1997 Abstracts from the Bloomfield Lab

Abstracts of 1997 Publications

Rouzina, I. and Bloomfield, V.A. (1997) Competitive Electrostatic Binding of Charged Ligands to Polyelectrolytes: Practical Approach Using the Nonlinear Poisson-Boltzmann Equation. Biophys. Chem. 64: 139-155.

We have developed a practical analytical treatment of the nonlinear Poisson-Boltzmann equation to characterize the strong but nonspecific binding of charged ligands to DNA and other highly charged macromolecules. These reactions are notable for their strong salt dependence and anticooperativity, features which the theory fully explains. We summarize analytical results for concentration profiles and ion binding in various regimes of surface curvature and ionic strength, and show how counterion size and charge distribution may influence competitive binding. We present several practical applications of the formalism, showing how to estimate the ligand concentration needed to effectively compete with a given buffer salt, and how to calculate the amounts of counterion species bound at various distances from the DNA surface under given bulk solution conditions. We cast our results into the form of a Scatchard binding isotherm, showing how the apparent binding constant Kobs and S = - d log Kobs / d log [M+] can be predicted from the basic theory. Anticooperativity arises naturally without steric repulsion, and binding curves can be fit with Kobs and effective charge as the only free parameters. We extend the analytical P-B analysis to an arbitrary number of counterion species, and apply the results to fit and predict three-ion competition data.

Baumann, C.G., Smith, S.B., Bloomfield, V.A. and Bustamante, C. (1997) Ionic Effects on the Elasticity of Single DNA Molecules. Proc. Nat. Acad. Sci. USA 94: 6185-6190.

We used a force-measuring laser tweezers apparatus to determine the elastic properties of l-bacteriophage DNA as a function of ionic strength and in the presence of multivalent cations. We found that the electrostatic contribution to the persistence length P varies as the inverse of the ionic strength in monovalent salt, as predicted by the standard smoothly charged cylinder model. However, ionic strength is not always the dominant variable in determining the elastic properties of DNA. Monovalent and multivalent ions have quite different effects even when present at the same ionic strength. Multivalent ions lead to P values as low as 250 - 300 Å, well below the high salt, "fully neutralized" value of 450 - 500 Å characteristic of DNA in monovalent salt. The ions Mg²⁺ and Co(NH₃)₆³⁺, in which the charge is centrally concentrated, yield lower P values than the polyamines putrescine²⁺ and spermidine3+, in which the charge is linearly distributed. The stretch modulus and persistence length display opposite trends with ionic strength, in contradiction to predictions of macroscopic elasticity theory. DNA is well described as a wormlike chain at concentrations of trivalent cations capable of inducing condensation, if condensation is prevented by keeping the molecule stretched. No evidence of the buckling transition that has been postulated to underlie condensation is observed. Instead, a retractile force appears in the presence of multivalent cations at molecular extensions that allow intramolecular contacts, suggesting the existence of a thermal ratchet condensation mechanism in stretched DNA.

Last updated 5/27/98

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