Labeling of cytosine residues with biliproteins for use as fluorescent DNA probes

The fluorescent properties of biliproteins (B-phycoerythrin, BPE; C-phycocyanin, CPC and allophycocyanin, APC) have been utilized as labels of nucleic acids to detect hybridization by means of steady-state fluorescence anisotropy in a homogeneous aqueous solution of model system in which poly(C) and poly(I) are, respectively, the probe and target sequences. An easy method to obtain biliprotein–DNA conjugates by a two-stage procedure is described. The first stage was a modification of the cytosine amino group of poly(C) at the N4 position which then reacted with N-succinimidyl 3-(2-pyridyldithio) propionate (SPDP) to obtain poly(C)-bound 2-pyridyl disulfide. In the second stage biliproteins were directly reacted with SPDP to obtain biliprotein-bound 2-pyridyl disulfide, dithiotreitol was added for reduction to biliprotein-bound thiol and was then mixed with the poly(C)-bound 2-pyridyl disulfide to obtain the biliprotein–poly(C) conjugate. The three biliproteins studied bind to nucleic acids without noticeable change of their spectral properties (absorption, fluorescence efficiency and fluorescence lifetime). Consequently, our labeling methodology can be applied to obtain any type of biliprotein-labeled nucleic acid probe. The increase of the steady-state fluorescence anisotropy from biliprotein–poly(C) upon hybridization with poly(I) can be used to readily detect the hybridization with the target poly(I) in a sample without having to separate free and bound labeled probes. The small decreases in lifetime displayed by the biliprotein–poly(C) conjugates upon hybridization are not sufficient to explain the steady-state anisotropy increase. Apparently, the rotational motion of the overall macrostructure is principally responsible for the increase in anisotropy. The greater fluorescence efficiency and lifetime from BPE with respect to those from CPC or APC allows us recommend that protein as the most suitable label.