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Register a new userSupercoil formation in DNA denaturation
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Alkan Kabak\\c{c}io\\u{g}lu
Publication date
2009
fields
Physics
and research's language is
English
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We generalize the Poland-Scheraga (PS) model to the case of a circular DNA, taking into account the twisting of the two strains around each other. Guided by recent single-molecule experiments on DNA strands, we assume that the torsional stress induced by denaturation enforces formation of supercoils whose writhe absorbs the linking number expelled by the loops. Our model predicts that, when the entropy parameter of a loop satisfies $c le 2$, denaturation transition does not take place. On the other hand for $c>2$ a first-order denaturation transition is consistent with our model and may take place in the actual system, as in the case with no supercoils. These results are in contrast with other treatments of circular DNA melting where denaturation is assumed to be accompanied by an increase in twist rather than writhe on the bound segments.
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The problem of the helix-coil transition of biopolymers in explicit solvents, like water, with the ability for hydrogen bonding with solvent is addressed analytically using a suitably modified version of the Generalized Model of Polypeptide Chains. Besides the regular helix-coil transition, an additional coil-helix or reentrant transition is also found at lower temperatures. The reentrant transition arises due to competition between polymer-polymer and polymer-water hydrogen bonds. The balance between the two types of hydrogen bonding can be shifted to either direction through changes not only in temperature, but also by pressure, mechanical force, osmotic stress or other external influences. Both polypeptides and polynucleotides are considered within a unified formalism. Our approach provides an explanation of the experimental difficulty of observing the reentrant transition with pressure; and underscores the advantage of pulling experiments for studies of DNA. Results are discussed and compared with those reported in a number of recent publications with which a significant level of agreement is obtained.
The hydrophobic effect stabilizes the native structure of proteins by minimizing the unfavourable interactions between hydrophobic residues and water through the formation of a hydrophobic core. Here we include the entropic and enthalpic contributions of the hydrophobic effect explicitly in an implicit solvent model. This allows us to capture two important effects: a length-scale dependence and a temperature dependence for the solvation of a hydrophobic particle. This consistent treatment of the hydrophobic effect explains cold denaturation and heat capacity measurements of solvated proteins.
The dynamics of a loop in DNA molecules at the denaturation transition is studied by scaling arguments and numerical simulations. The autocorrelation function of the state of complementary bases (either closed or open) is calculated. The long-time decay of the autocorrelation function is expressed in terms of the loop exponent c both for homopolymers and heteropolymers. This suggests an experimental method for measuring the exponent c using florescence correlation spectroscopy.
The problem of inhibiting viral DNA ejection from bacteriophages by multivalent counterions, specifically Mg$^{+2}$ counterions, is studied. Experimentally, it is known that MgSO$_4$ salt has a strong and non-monotonic effect on the amount of DNA ejected. There exists an optimal concentration at which the minimum amount of DNA is ejected from the virus. At lower or higher concentrations, more DNA is ejected from the capsid. We propose that this phenomenon is the result of DNA overcharging by Mg$^{+2}$ multivalent counterions. As Mg$^{+2}$ concentration increases from zero, the net charge of DNA changes from negative to positive. The optimal inhibition corresponds to the Mg$^{+2}$ concentration where DNA is neutral. At lower/higher concentrations, DNA genome is charged. It prefers to be in solution to lower its electrostatic self-energy, which consequently leads to an increase in DNA ejection. By fitting our theory to available experimental data, the strength of DNA$-$DNA short range attraction energies, mediated by Mg$^{+2}$, is found to be $-$0.004 $k_BT$ per nucleotide base. This and other fitted parameters agree well with known values from other experiments and computer simulations. The parameters are also in aggreement qualitatively with values for tri- and tetra-valent counterions.
In living cells, proteins combine 3D bulk diffusion and 1D sliding along the DNA to reach a target faster. This process is known as facilitated diffusion, and we investigate its dynamics in the physiologically relevant case of confined DNA. The confining geometry and DNA elasticity are key parameters: we find that facilitated diffusion is most efficient inside an isotropic volume, and on a flexible polymer. By considering the typical copy numbers of proteins in vivo, we show that the speedup due to sliding becomes insensitive to fine tuning of parameters, rendering facilitated diffusion a robust mechanism to speed up intracellular diffusion-limited reactions. The parameter range we focus on is relevant for in vitro systems and for facilitated diffusion on yeast chromatin.
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