Effect of chain length on the conformation and friction behaviour of DNA

Abstract

Four double-stranded DNA films with different chain lengths were prepared on 3-aminopropyltriethoxysilane (APS)-modified mica surfaces in the NaCl solution with concentration ranging from 0.001 to 0.1 M. By using an atomic force microscope, the force-distance curves and friction behaviour of each DNA film were studied in the NaCl solution that was used in the sample preparation. When adsorbed on mica as films in salt solution, the conformation of DNA molecules would be a combination of loops and “train-like”. As the chain length increased from 50 to 20000 bp, the extension rate of DNA film increased from 7.1 to 11.5 in 0.001 mol/L NaCl solution, which suggested that the DNA molecule with long chain likely resulted in more extended conformation. In addition, under low normal load, low NaCl concentration could increase the friction of DNA film and the chain length revealed insignificant effect on the friction force of DNA film. Therefore, long chain DNA with low salt concentration is more conducive to the nanopore sequencing process, since extended conformation can make DNA molecules easier to reach into nanopore and the high friction can reduce the translocation speed. These results may benefit the development of the third-generation sequencing technique based on nanopore.