Interaction Between Ions And Poly Electrolytes:from Macroions To Nucleic Acids

Ions play an essential role in polyelectrolyte system,such as macroion and nucleic acid(DNA/RNA).For example,ion can mediate the folding,structure stability and fluctuation of nucleic acids,which can further influence the biological functions.In this thesis,we investigated macroion and nucleic acid from different models,in order to understand the physical nature of polyelectrolyte in salt solution more comprehensively.The main research contents of the thesis are as follows:1.Ion-mediated interaction is important for the properties of polyelectrolytes such as colloids and nucleic acids.The effective pair interactions between two polyelectrolytes have been investigated extensively,but the many-body effect for multiple polyelectrolytes still remains elusive.In this work,the many-body effect in potential of mean force(PMF)between like-charged macroions in various salt solutions was examined comprehensively by Monte Carlo(MC)simulation and the nonlinear Poisson-Boltzmann theory.Our calculations showed that,at high 1:1 salt,the PMF is weakly repulsive and appears additive,while at low 1:1 salt,the additive assumption overestimates the repulsive many-body PMF.At low 2:2 salt,the pair PMF appears weakly repulsive while the many-body PMF can become attractive.In contrast,at high 2:2 salt,the pair PMF is apparently attractive while the many-body effect can cause a weaker attractive PMF than that from the additive assumption.Our microscopic analyses suggested that the elusive many-body effect is attributed to ion-binding which is sensitive to ion concentration,ion valence,number of macroions and charges on macroions.2.Ion can mediate an attractive PMF from repulsive Columbic interaction between like-charged polyelectrolytes,such as two nucleic acids or like-charged macroions.However,whether ion can mediate a repulsive PMF between two oppositely charged macroions still remains elusive.In this study,we employed MC simulation to study the PMF of oppositely charged macroions in trivalent salt solution.Our simulations showed that,for 3:3 salt,the PMFs are long-range attraction;for 3:1 salt,the PMFs can be long-range repulsive.Our detailed analyses and theoretical model suggested that the long-range repulsion is attributed to the overcharge effect caused by the binding of trivalent ions.3.Radial distribution of end-to-end distance Ree is crucial for quantifying global size and flexibility of a linear polymer.For semiflexible polymers,several analytical formulas have been derived for the radial distribution of Ree with ignoring stretching flexibility.However,for DNA-like semiflexible oligomers,stretching flexibility is rather pronounced and can significantly affect the radial distribution of Ree.In this study,with involving stretch modulus,we obtained an extended formula to describe the distributions of end-to-end distance for DNA/RNA-like semiflexible oligomers,based on previous formulas for semiflexible polymers without stretching flexibility.In different concentrations of salt solution,persistence length of DNA/RNA had been shown to be very different.Therefore,the extended formula was validated by extensive MC simulations over the wide ranges of stretch modulus and persistence length,as well as the all-atom molecular dynamics(MD)simulations for short DNAs and RNAs.Additionally,our analyses showed that stretching flexibility would become negligible in the distribution of Ree for DNAs longer than?130 base pairs and for RNAs longer than?240 base pairs.4.Ion correlation and fluctuation are important for polyelectrolyte system.Tightly bound ion(TBI)model,originally raised by Tan and Chen,can take the ion correlation and fluctuation into consideration by separating ions into tightly bound ions and diffusive ions.However,TBI model was limited because it cannot deal with all-atom charged polyelectrolytes.In this study,based on the original TBI model,we developed an extended TBI model that not only can treat the ion correlation and fluctuation,but also can deal with all-atom charged polyelectrolyte.With the extended model,we first calculated the PMF between macroions in 2:2 salt solution and made comparison with MC simulation.In addition,we made predictions on monovalent/divalent ion competitions in nucleic acid systems,which are in good agreements with experiments.Moreover,we calculated the radial ion distribution of DNA triplex,and made comparisions with MD simulation.Finally,detailed ion spatial distributions can be obtained with the extended TBI model.