Abstracts of 1998 Publications


Bloomfield, V.A. and Rouzina, I. (1998) Practical use of the Poisson-Boltzmann equation to analyze ion binding to DNA. Meth. Enzymol. 265: 364-378.

We present in this article an approach, based on fundamental, well-established physical principles, which accomplishes the goal of enabling straightforward calculation and interpretation of electrostatic binding of charged ligands to polyelectrolytes. The theory is approximate but reasonably accurate, does not require detailed numerical calculations, and is explicit in its dependence on parameters. Our treatment uses the nonlinear Poisson-Boltzmann (P-B) equation. The P-B theory of two spherical ions near a charged cylinder or wall is adequate for most purposes.

Schnell, J.R., Berman, J., and Bloomfield, V.A. (1998) Insertion of Telomere Repeat Sequence Decreases Plasmid DNA Condensation by Cobalt (III) Hexaammine. Biophys. J. 74: 1484-1491.

Telomere Repeat Sequence (TRS) DNA is found at the termini of most eukaryotic chromosomes. The sequences are highly repetitive and G-rich (e.g., [C1-3A/TG1-3]n for the yeast Saccharomyces cerevisiae) and are packaged into non-nucleosomal protein-DNA structures in vivo. We have used total intensity light scattering and electron microscopy to monitor the effects of yeast TRS inserts on in vitro DNA condensation by cobalt (III) hexaammine. Insertion of 72 bp of TRS into a 3.3 kb plasmid depresses condensation as seen by light scattering and results in a 22% decrease in condensate thickness as measured by EM. Analysis of toroidal condensate dimensions suggests that the growth stages of condensation are inhibited by the presence of a TRS insert. The depression in total light scattering intensity is greater when the plasmid is linearized with the TRS at an end (39-49%) than when linearized with the TRS in the interior (18-22%). Circular dichroism of a 95 bp fragment containing the TRS insert gives a spectrum which is intermediate between A- and B-form, and the anomalous condensation behavior of the TRS suggest a non-canonical DNA structure. We speculate that under conditions in which the plasmid DNA condenses, the telomeric insert assumes a helical geometry which is similar to A-form and which is incompatible with packing into the otherwise B-form lattice of the condensate interior.


Bloomfield, V.A. (1998) DNA Condensation by Multivalent Cations. Biopolymers/Nucleic Acid Sci. 44: 269-282.

In the presence of multivalent cations, high molecular weight DNA undergoes a dramatic condensation to a compact, usually highly ordered toroidal structure. This review begins with an overview of DNA condensation:condensing agents, morphology, kinetics and reversibility, and the minimum size required to form orderly condensates. It then summarizes the statistical mechanics of the collapse of stiff polymers, which shows why DNA condensation is abrupt and why toroids are favored structures. Various ways to estimate or measure intermolecular forces in DNA condensation are discussed, all of them agreeing that the free energy change per base pair is very small, on the order of 1% of thermal energy. Experimental evidence is surveyed showing that DNA condensation occurs when about 90% of its charge is neutralized by counterions. The various intermolecular forces whose interplay gives rise to DNA condensation are then reviewed. The entropy loss upon collapse of the expanded wormlike coil costs free energy, and stiffness sets limits on tight curvature. However, the dominant contributions seem to come from ions and water. Electrostatic repulsions must be overcome by high salt concentrations or by the correlated fluctuations of territorially bound multivalent cations. Hydration must be adjusted to allow a cooperative accommodation of the water structure surrounding surface groups on the DNA helices as they approach. Undulations of the DNA in its confined surroundings extend the range of the electrostatic forces. The condensing ions may also subtly modify the local structure of the double helix.


Rouzina, I. and Bloomfield, V.A. (1998) DNA bending by small, mobile multivalent cations. Biophys. J. 74: 3152-3164.

We propose a purely electrostatic mechanism by which small, mobile, multivalent cations can induce DNA bending. A multivalent cation binds at the entrance to the B-DNA major groove, between the two phosphate strands, electrostatically repelling sodium counterions from the neighboring phosphates. The unscreened phosphates on both strands are strongly attracted to the groove-bound cation. This leads to groove closure, accompanied by DNA bending towards the cationic ligand. We explicitly treat the dynamic character of the cation-DNA interaction using an adiabatic approximation, noting that DNA bending is much slower than the diffusion of nonspecifically bound, mobile cations. We make semiquantitative estimates of the free energy components of bending - electrostatic (with a sigmoidal distance-dependent dielectric function), elastic, and entropic cation localization - and find that the equilibrium state is bent B-DNA stabilized with a self-localized cation. This is a bending polaron, formation of which should be critically dependent on the strength of electrostatic interaction and the concentration of highly mobile cations available for self-localization. We predict that the resultant bend will be large (ca. 20-40 deg), smooth since it is spread over six base pairs, and infrequent. The stability of such a bend can be variable, from transient to highly stable (static) bending observable with standard curvature-measuring techniques. We further predict that this bending mechanism will have an unusual sequence dependence: sequences with less binding specificity will be more bent, unless the specific binding site is in the major groove.


Munshi, C., Baumann, C., Levitt, D., Bloomfield, V.A. and Lee, H.C. (1998) Biochim. Biophys. Acta 1388: 428-436. The Homo-Dimeric Form of ADP-Ribosyl Cyclase in Solution.

ADP-ribosyl cyclase is a multi-functional enzyme that catalyzes the formation of two Ca2+ signaling molecules, cyclic ADP-ribose (cADPR) and nicotinic acid adenine dinucleotide phosphate (NAADP). X-ray crystallography of three different crystal forms shows that it is a non-covalent dimer. Chemical cross-linking and dynamic light scattering were used in this study to determine if the cyclase is also a non-covalent dimer in solution. Treatment of the cyclase in dilute solution (0.05 mg/ml ) with dimethylsuberimidate resulted in complete conversion to a species with molecular weight about twice that of the monomeric cyclase. Prolonged cross-linking of the cyclase at four times higher concentration produced also only the covalently linked dimers and no multimer formation was observed. The cross-linked dimer retained full enzymatic activity and readily catalyzed the formation of cADPR from NAD, NAADP from NADP, cyclic ADP-ribose phosphate from NADP, and cyclic GDP-ribose from nicotinamide guanine dinucleotide. Analysis of the autocorrelation functions obtained from dynamic light scattering measurements indicated the cyclase solution (2 mg/ml) was composed of a single molecular species and its diffusion coefficient was measured to be 7.4x10(-7) cm(2)/s. Computer modeling using the crystallographic dimensions of the non-covalent cyclase dimer, a donut shaped molecule with a central cavity and overall dimensions of 7x6x3 nm, gave a value for the diffusion coefficient essentially the same as that measured. These results indicate the cyclase is a non-covalent dimer in solution.

Last updated 8/28/99

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