SOLID-STATE DNA SIZING BY ATOMIC-FORCE MICROSCOPY

Atomic force microscopy (AFM) allows rapid, accurate, and reproducible visualization of DNA adsorbed onto solid supports, The images reflect the lengths of the DNA molecules in the sample. Here we propose a sol id-state DNA sizing (SSDS) method based on AFM as an analytical method for high-throughput applications such as fingerprinting, restriction mapping, +/- screening, and genotyping, For this process,the sample is first deposited onto a solid support by adsorption from solution, It is then dried and imaged under ambient conditions by AFM. The resultin g images are subjected to automated determination of the lengths of th e DNA molecules on the surface. The result is a histogram of sizes tha t is similar to densitometric scans of DNA samples separated on gels. A direct comparison of SSDS with agarose gel electrophoresis for +/- s creening shows that it produces equivalent results. Advantages of SSDS include reduced sample size (i.e., lower reagent costs), rapid analys is of single samples, and potential for full automation using availabl e technology. The high sensitivity of the method also allows the numbe r of polymerase chain reaction cycles to be reduced to 15 or less. Bec ause the high signal-to-noise ratio of the AFM allows for direct visua lization of DNA-binding proteins, different DNA conformations, restric tion enzymes, and other DNA modifications, there is potential for dram atically improving the information content in this type of analysis.