Investigation of nonspecific effects of different dyes in the screening of labeled carbohydrates against immobilized proteins

Carbohydrates play an important role in life processes, and combinatorial chemistry can provide useful sources of thousands of synthetic carbohydrates as potential ligands for biological receptors. To accelerate the detection of positive hits arising from specific interactions between a carbohydrate and a protein, the use of fluorescent dyes can serve as a reliable detecting tool. A study of labeled carbohydrates to lectins conjugated to a solid-support shows that succinimidyl 6-(N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino)hexanoate (NBD-X) dye provides by far the lowest level of nonspecific interaction with immobilized protein. This observation is in stark contrast with the commonly used labeling reagents constituted of charged and aromatic groups, for instance, FITC and TAMRA dyes.