A unified view of polymer, dumbbell, and oligonucleotide nearest-neighbor (NN) thermodynamics is presented DNA NN DG° 37 parameters from seven laboratories are presented in the same format so that careful comparisons can be made The seven studies used data from natural polymers, synthetic polymers, oligonucleotide dumbbells, and oligonucleotide duplexes to derive NN parameters; used dif- ferent methods of data analysis; used different salt concen- trations; and presented the NN thermodynamics in different formats As a result of these differences, there has been much confusion regarding the NN thermodynamics of DNA poly- mers and oligomers Herein I show that six of the studies are actually in remarkable agreement with one another and explanations are provided in cases where discrepancies re- main Further, a single set of parameters, derived from 108 oligonucleotide duplexes, adequately describes polymer and oligomer thermodynamics Empirical salt dependencies are also derived for oligonucleotides and polymers

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A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics

A major revival in the use of classical electrostatics as an approach to the study of charged and polar molecules in aqueous solution has been made possible through the development of fast numerical and computational methods to solve the Poisson-Boltzmann equation for solute molecules that have complex shapes and charge distributions. Graphical visualization of the calculated electrostatic potentials generated by proteins and nucleic acids has revealed insights into the role of electrostatic interactions in a wide range of biological phenomena. Classical electrostatics has also proved to be successful quantitative tool yielding accurate descriptions of electrical potentials, diffusion limited processes, pH-dependent properties of proteins, ionic strength-dependent phenomena, and the solvation free energies of organic molecules.

https://science.sciencemag.org/content/sci/268/5214/1144.full.pdf

Classical Electrostatics in Biology and Chemistry

Formulas are derived for the osmotic coefficient, the Donnan salt‐exclusion factor, and the mobile‐ion activity coefficients in a polyelectrolyte solution with or without added sample salt. The formulas, which contain no adjustable parameters, are based on the (theoretical) observation by several workers that counterions will “condense” on the polyion until the charge density on the polyion is reduced below a certain critical value. The uncondensed mobile ions are treated in the Debye–Huckel approximation. In a restricted sense, the formulas are “limiting laws,” and this aspect is discussed at length. Detailed comparison with experimental data in the literature is given; agreement of the theory with experiment is usually found to be quantitative.

Limiting Laws and Counterion Condensation in Polyelectrolyte Solutions I. Colligative Properties

Although the importance of the polyelectrolyte character of DNA has been recognized for some time (Felsenfeld & Miles 1967), few of the implications have been explored, primarily because of a lag in translating the breakthroughs in polyelectrolyte theory of the last decade into a form that is well adapted to the analysis of the specialized problems of biophysical chemistry. Perhaps an analogous situation existed in the field of protein chemistry during the period after the formulation and confirmation of the Debye—Huckel theory of ionic solutions but before Scatchard's incorporation of the theory into his analysis of the binding properties of proteins. An achievement for polynucleotide solutions parallel to Scatchard's was recently presented by Record, Lohman, & de Haseth (1976) and further developed and reviewed by Record, Anderson & Lohman (1978).

https://www.cambridge.org/core/services/aop-cambridge-core/content/view/S0033583500002031

The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides.

Single molecules of double-stranded DNA (dsDNA) were stretched with force-measuring laser tweezers. Under a longitudinal stress of approximately 65 piconewtons (pN), dsDNA molecules in aqueous buffer undergo a highly cooperative transition into a stable form with 5.8 angstroms rise per base pair, that is, 70% longer than B form dsDNA. When the stress was relaxed below 65 pN, the molecules rapidly and reversibly contracted to their normal contour lengths. This transition was affected by changes in the ionic strength of the medium and the water activity or by cross-linking of the two strands of dsDNA. Individual molecules of single-stranded DNA were also stretched giving a persistence length of 7.5 angstroms and a stretch modulus of 800 pN. The overstretched form may play a significant role in the energetics of DNA recombination.

/pdf/overstretching-b-dna-the-elastic-response-of-individual-16c6cujz0e.pdf

Overstretching B-DNA: The Elastic Response of Individual Double-Stranded and Single-Stranded DNA Molecules

The concepts developed in Part I of this series are applied to the self‐diffusion of counterions and co‐ions. The condensed counterions are assumed to have no mobility, while the uncondensed counterions and all co‐ions execute Brownian motion subject to the locally inhomogeneous electric field created by the polyelectrolyte molecules. The polyelectrolyte field is assumed to have small amplitude, in analogy to the Debye–Huckel treatment of uncondensed mobile ions in Part I. The self‐diffusion coefficients of the counterion and the co‐ion are both less than the coresponding values in the absence of polyelectrolyte, but the coefficient for the counterion is much less than that for the co‐ion. The results for the self‐diffusion coefficient of the counterion in a salt‐free polyelectrolyte solution are in good agreement with experimental data.

Limiting Laws and Counterion Condensation in Polyelectrolyte Solutions II. Self‐Diffusion of the Small Ions

Limiting laws and counterion condensation in polyelectrolyte solutions: IV. The approach to the limit and the extraordinary stability of the charge fraction

The interaction with point ions of a line charge supplemented by a distance of closest approach is studied by means of the Mayer theory of ionic solutions. A number of points involved in a recent theory of polyelectrolyte solutions (Papers I and II of this series) are thereby clarified. It is demonstrated that the counterion condensation phenomenon occurs in the limit of zero concentration, that the Debye–Huckel approximation is applicable to the coions and uncondensed counterions, and that the relevant dielectric constant is that of the pure bulk solvent.

Gerald S. Manning

Papers

Limiting Laws and Counterion Condensation in Polyelectrolyte Solutions I. Colligative Properties

The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides.

Limiting Laws and Counterion Condensation in Polyelectrolyte Solutions II. Self‐Diffusion of the Small Ions

Limiting laws and counterion condensation in polyelectrolyte solutions: IV. The approach to the limit and the extraordinary stability of the charge fraction

Limiting Laws and Counterion Condensation in Polyelectrolyte Solutions. III. An Analysis Based on the Mayer Ionic Solution Theory