Preparation and Atomic Force Microscopy (AFM) Characterization of DNA Scaffolds as a Template for Protein Immobilization

Abstract

The design of DNA nanostructures is of fundamental importance, the intrinsic value of DNA as a building-block material lies in its ability to organize other bio-molecules with nanometer-scale spacing. Here, we report the fabrication of DNA scaffolds with nano-pores (<10 nm size) that formed easily without the use of additives (i.e., avidin, biotin, polyamine, or inorganic materials) into large scale DNA nanostructures by controlling buffer pH and reaction temperature. Large scale DNA scaffolds with porous structures are stable and uniform at slightly acidic buffer pH values (pH 5.5) and at approximately room temperature (similar to 30 degrees C). The depth of the DNA scaffolds with randomly porous size (<10 nm) was a maximum of approximately 8 nm. Protein immobilization results also confirmed that a fibronectin (FN) proteins/large scale DNA scaffolds/aminopropylytriethoxysilane (APS)/SiO2/Si substrate with high sensitivity formed in a well-defined manner. The DNA scaffolds can be applied for use with DNA based biochips, biophysics, and cell biology.