Using Single-Molecule DNA Flow-Stretching Experiments to See the Effects of Temperature and Viscosity

Abstract

Deoxyribonucleic acid (DNA) is a highly charged long and semi-flexible polymer of which length is much longer than cell dimensions at least by 1,000-folds. A long linear DNA turns into a crumpled structure to fit into a tiny cell volume by the process known as DNA compaction. In nature, DNA fits into the volume of the cell using DNA compaction by packaging genome material. Various types of protein are involved in DNA compaction. To experiment with various proteins as DNA compaction agents, DNA needs to be stretched out. In our thesis, the effect of temperature and buffer viscosity on DNA stretching and fluctuation was observed using steady-state laminar flow. From experimental data, a slight increase in length, with the increase of temperature and viscosity was found out. The total change of the stretched length of DNAs was almost 0.7 μm–0.8 μm for 0 %PEG in EBB buffer to 5% PEG in EBB buffer solution in our experiment. The total increase of length from 4 °C to 30 °C was almost 0.5 μm which is almost linear. It was observed that temperature changes did not lead to a noticeable change in the fluctuation of DNA, but when buffer viscosity was increased, the fluctuation of DNA decreased. The average fluctuation of DNAs for 3% PEG and 5% PEG are 15% and 28% lower than the fluctuations of DNAs for EBB buffer. Thus, it can be concluded that DNA length and fluctuation are a function of viscosity.