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The inventors have engineered proteins capable of recognizing carbohydrate epitopes for use as antibody and lectin alternatives. Using directed evolution, the inventors engineered small DNA-binding proteins to tightly bind and specifically recognize targeted monosaccharides, disaccharides and more complex carbohydrates. These proteins are highly thermostable, small enough to recognize single-atom differences between sugars, and do not face the steric hindrance challenges of antibodies and lectins. Importantly, multiple glycan-binding proteins can be assembled together to form customized reagents for recognition and manipulation of complex oligosaccharide structures. These engineered glycan-binding proteins can be easily functionalized and can substitute for antibodies in a wide range of immunological or diagnostic techniques, including flow cytometry and histology for cells expressing a glycosylated biomolecule of interest. Furthermore, these proteins can be utilized in microarray-based detection methods or for affinity purification of specific glycosylated biomolecules. In summary, these engineered glycan-binding proteins enable recognition and manipulation of carbohydrates of user interest, regardless of size and composition, with greater specificity and affinity than currently existing tools.