Water-soluble carbon nanodots (C-dots) prepared from food, or food wastes generally have a size below 10 nm and emit fluorescence upon the UV radiation with environmental safe specialty. These features of C-dots have been taken advantages in the areas of drug delivery as well as the inhibition of cancer cell growth as green carbon nanoparticles. The electrically physical, chemical characteristics and the mechanisms of their various applications, however, remain unclear. In the present work, we were attempted to develop the C-dots that carry charges which can be later embedded in the glass beads to achieve a specific biological microscopic process. The prepared C-dots were discovered to be able to be used in DNA extraction without affecting DNA cleavage; in addition, they can be used in semi-3D cell culture especially for cancer cells. These electrically charged C-dots@glass beads developed in the present work showed a great potential in diagnosis and drug delivery targeting tumor cells.