The effect of the structure of cosolutes on the DNA duplex formation.

A living cell generally contains macromolecules occupying 20 approximately 40% of the total volume. In order to mimicking the crowded cellular environment, we chose different structure molecules, glycerol, ethylene glycol (EG) and poly(ethylene glycol) (PEG), as cosolutes. The thermodynamics and kinetics of DNA duplex formation in the presence of high concentration of glycerol, EG and PEG were investigated to discern nucleic acid behavior under molecular crowding condition. Comparing with the data obtained in the dilute solution, the melting temperature (T(m)) of a 10-mer DNA duplex (5'-TAGGTTATAA-3'/5'-TTATAACCTA-3') decreased by 4.8 degrees C, 5.6 degrees C, or 7.0 degrees C in the presence of 20 wt% glycerol, EG, or PEG200, respectively. The kinetic results revealed that the destabilization was not only caused by decreasing the association rate constant but also caused by great increasing the dissociation rate constant. These results are useful for understanding nucleic acid behavior in cell.