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A novel method of DNA patterning on silicon surface based on atomic force microscopy (AFM) is presented. This method is based on the AFM anodic oxidation technique, which has the ability to make nano-level oxide patterns on the silicon surface. The oxide patterns drawn by the AFM anodic oxidation is used as a template for nano-patterning of biomolecules such as protein and DNA. We describe the protocols and preliminary results of experiments and discusses its applicability to DNA-based nanotechnology armed with DNA computation method.