DNA Manipulation in Biological Liquid Environment Based on Atomic Force Microscopy

Abstract

During the recent years, one of the most important progresses in nano world was the development of methods for direct access to single mo lecules on the nanometer scale. The most significant ones have been the scanning probe microscopes such as the atomic fo rce microscope (AFM). AFM is a versatile tool for imag ing, force measurement and manipulation of different nanoparticles including p roteins, DNA, and living cells. This work is focused on manipulat ion of biological cells specially DNA in b iological liquid and is analy zed dynamics of the spherical nanoparticle manipulation based on Atomic Force M icroscopy (AFM). In prev ious investigations, pushing of the gold nanoparticle using AFM was modeled in air and liquid and the dynamic behavior of t ip and nanoparticle was investigated. The problem is simu lated for DNA nanoparticle pushing on a silicon substrate in b iological liquid using AFM. The biological liquid is ethanol in all the parts, but a co mparison has been made between three liquids (ethanol, methanol and blood) in order to investigate the effect o f env i-ronment on the results. The results show that, for DNA (as compared to gold), the required manipulation force and time for nanoparticle sliding and rolling increase by 17.9 and 18.9%, for sliding and 24.7 and 24.2% for ro lling, respectively. The results also make it clear that in comparison to gold, there is an increase in the type of particle movement; in case of gold, the particles with radiuses larger than 480 n m starts to rolling before sliding, wh ile for DNA it happens for particles with radiuses larger than 530 n m. The co mparison between three important contact theories (JKR, DMT and Hert z) shows that there is a small d ifference between the crit ical t imes and forces of them.