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In the study, we investigated the influence of ND origin (detonation vs. high-pressure high-temperature), surface modification, size and separation/purification steps on the sequestration ability and binding affinity of FGF2, a representative member of the FGF family. We found that hydrogenated detonation NDs showed the highest binding capacity. Based on the obtained results, we proposed that NDs can potentially be used in vivo as selective FGF traps to regulate disorders caused by aberrant FGF signaling. The study also employed well-hydrogenated HPHT nanodiamonds achieved for the first time and provided their initial structural, surface chemical, and colloidal characteristics.