In order to realize an efficient absorption measurement based evanescent-wave sensor, a long interaction length and a strong penetration of the optical field into the sample space is required. For an optical fiber based device, with a solid silica core immersed into a liquid sample, the strength of the evanescent field increases with decreasing core radius. When the core diameter is comparable to the wavelength of the light, a large fraction of the light propagates in the evanescent field. We demonstrate evanescent-wave sensing on aqueous solutions of fluorophore labeled biomolecules positioned in the air holes of a hollow-core photonic crystal fiber (PCF). The aqueous solutions can be positioned in close proximity to light guided in small cores without removing the coating and cladding, thus ensuring a very robust device. In order to make selective DNA detection, we coated the inside of the hollow-core PCF with a sensing layer, which by hybridization selectively immobilize specific molecules. A fluorescence measurement method, where a line-shaped laser beam expose the fiber from the side and excites the fluorophore molecules, was realized. The emitted fluorescence tunnels via the evanescent field into the fiber core(s) and is analyzed by a spectrometer at the fiber end.