Abstracts of 2002 Publications
Thermodynamics of DNA Interactions from Single Molecule Stretching Experiments
V.A. Bloomfield, M.C. Williams, and I. Rouzina (2002), Accts. Chem. Res. 35: 159-166. pdf
On the basis of our analysis of detailed measurements of the
dependence of the overstretching transition of double-stranded
DNA (dsDNA) on temperature, pH, and ionic strength, we have
demonstrated that a model of force-induced melting accurately
describes the thermodynamics of DNA overstretching. Measurements
of this transition allow us to determine the stability of dsDNA
and obtain information similar to that obtained in thermal melting
studies. This single-molecule technique has the advantage that it
can be used to measure DNA stability at any temperature. We
discuss the use of this technique to study the nucleic acid
chaperone activity of the HIV-1 nucleocapsid protein.
Salt Dependence of the Elasticity and Overstretching Transition of Single DNA Molecules
J.R. Wenner, M.C. Williams, I. Rouzina, and V.A. Bloomfield (2002)
Biophys. J. 82: 3160-3169
pdf
As double-stranded DNA is stretched to its B-form contour length, models of polymer elasticity can describe the dramatic increase in measured force. When the molecule is stretched beyond this contour length, it shows a highly cooperative overstretching transition. We have measured the elasticity and overstretching transition as a function of monovalent salt concentration by stretching single DNA molecules in an optical tweezers apparatus. As the sodium ion concentration was decreased from 1000 to 2.57 mM, the persistence length of DNA increased from 46 nm to 59 nm, while the elastic stretch modulus remained approximately constant. These results are consistent with the model of Podgornik et al. [R. Podgornik, P. L. Hansen, and V. A. Parsegian, J. Chem. Phys. 113: p. 9343-9350.] using an effective DNA length per charge of 0.85 nm. As the monovalent salt concentration was decreased over the same range, the overstretching transition force decreased from 68 pN to 52 pN. This reduction in force is attributed to a decrease in the stability of the DNA double helix with decreasing salt concentration. While we have previously shown that the base pairs holding DNA in a helical conformation separate as DNA is overstretched, these data indicate that both strands remain close together during the transition.
Assessing accumulated solvent near a macromolecular solute by preferential interaction coefficients
K.S. Tang and V.A. Bloomfield (2002), Biophys. J. 82: 2876-2891
pdf
Biological macromolecules are often studied in mixed solvents. To
understand cosolvent-macromolecule interactions, the preferential
interaction coefficient, G3, may help determine surface solvent
compositions. G3 measures the amounts of water, B1, and cosolvent,
B3, within the ''local domain'', the (possibly far-reaching) region
surrounding the macromolecule where the solvent is nonbulk-like. The
local domain's boundary is, however, vague and it is unclear which
molecules are counted in B1. It is useful to explore a simple model
system to make Bi more concrete and to understand which aspects of the
surface solvent distribution, p(x), are sampled by G3. We
performed computer simulations on a two-dimensional system consisting of
a hard-wall solute (the macromolecule) in a mixed solvent (hard disks of
different radii). We simultaneously calculated G3 and p(x). We
found that, 1) in practice, the local domain's boundary is demarked by
the outer limit of the first cosolvent (not water) layer; B1 mainly
counts the solvent near the macromolecule. 2) Assuming B1 to count
only the waters within the first water layer is a poor approximation.
3) When determining B1 and B3, water and cosolvent molecules must be
counted from the same region of space. We speculate that these 2D
results may serve as a first-order approximation for the dominant
contributions to G3 even in 3D, so long as the cosolvent is not
strongly excluded from the macromolecular surface and there is no
significant long-ranged solvent structure.
Thermodynamics of Cationic Lipid Binding to DNA and DNA Condensation: Roles of Electrostatics and Hydrophobicity
Daumantas Matulis, Ioulia Rouzina, and Victor A. Bloomfield (2002) J. Amer. Chem. Soc. 124: 7331-7342 pdf
Alkylammonium binding to DNA was studied by isothermal titration calorimetry. Experimental data, obtained as functions of alkyl chain length, salt concentration, DNA concentration, and temperature, provided a detailed thermodynamic description of lipid-DNA binding reactions leading to DNA condensation. Lipid binding, counterion displacement, and DNA condensation were highly cooperative processes, driven by a large increase in entropy and opposed by a relatively small endothermic enthalpy at room temperature. Large negative heat capacity change indicated a contribution from hydrophobic interactions between aliphatic tails.An approximation of lipid-DNA binding as dominated by two factorssionic and hydrophobic interactionssyielded a model that was consistent with experimental data. Chemical group contributions to the energetics of binding were determined and could be used to predict energetics of other lipid binding to DNA. Electrostatic and hydrophobic contributions to Gibbs free energy, enthalpy, entropy, and heat capacity could be distinguished by applying additivity principles. Binding of lipids with two, three, and four aliphatic tails was investigated and compared to single-tailed lipid binding. Structurally, the model suggests that lipid cationic headgroups and aliphatic tails distribute evenly and lay down on DNA surface without the
formation of micelles.
Last updated 3-8-03
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