Direct detection of mutation sites on stretched DNA by atomic force microscopy

Abstract Based on MutS protein recognition of heteroduplex DNA, here we report an approach by using atomic force microscopy (AFM) in combination with a DNA stretching technique for detecting small DNA alternations. The AFM studies showed that the binding ratio of heteroduplex DNA to MutS was higher than that of homoduplex DNA. The data also showed that the stretching operation caused little change to the binding ratios of both heteroduplex and homoduplex DNA. By stretching the MutS‐bound DNA, the distances from MutS binding sites to the DNA ends could be measured directly using AFM and the position of the binding sites could be measured. Because of the DNA stretching operation, this method will be competent to detect unpaired or mismatched sites on long DNA molecules in a direct and visual way. Copyright © 2002 John Wiley & Sons, Ltd.