Detailed characterization of conditions for alignment of Single-Stranded and double-stranded DNA fragments on surfaces

DNA is expected to play a critical role in biomolecular nanotechnology because nucleic acids offer a range of desirable properties for nanometer scale manipulations. We report here a thorough characterization and optimization of conditions for alignment of well extended single- and double-stranded DNA molecules on mica surfaces. The optimum poly-L-lysine concentration range for surface treatment in DNA alignment experiments is 0.5-2 ppm. DNA is best aligned, and the greatest surface density of DNA molecules is observed in the center of the path traversed by the DNA solution droplet during deposition. The alignment procedure induces only a small amount of fragmentation of deposited DNA molecules. Knowledge of the optimum conditions for nucleic acid alignment on surfaces should facilitate the use of DNA based nanotechnology.