Effect of ethidium binding and superhelix density on the apparent supercoiling free energy and torsion constant of pBR322 DNA

Supercoiling-dependent DNA binding: quantitative modeling and applications to bulk and single-molecule experiments

DNA stores our genetic information and is ubiquitous in applications, where it interacts with binding partners ranging from small molecules to large macromolecular complexes. Binding is modulated by mechanical strains in the molecule and can change local DNA structure. Frequently, DNA occurs in closed topological forms where topology and supercoiling add a global constraint to the interplay of binding-induced deformations and strain-modulated binding. Here, we present a quantitative model with a straight-forward numerical implementation of how the global constraints introduced by DNA topology modulate binding. We focus on fluorescent intercalators, which unwind DNA and enable direct quantification via fluorescence detection. Our model correctly describes bulk experiments using plasmids with different starting topologies, different intercalators, and over a broad range of intercalator and DNA concentrations. We demonstrate and quantitatively model supercoiling-dependent binding in a single-molecule assay, where we directly observe the different intercalator densities going from supercoiled to nicked DNA. The single-molecule assay provides direct access to binding kinetics and DNA supercoil dynamics. Our model has broad implications for the detection and quantification of DNA, including the use of psoralen for UV-induced DNA crosslinking to quantify torsional tension in vivo, and for the modulation of DNA binding in cellular contexts.

A quantitative model of a cooperative two-state equilibrium in DNA: experimental tests, insights, and predictions

Quantitative parameters for a two-state cooperative transition in duplex DNAs were finally obtained during the last 5 years. After a brief discussion of observations pertaining to the existence of the two-state equilibrium per se, the lengths, torsion, and bending elastic constants of the two states involved and the cooperativity parameter of the model are simply stated. Experimental tests of model predictions for the responses of DNA to small applied stretching, twisting, and bending stresses, and changes in temperature, ionic conditions, and sequence are described. The mechanism and significance of the large cooperativity, which enables significant DNA responses to such small perturbations, are also noted. The capacity of the model to resolve a number of long-standing and sometimes interconnected puzzles in the extant literature, including the origin of the broad pre-melting transition studied by numerous workers in the 1960s and 1970s, is demonstrated. Under certain conditions, the model predicts significant long-range attractive or repulsive interactions between hypothetical proteins with strong preferences for one or the other state that are bound to well-separated sites on the same DNA. A scenario is proposed for the activation of the ilvPG promoter on a supercoiled DNA by integration host factor.

Local elasticity of strained DNA studied by all-atom simulations

Genomic DNA is constantly subjected to various mechanical stresses arising from its biological functions and cell packaging. If the local mechanical properties of DNA change under torsional and tensional stress, the activity of DNA-modifying proteins and transcription factors can be affected and regulated allosterically. To check this possibility, appropriate steady forces and torques were applied in the course of all-atom molecular dynamics simulations of DNA with AT- and GC-alternating sequences. It is found that the stretching rigidity grows with tension as well as twisting. The torsional rigidity is not affected by stretching, but it varies with twisting very strongly, and differently for the two sequences. Surprisingly, for AT-alternating DNA it passes through a minimum with the average twist close to the experimental value in solution. For this fragment, but not for the GC-alternating sequence, the bending rigidity noticeably changes with both twisting and stretching. The results have important biological implications and shed light on earlier experimental observations.

Torsional mechanics of DNA are regulated by small-molecule intercalation

Whether the bend and twist mechanics of DNA molecules are coupled is unclear. Here, we report the direct measurement of the resistive torque of single DNA molecules to study the effect of ethidium bromide (EtBr) intercalation and pulling force on DNA twist mechanics. DNA molecules were overwound and unwound using recently developed magnetic tweezers where the molecular resistive torque was obtained from Brownian angular fluctuations. The effect of EtBr intercalation on the twist stiffness was found to be significantly different from the effect on the bend persistence length. The twist stiffness of DNA was dramatically reduced at low intercalator concentration (<10 nM); however, it did not decrease further when the intercalator concentration was increased by 3 orders of magnitude. We also determined the dependence of EtBr intercalation on the torque applied to DNA. We propose a model for the elasticity of DNA base pairs with intercalated EtBr molecules to explain the abrupt decrease of twist stiffness at low EtBr concentration. These results indicate that the bend and twist stiffnesses of DNA are independent and can be differently affected by small-molecule binding.

Anharmonic torsional stiffness of DNA revealed under small external torques

DNA supercoiling plays an important role in a variety of cellular processes. The torsional stress related to supercoiling may also be involved in gene regulation through the local structure and dynamics of the double helix. To check this possibility, steady torsional stress was applied in the course of all-atom molecular dynamics simulations of two DNA fragments with different base pair sequences. For one fragment, the torsional stiffness significantly varied with small twisting. The effect is traced to sequence-specific asymmetry of local torsional fluctuations, and it should be small in long random DNA due to compensation. In contrast, the stiffness of special short sequences can change significantly, which gives a simple possibility of gene regulation via probabilities of strong fluctuations. These results have important implications for the role of DNA twisting in complexes with transcription factors.

Gel mobilities of linking-number topoisomers and their dependence on DNA helical repeat and elasticity

Agarose-gel electrophoresis has been used for more than thirty years to characterize the linking-number (Lk) distribution of closed-circular DNA molecules. Although the physical basis of this technique remains poorly understood, the gel-electrophoretic behavior of covalently closed DNAs has been used to determine the local unwinding of DNA by proteins and small-molecule ligands, characterize supercoiling-dependent conformational transitions in duplex DNA, and to measure helical-repeat changes due to shifts in temperature and ionic strength. Those results have been analyzed by assuming that the absolute mobility of a particular topoisomer is mainly a function of the integral number of superhelical turns, and thus a slowly varying function of plasmid molecular weight. In examining the mobilities of Lk topoisomers for a series of plasmids that differ incrementally in size over more than one helical turn, we found that the size-dependent agarose-gel mobility of individual topoisomers with identical values of Lk (but different values of the excess linking number, DeltaLk) vary dramatically over a duplex turn. Our results suggest that a simple semi-empirical relationship holds between the electrophoretic mobility of linking-number topoisomers and their average writhe in solution.

A structural transition in duplex DNA induced by ethylene glycol

The twist energy parameter ( E T) that governs the supercoiling free energy, and the linking difference (Delta l) are measured for p30delta DNA in solutions containing 0-40 w/v % ethylene glycol (EG). A plot of E T vs -ln a w, where a w is the water activity, displays the full (reverse) sigmoidal profile of a discrete structural transition. A general theory for the effect of added osmolyte on a cooperative structural transition between two duplex states, 1 right arrow over left arrow 2, is formulated in terms of parameters applicable to individual base-pair subunits. The resulting fraction of base pairs in the 2-state ( f 2 (0)) is incorporated into expressions for the effective torsion and bending elastic constants, the effective twist energy parameter ( E T (eff)), and the change in intrinsic twist (delta l 0). Fitting the expression for E T (eff) to the measured E T values yields reasonably unambiguous estimates of E T 1 and E T 2 , the midpoint value (ln a w) 1/2, and the midpoint slope ( partial differential E T/ partial differential ln a w) 1/2, but does not yield unambiguous estimates of the equilibrium constant ( K 0), the difference in DNA-water preferential interaction coefficient (DeltaGamma), or the inverse cooperativity parameter ( J). Fitting a noncooperative model (assumed J = 1.0) to the data yields K 0 = 0.067 and DeltaGamma = -30.0 per base pair (bp). Essentially equivalent fits are provided by models with a wide range of correlated J, DeltaGamma, and K 0 values. Other results favor DeltaGamma in the range -1.0 to 0, which then requires K 0 > or = 0.914, and a cooperativity parameter, 1/ J > or = 30.0 bp. The measured delta l 0 and circular dichroism (CD) at 272 nm are found to be compatible with curves predicted using the same f 2 (0) values that best-fit the E T data. At least 7-10% of the base pairs are inferred to exist in the 2-state in 0.1 M NaCl in the complete absence of added osmolyte. Compared with the 1-state, the 2-state has a approximately 2.0- to 2.1-fold greater torsion elastic constant, a approximately 0.70-fold smaller bending elastic constant, a approximately 0.91-fold smaller E T value, a approximately 0.2% lower intrinsic twist, a somewhat lower CD near both 272 and 245 nm, and less water and/or more EG in its neighborhood. However, the relative change in preferential interaction coefficient associated with the transition is likely rather slight.

The effect of changes in the bulk dielectric constant on the DNA torsional properties

The effect of changes in the bulk dielectric constant on the DNA torsional properties was evaluated from plasmid circularization reactions. In these reactions, pUC18 previously linearized by EcoRI digestion was recircularized with T4 DNA ligase. The bulk dielectric constant of the reaction medium was decreased by the addition of different concentrations of neutral solutes: ethylene glycol, glycerol, sorbitol, and sucrose, or increased by the addition of glycine. The topoisomers generated by the ligase reaction were resolved by agarose-gel electrophoresis. The DNA twist energy parameter (kappa), which is an apparent torsional constant, was determined by linearization of the Gaussian topoisomers' distribution. It was observed that the twist energy parameter for the given solutes is almost linearly dependent on the bulk dielectric constant. In the reaction buffer, the twist energy parameter was determined to be 1100 +/- 100. By decreasing the dielectric constant to 74 with the addition of sorbitol, the value of the parameter reaches kappa = 900 +/- 100, whereas the addition of ethylene glycol leads to kappa = 400 +/- 50. Upon addition of glycine, which resulted in a dielectric constant equal to 91, the value of the twist energy parameter increased to kappa = 1750 +/- 100.

Effects of ethylene glycol on the torsion elastic constant and hydrodynamic radius of p30δ DNA

Upon increasing the concentration of ethylene glycol (EG) at 37 degrees C, the twist energy parameter, E(T), which governs the supercoiling free energy, was recently found to undergo a decreasing (or reverse) sigmoidal transition with a midpoint near 20 w/v % EG. In this study, the effects of adding 20 w/v % EG on the torsion elastic constant (alpha) of linear p30delta DNA and on the hydrodynamic radius (R(H)) of a synthetic 24 bp duplex DNA were examined at both 40 and 20 degrees C. The time-resolved fluorescence intensity and fluorescence polarization anisotropy (FPA) of intercalated ethidium were measured in order to assess the effects of 20 w/v % EG on: (1) alpha; (2) R(H); (3) the lifetimes of intercalated and non-intercalated dye; (4) the amplitude of dye wobble in its binding site; and (5) the binding constant for intercalation. The effects of 20 w/v % EG on the circular dichroism (CD) spectrum of the DNA and on the emission spectrum of the free dye were also measured. At 40 degrees C, addition of 20 w/v % EG caused a substantial (1.27- to 1.35-fold) increase in alpha, a significant change in the CD spectrum, and a very small, marginally significant increase in R(H), but little or no change in the amplitude of dye wobble in its binding site or the lifetime of intercalated dye. Together with previously reported measurements of E(T), these results imply that the bending elastic constant of DNA is significantly decreased by 20 w/v % EG at 40 degrees C. At 20 degrees C, addition of 20 w/v % EG caused a marginally significant decrease in alpha and very little change in any other measured properties. Also at 20 degrees C, addition of 30 w/v % betaine caused a marginally significant increase in alpha and significant but modest change in the CD spectrum, but very little change in any other properties.

Torsional rigidities of weakly strained DNAs

Measurements on unstrained linear and weakly strained large (> or =340 bp) circular DNAs yield torsional rigidities in the range C = 170-230 fJ fm. However, larger values, in the range C = 270-420 fJ fm, are typically obtained from measurements on sufficiently small (< or =247 bp) circular DNAs, and values in the range C = 300-450 fJ fm are obtained from experiments on linear DNAs under tension. A new method is proposed to estimate torsional rigidities of weakly supercoiled circular DNAs. Monte Carlo simulations of the supercoiling free energies of solution DNAs, and also of the structures of surface-confined supercoiled plasmids, were performed using different trial values of C. The results are compared with experimental measurements of the twist energy parameter, E(T), that governs the supercoiling free energy, and also with atomic force microscopy images of surface-confined plasmids. The results clearly demonstrate that C-values in the range 170-230 fJ fm are compatible with experimental observations, whereas values in the range C > or = 269 fJ fm, are incompatible with those same measurements. These results strongly suggest that the secondary structure of DNA is altered by either sufficient coherent bending strain or sufficient tension so as to enhance its torsional rigidity.

Monte Carlo simulations of locally melted supercoiled DNAs in 20 mM ionic strength

Mesoscopic models of unmelted and locally melted supercoiled DNAs in 20 mM ionic strength are simulated over a range of linking difference from deltal = 0 to -26 turns, or superhelix density from sigma = 0 to -0.062. A domain containing m = 0, 28, or 56 melted basepairs (out of 4349 total) is modeled simply by a region of suitable length with substantially reduced torsion and bending elastic constants. Average structural properties are calculated from the saved configurations, and a reversible work protocol is used to calculate the supercoiling free energy, The cross-writhe between duplex and melted regions (defined herein) is found to be negligibly small. The total writhe, radius of gyration, and ordered elements of the diagonalized inertial tensor are found to be nearly universal functions of the residual linking difference (deltal(r)) associated with the duplex region, independent of m. However, deformability of the tertiary structure, as manifested by the variance of those same properties, is not a universal function of deltal(r)), but depends upon m.delta (SC) varies with deltal(r)) more strongly than deltal(r)) (2)due to the low ionic strength. The twist energy parameter, E (T) obtained from the simulated delta G(SC), deltal(r)), and net twisting strain of the melted region T (D), is found to be independent of m, hence also of the torsion and bending elastic constants of the melted region. However, E(T) increases linearly with -deltalr), which leads to 1). a small overestimation of E (T) for any given deltal(r)) when E(T) is determined from the observed deltal and deltal (r) by the protocol of Bauer and Benham; and 2). a significant enhancement of the apparent slope, -dE(T)/d(T), obtained via the protocol of Bauer and Benham, relative to the actual slope at fixed delta l(r). After taking these two effects into account, the theoretical and experimental values E(T) and -dE(T)/d(T) values agree rather well. For the larger deltal the melted regions are found preferentially in the linker domains between interwound arms, rather than in the apical regions at the ends of interwound arms.

Effects of small neutral osmolytes on the supercoiling free energy and intrinsic twist of p30? DNA

Both theory and experiments are employed to investigate the effects of small neutral osmolytes on the average intrinsic twist (l0), the torsion and bending elastic constants, and the twist energy parameter (ET) that governs the supercoiling free energy. The experimental data for ethylene glycol and acetamide at 37 degrees C suggest, and are interpreted in terms of, a model wherein the DNA exhibits an equilibrium between two distinct conformational states that possess different numbers of bound water molecules and exhibit different intrinsic twists and torsion and bending elastic constants. Expressions are derived to relate the effective ET and l0 to the equilibrium constant, water activity (aw), and number (n) of bound water molecules released per cooperative domain undergoing the two-state transition. The variations of l0 and ET with -ln(aw) are similar for acetamide and ethylene glycol at 37 degrees C. Fitting the theory to those data yields the range n = 103-125 for ethylene glycol and n = 71-113 for acetamide, depending on the assumed value of ET for the dehydrated state. The cooperative domain size of the two-state transition is estimated to exceed about 25-30 base pairs (bp). Between 0 and 19.4 w/v % ethylene glycol, the torsion elastic constant, measured by time-resolved fluorescence polarization anisotropy (FPA), increases by 1.37-fold, whereas the measured ET decreases by 1.15-fold over that same range. The implied decrease in bending rigidity over that range is by a factor of about 0.7. The variations of l0 and ET with increasing -ln(aw) due to added ethylene glycol at 37 degrees C are far smaller than the corresponding variations observed previously at 14 and 15 degrees C. However, at 21 degrees C, upon adding either ethylene glycol or acetamide, l0 and ET initially decline steeply with increasing -ln(aw), with slopes possibly comparable to those seen at 14 and 15 degrees C, but then flatten out and follow curves similar to those at 37 degrees C. Possible origins of such mixed behavior are discussed. The effects of betaine at both 37 and 21 degrees C differ qualitatively and quantitatively in various respects from those of ethylene glycol and acetamide. Upon adding sucrose, l0 initially jumps to higher plateaus at both 37 and 21 degrees C, but its effects on ET cannot be reliably assessed, due to the limited range of -ln(aw).

The question of long-range allosteric transitions in DNA

The question of long-range allosteric transitions of DNA secondary structure and their possible involvement in transcriptional activation is discussed in the light of new results. A variety of recent evidence strongly supports a fluctuating long-range description of DNA secondary structure. Balanced equilibria between two or more different secondary structures, and the occurrence of very large domain sizes, have been documented in several instances. Long-range allosteric effects stemming from changes in sequence or secondary structure over a small region of the DNA have been observed to extend over distances up to hundreds of base pairs in some cases. The discovery that coherent bending strain beyond a threshold level in small (N < or = 250 base pairs (bp)] circular DNAs significantly alters the DNA secondary structure has important implications, especially for transcriptional activators that either bend the DNA directly or are involved in the formation of DNA loops of sufficiently small size (N < or = 250 bp). Whether the RNA polymerase is activated primarily via protein: protein contacts, as is widely believed, or instead via a bend-induced allosteric transition of the DNA in such a small loop, is now an open question. Binding of the transcriptional activator Sp1 to linear DNA induces a remarkably long-range change in its secondary structure, and catabolite activator protein binding to a supercoiled DNA behaves similarly, though possibly for different reasons. Compelling evidence for a bend-induced long-range structural transmission effect of the transcriptional activator integration host factor on RNA polymerase activity was recently reported. These results may augur a new paradigm in which allosteric transitions of duplex DNA, as well as of the proteins, are involved in the regulation of transcription.

Dynamic twisting correlations in a model DNA with uniform torsion elastic constant

The extent to which the twisting motions of two separate subunits (base pairs) in an elastic filament are correlated is discussed in terms of the two-point correlation function of their azimuthal angular displacements C(Delta,t) identical with <(phi(m)(t) - phi(m)(0))(phi(n)(t) - phi(n)(0))>, where m,n are the sequential subunit indices and Delta = |m - n| is their absolute difference. An approximate expression is derived for C(Delta,t) for an infinitely long model DNA from the analytical theory developed previously to treat the decay of the fluorescence polarization anisotropy of intercalated ethidium. C(Delta,t) is numerically evaluated as a function of Delta for a range of times (20, 40, 60, 80, 100, and 120 ns) for a model DNA with a typical torsion elastic constant. By t = 120 ns, significant dynamic correlations are observed to extend over a domain (Delta) several hundred base pairs. Copyright 1999 John Wiley & Sons, Inc.

Effect of temperature on DNA secondary structure in the absence and presence of 0.5 M tetramethylammonium chloride

Changes in the average secondary structures of three different linear DNAs over the premelting region from 5 to 60 degrees C were investigated by measuring their CD spectra and also their torsion elastic constants (<alpha>) by time-resolved fluorescence polarization anisotropy. For one of these DNAs, the Haell fragment of pBR322, the apparent diffusion coefficients [Dapp(k)] at small and large scattering vectors (k) were also measured by dynamic light scattering. With increasing temperature, all three DNAs exhibited typical premelting changes in their CD spectra, and these were accompanied by 1.4- to 1.7-fold decreases in <alpha>. Also for the 1876 base pair fragment, Dapp(k) at large scattering vectors, which is sensitive to the dynamic bending rigidity, decreased by 17%, even though there was no change at small scattering vectors, where Dapp(k) = D0 is the translational diffusion coefficient of the center-of-mass. These observations demonstrate conclusively that the premelting CD changes of these DNAs are associated with a significant change in average secondary structure and mechanical properties, though not in persistence length. In the presence of 0.5 M tetramethylammonium chloride (TMA-Cl) the premelting change in CD is largely suppressed, and the corresponding changes in <alpha> and Dapp(k) at large scattering vectors are substantially diminished. These observations suggest that TMA-Cl, which binds preferentially to A.T-rich regions and stabilizes those regions (relative to G.C-rich regions) against melting, effectively stabilizes the prevailing low-temperature secondary structure sufficiently that the DNA is effectively trapped in that state over the temperature range observed.

On the origin of the temperature dependence of the supercoiling free energy

Monte Carlo simulations using temperature-invariant torsional and bending rigidities fail to predict the rather steep decline of the experimental supercoiling free energy with increasing temperature, and consequently fail to predict the correct sign and magnitude of the supercoiling entropy. To illustrate this problem, values of the twist energy parameter (E(T)), which governs the supercoiling free energy, were simulated using temperature-invariant torsion and bending potentials and compared to experimental data on pBR322 over a range of temperatures. The slope, -dE(T)/dT, of the simulated values is also compared to the slope derived from previous calorimetric data. The possibility that the discrepancies arise from some hitherto undetected temperature dependence of the torsional rigidity was investigated. The torsion elastic constant of an 1876-bp restriction fragment of pBR322 was measured by time-resolved fluorescence polarization anisotropy of intercalated ethidium over the range 278-323 K, and found to decline substantially over that interval. Simulations of a 4349-bp model DNA were performed using these measured temperature-dependent torsional rigidities. The slope, -dE(T)/dT, of the simulated data agrees satisfactorily with the slope derived from previous calorimetric measurements, but still lies substantially below that of Duguet's data. Models that involve an equilibrium between different secondary structure states with different intrinsic twists and torsion constants provide the most likely explanation for the variation of the torsion constant with T and other pertinent observations.

Buckling transitions in superhelical DNA: dependence on the elastic constants and DNA size

Buckling transitions in superhelical DNA are sudden changes in shape that accompany a smooth variation in a key parameter, such as superhelical density. Here we explore the dependence of these transitions on the elastic constants for bending and twisting. A and C, important characteristics of DNA's bending and twisting persistence lengths. The large range we explore extends to other elastic materials with self-contact interactions, modeled here by a Debye-Hückel electrostatic potential. Our collective description of DNA shapes and energies over a wide range of p = A/C reveals a dramatic dependence of DNA shape and associated configurational transitions on p: transitions are sharp for large p but masked for small p. In particular, at small p, a nonplanar circular family emerges, in agreement with Jülicher's recent analytical predictions: a continuum of forms (and associated writhing numbers) is also observed. The relevance of these buckling transitions to DNA in solution is examined through studies of size dependence and thermal effects. Buckling transitions smooth considerably as size increases, and this can be explained in part by the lower curvature in larger plasmids. This trend suggests that buckling transitions should not be detectable for isolated (i.e., unbound) DNA plasmids of biological interest, except possibly for very large p. Buckling phenomena would nonetheless be relevant for small DNA loops, particularly for higher values of p, and might have a role in regulatory mechanisms: a small change in superhelical stress could lead to a large configurational change. Writhe distributions as a function of p, generated by Langevin dynamics simulations, reveal the importance of thermal fluctuations. Each distribution range (and multipeaked shape) can be interpreted by our buckling profiles. Significantly, the distributions for moderate to high superhelical densities are most sensitive to p, isolating different distribution patterns. If this effect could be captured experimentally for small plasmids by currently available imaging techniques, such results suggest a slightly different experimental procedure for estimating the torsional stiffness of supercoiled DNA than considered to date.

Dynamical change of mitochondrial DNA induced in the living cell by perturbing the electrochemical gradient

Digital-imaging microscopy was used in conditions that allowed the native state to be preserved and hence fluorescence variations of specific probes to be followed in the real time of living mammalian cells. Ethidium bromide was shown to enter into living cells and to intercalate stably into mitochondrial DNA (mtDNA), giving rise to high fluorescence. When the membrane potential or the pH gradient across the inner membrane was abolished by specific inhibitors or ionophores, the ethidium fluorescence disappeared from all mtDNA molecules within 2 min. After removal of the inhibitors or ionophores, ethidium fluorescence rapidly reappeared in mitochondria, together with the membrane potential. The fluorescence extinction did not result from an equilibrium shift caused by leakage of free ethidium out of mitochondria when the membrane potential was abolished but was most likely due to a dynamical mtDNA change that exposed intercalated ethidium to quencher, either by weakening the ethidium binding constant or by giving access of a proton acceptor (such as water) to the interior of mtDNA. Double labeling with ethidium and with a minor groove probe (4',6-diamino-2-phenylindole) indicated that mtDNA maintains a double-stranded structure. The two double-stranded DNA states, revealed by the fluorescence of mitochondrial ethidium, enhanced or quenched in the presence of ethidium, seem to coexist in mitochondria of unperturbed fibroblast cells, suggesting a spontaneous dynamical change of mtDNA molecules. Therefore, the ethidium fluorescence variation allows changes of DNA to be followed, a property that has to be taken into consideration when using this intercalator for in vivo as well as in vitro imaging studies.

Linker histones affect patterns of digestion of supercoiled plasmids by single-strand-specific nucleases

The effect of histone H1 binding on the cleavage of superhelical plasmids by single-strand-specific nucleases was investigated. Mapping of P1 cleavage sites in pBR322, achieved by EcoRI digestion after the original P1 attack, showed an intriguing phenomenon: preexisting susceptible sites became "protected," whereas some new sites appeared at high levels of H1. Similar results were obtained with another single-strand-specific nuclease, S1. Disappearance of cutting at preexisting sites and appearance of new sites was also observed in a derivative plasmid that contains a 36-bp stretch of alternating d(AT) sequence that is known to adopt an altered P1-sensitive conformation. On the other hand, H1 titration of a dimerized version of the d(AT)18-containing plasmid led to protection of all preexisting sites except the d(AT)18 inserts, which were still cut even at high H1 levels; in this plasmid no new sites appeared. The protection of preexisting sites is best explained by long-range effects of histone H1 binding on the superhelical torsion of the plasmid. The appearance of new sites, on the other hand, probably also involves a local effect of stabilization of specific sequences in Pl-sensitive conformation, due to direct H1 binding to such sequences. That such binding involves linker histone N- and/or C-terminal tails is indicated by the fact that titration with the globular domain of H5, while causing disappearance of preexisting sites, does not lead to the appearance of any new sites.

Monte Carlo simulations of supercoiling free energies for unknotted and trefoil knotted DNAs

A new Monte Carlo (MC) algorithm is proposed for simulating inextensible circular chains with finite twisting and bending rigidity. This new algorithm samples the relevant Riemann volume elements in a uniform manner, when the constraining potential vanishes. Simulations are performed for filaments comprising 170 subunits, each containing approximately 28 bp, which corresponds to a DNA length of 4770 bp. The bending rigidity is chosen to yield a persistence length, P = 500 A, and the intersubunit potential is taken to be a hard-cylinder potential with diameter d = 50 A. This value of d yields the same second virial coefficient as the electrostatic potential obtained by numerical solution of the Poisson-Boltzmann equation for 150 mM salt. Simulations are performed for unknotted circles and also for trefoil knotted circles using two different values of the torsional rigidity, C = (2.0 and 3.0) x 10(-19) dyne cm2. In the case of unknotted circles, the simulated supercoiling free energy varies practically quadratically with linking difference delta l. The simulated twist energy parameter ET, its slope dET/dT, and the mean reduced writhe <w>/delta l for C = 3 x 10(-19) dyne cm2 all agree well with recent simulations for unknotted circles using the polygon-folding algorithm with identical P, d, and C. The simulated ET vs. delta l data for C = 2.0 x 10(-19) dyne cm2 agree rather well with recent experimental data for p30 delta DNA (4752 bp), for which the torsional rigidity, C = 2.07 x 10(-19) dyne cm2, was independently measured. The experimental data for p30 delta are enormously more likely to have arisen from C = 2.0 x 10(-19) than from C = 3.0 x 10(-19) dyne cm2. Serious problems with the reported experimental assessments of ET for pBR322 and their comparison with simulated data are noted. In the case of a trefoil knotted DNA, the simulated value, (ET)tre, exceeds that of the unknotted DNA, (ET)unk, by approximately equal to 1.40-fold at magnitude of delta l = 1.0, but declines to a plateau about 1.09-fold larger than (ET)unk when magnitude of delta l > or = 15. Although the predicted ratio, (ET)tre/(ET)unk approximately equal to 1.40, agrees fairly well with recent experimental measurements on a 5600-bp DNA, the individual measured ET values, like some of those reported for pBR322, are so large that they cannot be simulated using P = 500 A, d = 50 A, and any previous experimental estimate of C.

A model for the binding of E. coli single-strand binding protein to supercoiled DNA

A model is proposed for the binding of E. coli single strand binding protein (SSB) to supercoiled DNA. The basic tetrameric binding units of SSB are assumed to bind in pairs to the complementary single strands of a locally melted region. The cooperativity of the binding includes contributions from both protein-protein and base-pair stacking interactions. Each bound SSB tetramer is assumed to unwind l = 34 bp, which implies an unwinding angle of 3.27 turns. The resulting loss of superhelical strain is the essential driving force for binding SSB to supercoiled DNAs. All molecular parameters entering into the theory are estimated from available data, except for the composite binding constant (Ka), which is adjusted to best-fit the theory to the fluorescence quenching (FQ) and diffusion coefficient (D0) data of Langowski et al. Very good fits are obtained with optimum values of Ka that are consistent with estimates from other data. This binding model predicts several noteworthy features. (1) SSB binds essentially always in a single contiguous stack on a supercoiled plasmid, and relative fluctuations in stack length are quite small, in agreement with results of electron microscopy studies. (2) The progressive loss of superhelical strain with increasing bound ligand decreases the affinity of the DNA for SSB. This anti-cooperativity offsets the cooperativity of the binding and causes apparent saturation of the binding at rather low binding ratios. Consequently, over the limited span of the measurements, the FQ data can also be satisfactorily fitted by a non-cooperative model comprising a small number of independent sites. (3) When SSB binds to a population of different topoisomers, the distribution of linking differences of the resulting complexes is extremely narrow. Thus, SSB acts to level any differences in superhelical strain in a population of topoisomers. Finally, the effects of restricting binding to a region comprising only part of the plasmid are assessed.