ترغب بنشر مسار تعليمي؟ اضغط هنا

Grand-canonical simulation of DNA condensation with two salts, affect of divalent counterion size

311   0   0.0 ( 0 )
 نشر من قبل Toan T. Nguyen
 تاريخ النشر 2015
  مجال البحث علم الأحياء فيزياء
والبحث باللغة English
 تأليف Toan T. Nguyen




اسأل ChatGPT حول البحث

The problem of DNA$-$DNA interaction mediated by divalent counterions is studied using a generalized Grand-canonical Monte-Carlo simulation for a system of two salts. The effect of the divalent counterion size on the condensation behavior of the DNA bundle is investigated. Experimentally, it is known that multivalent counterions have strong effect on the DNA condensation phenomenon. While tri- and tetra-valent counterions are shown to easily condense free DNA molecules in solution into toroidal bundles, the situation with divalent counterions are not as clear cut. Some divalent counterions like Mg$^{+2}$ are not able to condense free DNA molecules in solution, while some like Mn$^{+2}$ can condense them into disorder bundles. In restricted environment such as in two dimensional system or inside viral capsid, Mg$^{+2}$ can have strong effect and able to condense them, but the condensation varies qualitatively with different system, different coions. It has been suggested that divalent counterions can induce attraction between DNA molecules but the strength of the attraction is not strong enough to condense free DNA in solution. However, if the configuration entropy of DNA is restricted, these attractions are enough to cause appreciable effects. The variations among different divalent salts might be due to the hydration effect of the divalent counterions. In this paper, we try to understand this variation using a very simple parameter, the size of the divalent counterions. We investigate how divalent counterions with different sizes can leads to varying qualitative behavior of DNA condensation in restricted environments. Additionally a Grand canonical Monte-Carlo method for simulation of systems with two different salts is presented in detail.



قيم البحث

اقرأ أيضاً

The problem of DNA-DNA interaction mediated by divalent counterions is studied using computer simulation. Although divalent counterions cannot condense free DNA molecules in solution, we show that if DNA configurational entropy is restricted, divalen t counterions can cause DNA reentrant condensation similar to that caused by tri- or tetra-valent counterions. DNA-DNA interaction is strongly repulsive at small or large counterion concentration and is negligible or slightly attractive for a concentration in between. Implications of our results to experiments of DNA ejection from bacteriophages are discussed. The quantitative result serves to understand electrostatic effects in other experiments involving DNA and divalent counterions.
Strongly correlated electrostatics of DNA systems has drawn the interest of many groups, especially the condensation and overcharging of DNA by multivalent counterions. By adding counterions of different valencies and shapes, one can enhance or reduc e DNA overcharging. In this papers, we focus on the effect of multivalent co-ions, specifically divalent co-ions such as SO$_4^{2-}$. A computational experiment of DNA condensation using Monte$-$Carlo simulation in grand canonical ensemble is carried out where DNA system is in equilibrium with a bulk solution containing a mixture of salt of different valency of co-ions. Compared to system with purely monovalent co-ions, the influence of divalent co-ions shows up in multiple aspects. Divalent co-ions lead to an increase of monovalent salt in the DNA condensate. Because monovalent salts mostly participate in linear screening of electrostatic interactions in the system, more monovalent salt molecules enter the condensate leads to screening out of short-range DNA$-$DNA like charge attraction and weaker DNA condensation free energy. The overcharging of DNA by multivalent counterions is also reduced in the presence of divalent co$-$ions. Strong repulsions between DNA and divalent co-ions and among divalent co-ions themselves leads to a {em depletion} of negative ions near DNA surface as compared to the case without divalent co-ions. At large distance, the DNA$-$DNA repulsive interaction is stronger in the presence of divalent co$-$ions, suggesting that divalent co$-$ions role is not only that of simple stronger linear screening.
136 - S.Oda , N.Tsuda , T.Yukawa 1997
The string susceptibility exponents of dynamically triangulated 2-dimensional surfaces with various topologies, such as a sphere, torus and double-torus, were calculated by the grand-canonical Monte Carlo method. These simulations were made for surfa ces coupled to $d$-Ising spins ($d$=0,1,2,3,5). In each simulation the area of surface was constrained to within 1000 to 3000 of triangles, while maintaining the detailed-balance condition. The numerical results show excellent agreement with theoretical predictions as long as $d leq 2$.
The effective DNA-DNA interaction force is calculated by computer simulations with explicit tetravalent counterions and monovalent salt. For overcharged DNA molecules, the interaction force shows a double-minimum structure. The positions and depths o f these minima are regulated by the counterion density in the bulk. Using two-dimensional lattice sum and free energy perturbation theories, the coexisting phases for DNA bundles are calculated. A DNA-condensation and redissolution transition and a stable mesocrystal with an intermediate lattice constant for high counterion concentration are obtained.
By means of computer simulations of a coarse-grained DNA model we show that the DNA hairpin zippering dynamics is anomalous, i.e. the characteristic time T scales non-linearly with N, the hairpin length: T ~ N^a with a>1. This is in sharp contrast wi th the prediction of the zipper model for which T ~ N. We show that the anomalous dynamics originates from an increase in the friction during zippering due to the tension built in the closing strands. From a simple polymer model we get a = 1+ nu = 1.59 with nu the Flory exponent, a result which is in agreement with the simulations. We discuss transition path times data where such effects should be detected.
التعليقات
جاري جلب التعليقات جاري جلب التعليقات
سجل دخول لتتمكن من متابعة معايير البحث التي قمت باختيارها
mircosoft-partner

هل ترغب بارسال اشعارات عن اخر التحديثات في شمرا-اكاديميا