If we model a double strain DNA as a rod of 2nm cross section with a charge dens
ID: 71087 • Letter: I
Question
If we model a double strain DNA as a rod of 2nm cross section with a charge density of -2 times 1O^-5 (C/cm^2), calculate The potential profile if the DNA is in a salt solution with a NaCI concentration of 10 mM. Na^+ and CI^- concentration right next to the DNA molecule. The concentration of Ca^+2 if we add 1uM of C_aCl_2 in the solution. Also comment how the concentration profile of bivalent ions is different than that of monovalent ions. Describe how the ionic strength may affect the hybridization and stability of dsDNA. What will happen if the salt concentration is too low (e.g. deionized water)? What will happen if the salt concentration is too high?Explanation / Answer
13.
a) the potential between DNA and solution can be calculated using the equation V=q1 * q2 /4*Phi*e0 * r, where e0 is the coulomb's constant and r is the distance between the two charges. q1= -2*10^-1 (SI units) , q2= 0.01 SI units from the data.
V = -0.2 * 0.01 / 4*Phi*e0 * r
coulomb's constant includes 1/4*Phi*E0 which is equal to 9*10^9 Nm2/C2
So, V= -0.002 * 9 * 109 / 2 * 10-9
V = 9 * 10 ^ 15 eVolts
b) the amounts of sodium and chloride ions in the solution surrounding DNA are 0.23gms and 0.35gms respectively in 0.01M solution.
c) Amount of calcium in 1uM of CaCl2 solution is 0.00004gms.
d) High salt concentrations make the negative charge repulsion between the two phosphodiester bonds to be covered up. Therefore, the backbone stability increases at high salt concentration. At low salt concentrations, the repulsion between the negative charges on phosphodiester bonds in teh backbone persists strongly leading to loss of DNA stability. Divalent cations in the solution like Mg2+ and Ca2+ are found to be more stabilizing the DNA than the monovalent cations like Na+. Magnesium and calcium have the ability to increase the melting temperature of DNA as per certain research studies.
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