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Antibodies were raised to three synthetic peptides, each constructed to match a different cytoplasmic region of the 43kD protein of the cardiac gap junction. These antibodies have all been used for immunohistochemical localization of gap junctions in the rat ventricle. Each is shown to have different staining characteristics which provide supporting evidence for the model proposed for the configuration of the gap junction protein within the membrane. Laser scanning confocal microscopy has confirmed that the localization of ventricular myocyte gap junctions is solely within intercalated disks. This technique is demonstrated to provide a greater overview of the three dimensional arrangement of the junctions than other microscopical techniques. Larger gap junctions occur typically at the periphery of the disk, with smaller junctions situated in the central zone. The analysis of the number and distribution of gap junctions over large volumes of myocardial tissue (three-dimensional tomography) is now feasible with this approach, and may be used to delineate conduction pathways.