DNA duplex stabilization in crowded polyanion solutions

Abstract

The melting temperature of duplex DNA is much higher in 5 polyanions than that in non-ionic polymers with similar ionic strength, suggesting an additional electrostatic contribution on top of the excluded volume effect.Biological fluids and the cytoplasm contain concentrated biopolymers such as nucleic acids and proteins. They occupy 10 ~20-40% of a live cell's volume, creating a crowded environment because of their mutual impenetrable property. 1A thermodynamic consequence of macromolecular crowding is to favor reactions that produce reduced excluded volumes, such as DNA hybridization and protein oligomerization.

Differential stability of DNA based on salt concentration

“…Through the schematic diagram and by calculating the free energy as a function of temperature and force, we explain the cause of the instability of the DNA molecule at higher concentrations. Our results are in very good agreement with the experimental findings [22]. However, due to unavailability of results for infinite chains we can not compare our results for force induced unzipping of DNA molecules at high salt concentration.…”

“…As discussed earlier, the parameter t plays an important role here. We calculate the phase diagram for different values of t and find the best match for t = 0.01 for the experimental results of Khimji [22]. The maximum deviation is at C = 5.0 which is about 0.8 K. Thus, we can say that our results are in close match with the experimental findings of [22].…”

“…7 & 8. Here we consider an infinite chain of 300 base pairs which is generated by repetition of the 12 base pair chain [22]. In vitro, experiments on DNA unzipping are executed either at constant displacement or at varying loading rates.…”

Compaction of double-stranded DNA by negatively charged proteins and colloids

“…Aiming to provide deeper insight into changes of DNA secondary structure, Liu et al studied denaturation of short duplex DNA in solutions of either neutral (PEG) of anionic (sodium polyacrylate, PAANa) polymers maintaining the same concentration of Na + counterions in solution [33]. In contrast to the destabilization of DNA secondary structure observed by Zinchenko et al [29], Liu et al reported a significant increase of DNA melting temperature in solutions containing high concentrations of polyanion.…”

Recent advances in molecular machines based on toehold‐mediated strand displacement reaction

“…This A-toehold design enables the dynamic selective activation of multiple strand displacement reactions [36]. Considering the critical role of solvent in the stability of DNA structural properties [37,38], organic solvents were used by Liu, Xia, and their coworkers to adjust the kinetics of DNA hybridization [39][40][41]. Their studies indicated that the hybridization kinetics of the DNA beacon progressively rise as the ethanol content in solvent increases, and a 70-fold rate enhancement is achieved for DNA in a solvent with 56% ethanol [40].…”