was evaluated, which is necessary for genotyping by the specific interaction between the fluorescently labeled PCR product and oligonucleotide probes on the microarray. It has been shown that the fluorescently labeled Cy7-dUTP, unlike Cy5-dUTP, provides greater sensitivity of the hybridization analysis.