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G S Manning

Publications and source records attributed to G S Manning.

At least 19 recordsLinked to original sources
PubMed2001

Counterion association with native and denatured nucleic acids: an experimental approach.

The melting temperature of the poly(dA) . poly(dT) double helix is exquisitely sensitive to salt concentration, and the helix-to-coil transition is sharp. Modern calorimetric instrumentation allows this transition to be detected and characterized with high precision at extremely low duplex concentrations. We have taken advantage of these properties to show that this duplex can be used as a sensitive probe to detect and to characterize the influence of other solutes on solution properties. We demonstrate how the temperature associated with poly(dA) . poly(dT) melting can be used to define the change in bulk solution cation concentration imparted by the presence of other duplex and triplex solutes, in both their native and denatured states. We use this information to critically evaluate features of counterion condensation theory, as well as to illustrate "crosstalk" between different, non-contacting solute molecules. Specifically, we probe the melting of a synthetic homopolymer, poly(dA) . poly(dT), in the presence of excess genomic salmon sperm DNA, or in the presence of one of two synthetic RNA polymers (the poly(rA) . poly(rU) duplex or the poly(rU) . poly(rA) . poly(rU) triplex). We find that these additions cause a shift in the melting temperature of poly(dA) . poly(dT), which is proportional to the concentration of the added polymer and dependent on its conformational state (B versus A, native versus denatured, and triplex versus duplex). To a first approximation, the magnitude of the observed tm shift does not depend significantly on whether the added polymer is RNA or DNA, but it does depend on the number of strands making up the helix of the added polymer. We ascribe the observed changes in melting temperature of poly(dA) . poly(dT) to the increase in ionic strength of the bulk solution brought about by the presence of the added nucleic acid and its associated counterions. We refer to this communication between non-contacting biopolymers in solution as solvent-mediated crosstalk. By comparison with a known standard curve of tm versus log[Na+] for poly(dA) . poly(dT), we estimate the magnitude of the apparent change in ionic strength resulting from the presence of the bulk nucleic acid, and we compare these results with predictions from theory. We find that current theoretical considerations correctly predict the direction of the t(m) shift (the melting temperature increases), while overestimating its magnitude. Specifically, we observe an apparent increase in ionic strength equal to 5% of the concentration of the added duplex DNA or RNA (in mol phosphate), and an additional apparent increase of about 9.5 % of the nucleic acid concentration (mol phosphate) upon denaturation of the added DNA or RNA, yielding a total apparent increase of 14.5 %. For the poly(rU) . poly(rA) . poly(rU) triplex, the total apparent increase in ionic strength corresponds to about 13.6% of the amount of added triplex (moles phosphate). The effect we observe is due to coupled equilibria between the solute molecules mediated by modulations in cation concentration induced by the presence and/or the transition of one of the solute molecules. We note that our results are general, so one can use a different solute probe sensitive to proton binding to characterize subtle changes in solution pH induced by the presence of another solute in solution. We discuss some of the broader implications of these measurements/results in terms of nucleic acid melting in multicomponent systems, in terms of probing counterion environments, and in terms of potential regulatory mechanisms.

Animals↗
PubMed1998

Excess counterion binding and ionic stability of kinked and branched DNA.

We compute the excess number of counterions associated with kinked and branched DNA, and the ionic stabilities of these structures as a function of chain length and both sodium and magnesium salt concentration, using numerical counterion condensation theory. The DNA structures are modeled as two or more finite lines of phosphate charges radiating from the kink or junction center. The number of excess counterions around the (40-90 degrees) kinked duplex is very small (at most four). The geometries of large three- and four-way DNA junctions (with > 50 base pairs per arm) in solutions containing low to moderate NaCl concentrations, by contrast, accumulate a substantial number of excess sodium ions (> 20) but no more than 15 magnesium counterions. The excess number of counterions surrounding the kinked linear chain and the branched DNA structures either remains invariant or increases with chain length, tending to reach a plateau value. Open configurations, such as the planar Y-shaped three-way junction (with three 120 degrees inter-arm angles) and the 90 degrees cross-shaped four-way junction, are ionically more stable than compact geometries, such as pyramidal three-way junctions and X-shaped four-way junctions, over the entire range of salt concentration considered (10(-5)-10(-1) M NaCl or MgCl2). The ionic stabilities of the compact forms increase with increasing salt concentration and become comparable to those of the extended geometries at high salt (especially when magnesium is the supporting salt).

Algorithms↗
PubMed1998

Counterion condensation revisited.

We review some of the characteristic properties of the structure of polyelectrolyte solutions: the condensed layer of counterions that forms abruptly at a critical threshold charge density on the polymer chain; the more diffuse Debye-Hückel cloud, which is spatially distinct from the condensed layer; and the entropic release of counterions from the condensed layer as a driving force for the binding of oppositely charged ligands. We present a reminder of the basis of our current understanding in a variety of experiments, simulations, and theories; and we attempt as well to clarify some misunderstandings. We present a new analysis of a lattice model that suggests why the limiting laws for polyelectrolyte thermodynamics have proved to be accurate despite the neglect of polymer-polymer interactions in their original derivation. We sketch recent progress in constructing a potential between counterion and polyion. A counterion located in the interface between condensed layer and Debye cloud is repelled from the polyion, creating a sharp boundary between the two counterion populations.

Electrolytes↗
PubMed1995

A theory of DNA dissociation from the nucleosome.

Previous analysis of an elastic model of the nucleosome indicated that 10 bp end segments of DNA can exist in a continuum of mechanically stable trajectories ranging from complete winding on the histone octamer to complete unwinding. Stable states of 20 bp and 40 bp end segments, however, are grouped in bands separated by gaps where DNA trajectories are unstable. We extend these results to cover the entire range up to a complete nucleosomal turn, 80 bp. We find that 10 to 60 bp segments have states intermediate between fully wound and fully unwound that are mechanically stable. In striking contrast, there is no stable intermediate trajectory for 70 bp or 80 bp segments. Segments of these lengths constitute a two-state system. A 70 or 80 bp segment is either fully wound or fully unwound, and the population of these states is governed by Boltzmann's thermal distribution. We have found a plausible dissociation pathway from the fully wound to the fully unwound state for the 80 bp segment. In a ponderous breathing motion that breaks all contacts with the histone ponderous breathing motion that breaks all contacts with the histone surface, the segment climbs to an activation peak of about 12 kcal/mol, then rapidly straightens away from the histone core to complete dissociation.

Algorithms↗
PubMed1995

An elastic model for conformational transitions of spacer DNA in chromatin; first results.

We study the elastic stability of the trajectory of DNA in the solenoid model for the 30 nm chromatin fiber, as extended by McGhee et al. [J.D. McGhee, J.M. Nickol, G. Felsenfeld and D.C. Rau, Cell 33, 831-841 (1983)] to visualize both internucleosomal (spacer) DNA and DNA bound to the core histones. Actually, we idealize this trajectory by neglecting the shallow pitch of the solenoid. The DNA trajectory is then transversely wound on a torus, like a helix on a cylinder. We then neglect the shallow pitch of the transverse winding. We find that there is a threshold length for the elastic stability of a DNA segment in the resulting trajectory, even if the DNA is not allowed to straighten away from the torus surface. For most organisms the length of spacer DNA exceeds the threshold. This result does not imply that anything is wrong with the solenoid model, wherein two nucleosomal turns of DNA are stabilized by interaction with core and linker histones. The result does suggest, however, that if internucleosomal DNA follows a path similar to nucleosomal DNA, then this path would also have to be stabilized, possibly by interaction with linker histone. A second result of the analysis is that the extent of instability depends significantly on the location of the starting point of the DNA. If the DNA starts on the outside of the torus, it is less unstable than if it starts on the inside. In the extended solenoid model, some turns of internucleosomal DNA are on the outside of the solenoid, some on the inside. This result thus suggests the possibility that localized structural disruptions are more likely for some nucleosome neighboring pairs than others. Of intrinsic theoretical interest is the reduction of the problem through a series of approximations to the solution of Mathieu's equation.

Chromatin↗
PubMed1994

Electrostatic effects in short superhelical DNA.

We present Monte Carlo simulations of the equilibrium configurations of short closed circular DNA that obeys a combined elastic, hard-sphere, and electrostatic energy potential. We employ a B-spline representation to model chain configuration and simulate the effects of salt on chain folding by varying the Debye screening parameter. We obtain global equilibrium configurations of closed circular DNA, with several imposed linking number differences, at two salt concentrations (specifically at the extremes of no added salt and the high salt regime), and for different chain lengths. Minimization of the composite elastic/long-range potential energy under the constraints of ring closure and fixed chain length is found to produce structures that are consistent with the configurations of short supercoiled DNA observed experimentally. The structures generated under the constraints of an electrostatic potential are less compact than those subjected only to an elastic term and a hard-sphere constraint. For a fixed linking number difference greater than a critical value, the interwound structures obtained under the condition of high salt are more compact than those obtained under the condition of no added salt. In the case of no added salt, the electrostatic energy plays a dominant role over the elastic energy in dictating the shape of the closed circular DNA. The DNA supercoil opens up with increasing chain length at low salt concentration. A branched three-leaf rose structure with a fixed linking number difference is higher in energy than the interwound form at both salt concentrations employed here.

DNA, Superhelical↗
PubMed1993

An elastic model for in-plane deformations of small DNA rings.

In-plane deformations of an elastic ring are analyzed as a model for structural distortions of small covalently-closed DNA rings with little or no writhe. The static conformation of an unconstrained elastic ring is a geometric circle, but thermal fluctuations away from the circle are found to be significant. An elastic ring confined in a cylindrical pore of rigid radius less than the radius of the free ring is studied as a model for a small DNA ring in a tight resolving gel. The model is extended to include deformability of the pore. Larger rings are relatively more deformed in the pore than smaller ones. This result may be pertinent to the observation that at constant linking number the mobility of small DNA rings in a resolving gel decreases as the number of base pairs increases.

Algorithms↗
PubMed1992

Theory of delocalized ionic binding to polynucleotides: structural and excluded-volume effects.

A previously developed theory for the delocalized binding of ions to polyelectrolytes was restricted to point ions and a structurally rigid polyelectrolyte. For the binding of substances like oligolysines and polyamines to DNA, the restriction to point ions would appear not to be realistic. For the binding of ions to flexible chains like single-stranded polynucleotides, the restriction to a rigid polyelectrolyte may not be realistic. In this article, we assess the effect of relaxation of these two restrictions. Excluded volume among bound ions is modeled by a hard-rod potential in the context of the theory of a one-dimensional fluid. The possibility that a flexible chain folds in some manner in the immediate vicinity of a bound ion is modeled by allowing the mean spacing between charged groups on the polymer to become smaller as the number of bound ions increases. We compare our results with recent data on the binding of a series of oligolysines to single-stranded polynucleotides, which conflict with the predictions of the original theory of delocalized binding of point ions to rigid polyelectrolytes. Inclusion of excluded volume among bound ions does not significantly improve agreement with the data. Substantial improvement in the level of agreement is obtained when the polyion chain is assumed to be flexible. One of our conclusions is that the excluded-site description of anticooperativity, which was designed for the binding of ligands to discrete sites on a polymer chain, and which does not include the effect of ionic forces, should not be used in cases of delocalized binding of ions.

Binding Sites↗
PubMed1991

The elastic resilience of DNA can induce all-or-none structural transitions in the nucleosome core particle.

DNA on the surface of the histone octamer in the native nucleosome core particle is modeled as a circumferentially wound elastic line on the surface of a cylinder. In a model for the radial transition, the line is allowed to straighten, and thus lose energy, by swinging off the surface, but it is impeded in such an excursion by a radial force field representing the attractive interaction between DNA and histone octamer. In a model for the axial transition, the line may straighten by becoming more parallel to a generator of the cylinder while remaining on the surface. In this mode of straightening, dimer-tetramer or tetramer-tetramer interfaces are disrupted, and the resulting energy gain impedes the transition. Both radial and axial transitions are predicted to occur in all-or-none fashion. We propose that these models are related to the abrupt transitions actually observed in the nucleosome core particle.

DNA↗
PubMed1990

Approach to the limit of counterion condensation.

According to counterion condensation theory, one of the contributions to the polyelectrolyte free energy is a pairwise sum of Debye-Hückel potentials between polymer charges that are reduced by condensed counterions. When the polyion model is taken as an infinitely long and uniformly spaced line of charges, a simple closed expression for the summation, combined with entropy-derived mixing contributions, leads to the central result of the theory, a condensed fraction of counterions dependent only on the linear charge density of the polyion and the valence of the counterion, stable against increases of salt up to concentrations in excess of 0.1 M. Here we evaluate the sum numerically for B-DNA models other than the infinite line of B-DNA charges. For a finite-length line there are end effects at low salt. The condensation limit is reached as a flat plateau by increasing the salt concentration. At a fixed salt concentration the condensation limit is reached by increasing the length of the line. At moderate salt even very short B-DNA line-model oligomers have condensed fractions not far from the infinite polymer limit. For a long double-helical array with charge coordinates at the phosphates of B-DNA, the limiting condensed fraction appears to be approached at low salt. In contrast to the results for the line of charges, however, the computed condensed fraction varies strongly with salt in the range of experimentally typical concentrations. Salt invariance is restored, in agreement with both the line model and experimental data, when dielectric saturation is considered by means of a distance-dependent dielectric function. For sufficiently long B-DNA line and helical models, as typical salt concentrations, the counterion binding fraction approaches the polymer limit as a linear function of 1/P, where P is the number of phosphate groups of B-DNA.

Animals↗
PubMed1990

A numerical counterion condensation analysis of the B-Z transition of DNA.

We examine the salt dependence of the B-Z transition in DNA by means of the counterion condensation theory adapted to structurally realistic coordinates of the phosphate groups. The ionic contribution to the free energy difference delta G is computed for both the ZI and ZII conformations over broad ranges of NaCl and MgCl2 concentrations and polymer lengths. For the solvent we employ both a constant-dielectric model (dielectric constant set to 78.3) and a dielectric saturation model (distance-dependent dielectric constant). Where comparison can be made, the results for the constant-dielectric model are similar to those obtained by other workers for the same model but with different computational methods. The existence of a low-salt transition, and its location when it does occur, depends strongly on the DNA length and on the dielectric model. The behavior of ZI and ZII are qualitatively similar throughout the entire salt range for the constant-dielectric model, but qualitatively different if dielectric saturation is simulated, as we think is necessary for a realistic description. The ionic delta G, in the presence of dielectric saturation, bears comparison with the high-salt trend of the measured total delta G if "Z-DNA" is predominantly ZI, but not if it is predominantly ZII.

Animals↗
PubMed1989

An estimate of the extent of folding of nucleosomal DNA by laterally asymmetric neutralization of phosphate groups.

We attempt quantitative implementation of a previous suggestion that asymmetric charge neutralization of DNA phosphate groups may provide part of the driving force for nucleosome folding. Polyelectrolyte theory can be used to estimate the effective compressive force acting along the length of one side of the DNA surface when a fraction of the phosphate groups are neutralized by histones bound to that side. A standard engineering formula then relates the force to the bending amplitude caused by it. Calculated bending amplitudes are consistent with the curvature of nucleosomal DNA and the overall extent of charge neutralization by the histones. The relation of the model to various aspects of nucleosome folding, including the detailed path of core-particle DNA, is discussed. Several other DNA-protein complexes are listed as examples of possible asymmetric charge-induced bending.

DNA↗
PubMed1989

Self-attraction and natural curvature in null DNA.

Forces of self-attraction inherent in DNA are unmasked when its ionic charge is neutralized. On the global level, self-attraction operates between segments to condense null (charge-neutralized) DNA into a segment-rich particle. Locally, self-attraction tends to contract an individual segment along its axis. If certain conditions are satisfied, the compressed segment buckles outward from the original line of the axis. Its most stable shape is then curved, or, as an extreme case, even completely folded. Buckling conditions are derived and shown to be met by DNA, thus explaining the high degree of ordered curvature and folding in the observed morphologies of condensed null DNA. The central concept employed is the buckling persistence length. It is evaluated for null DNA (40-50 bp) and agrees with experimental data (less than 60 bp). It helps in understanding the observed cooperative unit in the condensation/decondensation equilibrium (about 60 bp) and the observed size of digestion fragments unstable in the condensed phase (about 80 bp). The root-mean-square thermal compression/extension fluctuation in DNA is estimated at about 0.1 A/bp.

DNA↗
PubMed1985

Packaged DNA. An elastic model.

We review and deepen a theory of elastic bending of DNA on a persistence length scale. In a regime of extensive charge neutralization the axis of the double helix is elastically unstable when straight. Its stable bent conformation allows nucleation of DNA toruses and in principle could direct the supercoiled (solenoid) form of a polynucleosome. The Euler theory of elastic instability of macroscopic rods gives a partial description of the intrinsic ability of DNA to form locally stable bends. A different, quasi-Eulerian theory can be based on what is probably the dominant bending mechanism of DNA in solution-flexible kinking at the sites of open base pairs. This predictive theory is in quantitative agreement with the observed value (about 16 nm) for the minimum radius of torus holes. Stability of the inner torus ring is achieved when DNA phosphate groups are about 90% neutralized by trivalent cations, another prediction that is consistent with the observed formation of toruses in these conditions. The predicted stable radius of curvature of charge-neutralized DNA is also equal to the radial dimension of a maximally contracted polynucleosome supercoil as measured by neutron scattering (17 nm), but further experimental investigation of the geometrical disposition of the spacer DNA regions in the solenoid will be necessary to rule out the possibility of accidental agreement for this complex system. We stress again the experimental reality and probable importance of open base pairs in the equilibrium solution conformation of DNA.

Adenine Nucleotides↗
PubMed1985

The trajectory of a stiff rod in a curved potential energy trough. An initial result for short nucleosomal rods.

The equilibrium trajectory of the axis of a rod subject to an externally imposed curved potential energy trough tends to conform to the shape of the curved trough, but also tends to be straight because of elastic resistance to bending. The actual path of the axis is a balance between the two extremes. We consider a potential energy trough centered along a circular arc of radius R. For a rod of small length compared to R, we show that the axis at equilibrium forms an arc of a circle of radius greater than R. The value of the radius of the axial path depends on the relative values of the Hooke's Law bending constant for the rod and the depth and width of the trough. Motivation for the calculation is provided by nucleosomal DNA, which conforms to the surface of a roughly cylindrical histone core at physiological ionic strength, but is observed to unwind into a partially extended conformation at very low ionic strength. We suggest that the rigidity to bending of short DNA segments becomes sufficiently great at low ionic strength to overcome attractive interactions with the histone surface. Alternately, of course, if during the cell cycle mutually attractive forces between DNA and histone core are weakened at constant ionic strength, the same type of unfolding would be expected to occur as the strength of the DNA-histone contacts drops below the level required to overcome elastic resistance to bending of the DNA rod.

Animals↗