Time-resolved fluorescence polarization anisotropy of short restriction fragments: the friction factor for rotation of DNA about its symmetry axis

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.

Can reliable torsion elastic constants be determined from FPA data on 24 and 27 base-pair DNAs?

Torsion elastic constants obtained from fluorescence polarization anisotropy (FPA) measurements on fifty-three 24 and 27 base-pair (bp) DNAs were recently reported [F. Pedone, F. Mazzei, D. Santoni, Sequence-dependent DNA torsional rigidity: a tetranucleotide code, Biophys. Chem. 112 (2004) 77-88; F. Pedone, F. Mazzei, M. Matzeu, F. Barone, Torsional constant of 27-mer DNA oligomers of different sequences, Biophys. Chem. 94 (2001) 175-184]. The problem of extracting reliable torsion elastic constants (alpha) from FPA measurements on such short DNAs is examined in detail. The difficulty is illustrated by two (fictitious) 24 bp DNAs with approximately 5-fold different torsion elastic constants and 10% different initial anisotropies (r(0)), which exhibit practically indistinguishable anisotropy decays for all t>1 ns. FPA data were simulated for 24 bp DNAs with different input values of alpha and r(0) in the presence and absence of Poisson noise, and were fitted using different choices of the adjustable and fixed parameters. Experimental data for a 24 bp DNA were fitted in a similar manner. For either the simulated or experimental FPA data, it was not possible to determine both the initial anisotropy, r(0), and the torsion elastic constant, alpha, in a reliable (i.e. statistically significant) manner in the presence of Poisson noise. When r(0) is assumed to be fixed at any particular value in the fitting protocol, a unique best-fit value of alpha is obtained, but that best-fit alpha is extremely sensitive to small deviations of the assumed fixed value of r(0) away from the input r(0)-value of the simulated data. Pedone et al. fitted their FPA data by assuming that r(0)=0.360, and adjusting alpha, the hydrodynamic radius (R(H)), and effective length (L). In fact, the reported best-fit values of R(H) and L lay significantly outside their expected ranges. When this same fitting protocol is applied to simulated data for 27 bp DNAs, better overall agreement with the reported experimental values (alpha, R(H), and L) is obtained for a model, wherein all DNAs have the same typical input alpha=5.9 x 10(-12) dyn cm, R(H)=10.0 A, and L=27 (3.4)+2.7=94.5 A, but a 1.00- to 1.13-fold range of r(0)-values, than for the model of Pedone et al., wherein all DNAs have the same input r(0)=0.360, R(H)=10.0 A, and L=94.5 A, but a approximately 3-fold range of alpha-values. It is concluded that, in the absence of reliable independent estimates of r(0) for every DNA, the alpha-values reported for 24 and 27 bp DNAs cannot be regarded as experimentally justified. The reliability of the torsion elastic constants reported for the 136 distinct tetranucleotide steps, which are inferred from the values reported for the fifty-three 24 and 27 bp DNAs, is also briefly discussed.

Fluorescence anisotropy in the frequency domain by an optical microscope

Fluorescence anisotropy decay spectroscopy is a suitable tool for investigating the size and the shape of biological molecules. We coupled this technique to an optical microscope in order to reduce the excitation volume and to allow its application to spatially inhomogeneous samples. Phase modulated measurements of the fluorescence anisotropy decay were performed by feeding an intensity modulated linearly polarized laser beam to the epifluorescence port of a microscope. Here we report the test of the dynamic response of the microscope by comparing the lifetime and fluorescence polarization anisotropy decays obtained in cuvettes in a standard phase modulation fluorometer and on tiny drops on the microscope stage. We show that once a correction factor for the objective depolarization is introduced in the best-fit functions for the data analysis of the decays, the results obtained on the two setups are comparable. Some applications are reported here on long DNA tracts as well on short DNA fragments containing structural anomalies.

Phosphate backbone neutralization increases duplex DNA flexibility: a model for protein binding

An important component of protein-DNA recognition is the charge neutralization of DNA backbone phosphates and subsequent protein-induced DNA bending. Replacement of phosphates by neutral methylphosphonates has previously been shown to be a model for protein-induced bending. In addition to bending, the neutralization process may change the inherent flexibility of the DNA--a feature never before tested. We have developed a method to measure the differential flexibility of duplex DNA when methylphosphonate substitutions are made and find that the local flexibility is increased up to 40%. These results imply that backbone-neutralization-dependent DNA flexibility augments DNA-binding motifs in protein-DNA recognition processes.

The distribution of end-to-end distances of the weakly bending rod model

The weakly bending rod model is an approximation to a worm-like chain in the limit where the ratio L(0)/P of the contour length L(0) to the persistence length P is not too large. The range of validity of the weakly bending rod model is investigated by deriving analytical expressions for its distribution of end-to-end distances P(L) and its moments <L(m) > and numerically comparing the results with corresponding values for the worm-like chain model. No general, closed form analytical expression for either P(L) or the average length <L> of a worm-like chain exists, so those quantities are obtained by Monte Carlo simulations. Exact analytical expressions for <L(2)> and <L(4)> for the worm-like chain are employed in the comparison of the computed moments. Moments calculated for the approximate distributions of Daniels and Yamakawa and Stockmayer are also compared with the others. In addition, P(L) and its moments for the alternative model of Winkler et al. are compared with the others. The weakly bending rod model gives a reasonably good account of both P(L) and <L(m) >, m = 1,2,4, over the range L(0)/P </= 0.6, but deviates significantly for L(0)/P >/= 1.0. In contrast, the alternative model of Winkler et al. yields rather poor results in the rodlike domain.

Sequence-dependent dynamics in duplex DNA

The submicrosecond bending dynamics of duplex DNA were measured at a single site, using a site-specific electron paramagnetic resonance active spin probe. The observed dynamics are interpreted in terms of the mean squared amplitude of bending relative to the end-to-end vector defined by the weakly bending rod model. The bending dynamics monitored at the single site varied when the length and position of a repeated AT sequence, distant from the spin probe, were changed. As the distance between the probe and the AT sequence was increased, the mean squared amplitude of bending seen by the probe due to that sequence decreased. A model for the sequence-dependent internal flexural motion of duplex DNA, which casts the mean squared bending amplitudes in terms of sequence-dependent bending parameters, has been developed. The best fit of the data to the model occurs when the (AT)(n) basepairs are assumed to be 20% more flexible than the average of the basepairs within the control sequence. These findings provide a quantitative basis for interpreting the kinetics of biological processes that depend on duplex DNA flexibility, such as protein recognition and chromatin packaging.

Flexibility of duplex DNA on the submicrosecond timescale

Using a site-specific, Electron Paramagnetic Resonance (EPR)-active spin probe that is more rigidly locked to the DNA than any previously reported, the internal dynamics of duplex DNAs in solution were studied. EPR spectra of linear duplex DNAs containing 14-100 base pairs were acquired and simulated by the stochastic Liouville equation for anisotropic rotational diffusion using the diffusion tensor for a right circular cylinder. Internal motions have previously been assumed to be on a rapid enough time scale that they caused an averaging of the spin interactions. This assumption, however, was found to be inconsistent with the experimental data. The weakly bending rod model is modified to take into account the finite relaxation times of the internal modes and applied to analyze the EPR spectra. With this modification, the dependence of the oscillation amplitude of the probe on position along the DNA was in good agreement with the predictions of the weakly bending rod theory. From the length and position dependence of the internal flexibility of the DNA, a submicrosecond dynamic bending persistence length of around 1500 to 1700 A was found. Schellman and Harvey (Biophys. Chem. 55:95-114, 1995) have estimated that, out of the total persistence length of duplex DNA, believed to be about 500 A, approximately 1500 A is accounted for by static bends and 750 A by fluctuating bends. A measured dynamic persistence length of around 1500 A leads to the suggestion that there are additional conformations of the DNA that relax on a longer time scale than that accessible by linear CW-EPR. These measurements are the first direct determination of the dynamic flexibility of duplex DNA in 0.1 M salt.

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.

Site-specific dynamics in DNA: experiments

This chapter reviews the dynamics information obtained from experimental magnetic resonance studies of site-specifically labeled duplex DNA. A previous review (43) discusses the dynamics of duplex DNA; it develops a theory that shows how magnetic resonance experiments are used to detect those dynamics. The methods for obtaining information about dynamics as well as a summary of what is now known about the site-specific dynamics of DNA are presented. This review contains two methods sections which present results using electron paramagnetic resonance and nuclear magnetic resonance active probes.

Conformation of short DNA fragments by modulated fluorescence polarization anisotropy

The technique of fluorescence polarization anisotropy (FPA) decay of intercalated ethidium has been used to study DNA conformation and dynamics, which are being recognized as primary determinants in transcription control and other cellular processes. Frequency modulated FPA when applied to two DNA molecules, a "straight" 50 base-pairs duplex fragment, and a bent fragment of similar length, has yielded different rotational diffusion coefficients for the two fragments. The data have been processed with an analytical model and with Brownian dynamics simulations, obtaining a good fit and a quantitative agreement between the two models. Both analyses have confirmed that one fragment can be described as a straight cylinder, while the other fragment is bent, with an angle estimated to be 45 degrees +/- 3 degrees. FPA has proved to be very powerful in determining simple conformations of short DNA duplexes and also particularly apt to probe the dynamical features of DNA fragments where conventional methods are either too cumbersome or fail to give quantitative results. In addition, the ligand no longer behaves ideally due to its complex structure and charge distribution. Thus for the protein the slope is no longer related simply to the net ligand charge, and the PB model gives a much larger slope than the LL model.(ABSTRACT TRUNCATED AT 400 WORDS)

Influence of ligands on the fluorescence polarisation anisotropy of ethidium bound to DNA

The decay of the fluorescence polarisation anisotropy (FPA) of the ethidium-DNA complex has been measured by multifrequency phase fluorometry, in order to study the perturbations induced by the presence of different ligands on the torsional dynamics of DNA, a moderately flexible polymer that undergoes bending (flexure of the helix axis) and torsional (twisting of base pairs) motions. Two probes have been used together with ethidium: an intercalator, chloroquine, and a minor groove binding dye: hoechst 33258. Chloroquine is found to substantially modify the DNA torsional dynamics both in linear and in circularly closed DNAs only at high binding ratios, in agreement with previous reports [Wu et al. Biochem. 27 (1988) 8128]. The effective elastic constant becomes approximately three times larger when the dye/base pairs binding ratio is higher than 0.14. The minor groove ligand hoechst 33258, on the other hand, greatly increases the effective elastic constant to the point that at dye/base pairs ratios larger than 0.5, the effective elastic constant becomes stiffer by several orders of magnitude, suggesting a progressive hindering of internal motions. The results reported here show that DNA torsions are more effectively influenced by groove-binding molecules than by intercalators and it is expected that the large perturbation of the former ligand may be useful when describing the change in the dynamical properties induced by DNA binding proteins. FPA in the frequency domain, the technique adopted throughout this work, has proved to be very sensitive to changes of the elastic constant that describes DNA torsional dynamics. Several computer simulations performed in order to predict the FPA time decay of intercalated ethidium have led to good agreement with the observed results.

Effects of different cations on the hydrodynamic radius of DNA

The effects of different cations on the hydrodynamic radius (RH) of a 48-bp synthetic DNA are measured by time-resolved fluorescence polarization anisotropy of intercalated ethidium. Relative statistical errors in RH are only approximately 1%. With increasing cation concentration, Na+ causes a small decrease in RH, Cs+ causes a somewhat larger decrease by up to 0.5 A at 100 mM, and (CH3CH2)4N+ causes an increase in RH by approximately 0.5 A at 100 mM. The qualitatively different effects of these monovalent cations indicates that the changes in RH with cation concentration do not arise primarily from electrolyte friction. Divalent cations cause much larger increases in RH with increasing cation concentration. Mg2+ causes an increase in RH by up to 1.0 A at 24.4 mM, and Mn2+ causes an increase in RH by up to 1.6 A at 24.4 mM. These effects are independent of DNA concentration. There is some positive correlation between the order of effects of the different cations on RH and the order of their effects on interhelical hydration forces. It is suggested that these different ions affect RH either by altering the hydration layer or possibly by some effect on DNA structure, such as stabilizing bends.

The amplitude of local angular motion of purines in DNA in solution

Nuclear magnetic resonance and optical experiments are combined to determine the rms amplitude of local angular motion of purines in DNA in solution. A 12 base-pair duplex DNA with the sequence d(CGCGAATTCGCG)2 is deuterated at the H8 positions of adenine and guanine by exchange with solvent at 55 degrees C. The deuterium nmr spectrum of this DNA is measured at 30 mg/mL at 30 degrees C in an 11.76 Tesla magnet (76.75 MHz). The time-resolved fluorescence polarization anisotropies (FPA) of this same sample and also a greatly diluted sample (0.215 mg/mL) were measured after addition of ethidium. FPA measurements of the dilute sample yield the hydrodynamic radius, RH = 9.94 +/- 0.2 A, while those at the nmr concentration are employed to characterize the collective motions in terms of either an enhanced viscosity or dimer formation. The rms amplitude of local angular motion was determined by analyzing the 2H-nmr spectrum, in particular the line width, using recently developed theory for the transverse relaxation rate (RQ2) together with essential information about the collective motions from these and other optical studies. When the principal-axis frame of the electric field gradient tensor is assumed to undergo overdamped libration around each of its three body-fixed axes in an isotropic deflection potential, then the rms amplitude of local angular motion around any single axis is found to lie in the range 10 degrees-11 degrees, provided the high DNA concentration acts to enhance the viscosity, and is about 9 degrees-11 degrees, if it acts to produce end-to-end dimers. The proton nmr relaxation data of Eimer et al. are reanalyzed and shown to yield an rms amplitude of angular motion of the cytosine H5-H6 internuclear vector of 9 degrees-10 degrees, depending upon its orientation with respect to the helix axis. In all of these analyses, full account is taken of the collective twisting and bending deformations, which have a small but significant effect on the results. It is shown that the rms amplitudes of local angular motion do not depend strongly on the model (potential), provided that isotropic rotation around the same number of axes is allowed and that one compares rms angles of the same dimensionality. The rms amplitudes of local angular motion in solution are comparable to those observed for the same sequence at low levels of hydration in the solid state.

Dynamics and structures of DNA: long-range effects of a 16 base-pair (CG)8 sequence on secondary structure

The effects of inserting 16 base pair (bp) of alternating CG [(CG)8] near the middle of a much longer restriction fragment (1097 bp) are investigated by measuring various properties that are sensitive to secondary and tertiary structure. Results for this fragment are compared with those for a control fragment (1089 bp) with the identical sequence except at the insert. Another fragment (1382 bp), which contains a 296-bp extension at the 5'-end of the 1089-bp control fragment, is also used as a secondary control in some experiments. When the 1097-bp (CG)8 insert fragment is compared with the control fragments in 0.1 M NaCl buffer, the (CG)8 insert is found to induce disproportionately large relative changes in the molar ellipticity at 273 nm ([theta]273), the torsion constant (alpha) measured by fluorescence polarization anisotropy, the optical melting profile, and the susceptibility to S1 nuclease. Estimates of the minimum distance over which the (CG)8 insert alters the secondary structure range from 330 to 550 bp. With increasing NaCl concentration, the 1097-bp insert fragment undergoes a structural transition between 2.0 and 2.5 M that is manifested in the apparent diffusion coefficient (Dplat) from dynamic light scattering at large scattering vector. This transition, which is not exhibited by the control DNAs, is presumed to involve formation of Z-helix at the insert. However, the observed decrease in (Dplat) is attributed to an increase in bending rigidity, which perforce must be globally distributed far beyond the (CG)8 insert per se. In 4.25 M NaCl (but not in 0.1 M NaCl), the addition of 1 ethidium dye per 300 bp induces an extensive structural transition in the 1097 bp (CG)8 insert fragment. This transition, which also is not exhibited by the control DNAs, significantly decreases the bending rigidity, doubles [theta]273, and takes place on a time scale of a few days. Removal of ethidium and salt by dialysis vs 0.1 M NaCl buffer restores the original properties of the 1097-bp (CG)8 insert fragment. The present results are consistent with a (fluctuating, long-range) description of the secondary structure in which a given short sequence transiently fluctuates among two or more distinct secondary structures that extend over much larger domains of variable position and size, and whose relative stabilities depend on distant as well as close-lying base pairs.

DNA torsional dynamics by multifrequency phase fluorometry

The time decay of the fluorescence polarization anisotropy of calf thymus DNA-ethidium complexes is obtained from measurements with sine-modulated excitation employing the so-called multifrequency phase fluorometry. A torsional dynamics model developed by J. M. Schurr [(1984) Chemical Physics, Vol. 84, pp. 71-96] and translated into the frequency domain is found here to describe accurately DNA-ethidium fluorescence data collected under modulated excitation. At a low dye/DNA ratio (1:400) the value of the DNA torsional constant (alpha = 4.63 +/- 0.2 10(-12) dyne cm) fitting the data agrees very well with the known values of alpha. When the measurements are extended to a higher ethidium/DNA ratio, energy transfer effects between intercalated dyes are observed. A theoretical prediction of the donor and acceptor dye contributions to the fluorescence polarization anisotropy is made here, taking into account also dye-dye distance distributions.

Effect of ethidium on the torsion constants of linear and supercoiled DNAs

The torsion elastic constants (alpha) of linear pBR322 (4363 bp) and pUC8 (2717 bp) DNAs and supercoiled pBR322 and pJMSII (4375 bp) DNAs are measured in 0.1 M NaCl as a function of added ethidium/base-pair (EB/BP) ratio by studying the fluorescence polarization anisotropy (FPA) of the intercalated ethidium. The time-resolved FPA is measured by using a picosecond dye laser for excitation and time-correlated single photon counting detection. Previously developed theory for the emission anisotropy is generalized to incorporate rotations of the transition dipole due to excitation transfer. The excitation transfers are simulated by a Monte Carlo procedure (Genest et al., Biophys. Chem. 1 (1974) 266-278) and the consequent rotations of the transition dipole are superposed on the Brownian rotations. After accounting for excitation transfer, the torsion constants of the linear DNAs are found to be essentially independent of intercalated ethidium up to a binding ratio r = 0.10 dye/bp. Dynamic light scattering measurements on linear pUC8 DNA confirm that the torsion constant is independent of binding ratio up to r = 0.20 dye/bp. If alpha d denotes the torsion constant between ethidium and a base-pair, and alpha 0 that between two base-pairs, then our data imply that alpha d/alpha 0 lies in the range 0.65 to 1.64 with a most probable value of 1.0. The torsion constants of supercoiled DNAs decrease substantially with increasing binding ratio even after accounting for excitation transfer. At the binding ratio r* = 0.064, where the superhelix density vanishes and superhelical strain is completely relaxed, the torsion constant of the supercoiled pBR322 DNA/dye complex lies below that of the corresponding linear DNA/dye complex by about 30%. This contradicts the conventional view according to which linear, nicked circular, and supercoiled DNA/dye complexes with r = r* should coexist with the same concentration of free dye, display the same distribution of bound dye, and exhibit identical secondary structures, twisting and bending rigidities, and FPA dynamics. These and other observations imply the existence of metastable secondary structure in freshly relaxed supercoiled DNAs. A tentative explanation is presented for these and other unexpected observations on supercoiled DNAs.

Dynamic light scattering from weakly bending rods: estimation of the dynamic bending rigidity of the M13 virus

A theory is presented for the dynamic structure factor [S(K,t]) of weakly bending rods. This treatment is based on a discrete bead model for the Brownian dynamics in which all bead motions associated with bending are constrained to occur in a plane perpendicular to the end-to-end vector, thus prohibiting extension or contraction along that axis. Preset hydrodynamic interactions are incorporated in a numerically exact manner. The predicted normalized dynamic structure factor S(K,t)/S(K,0) should be valid for short times t such that the rms rotation of the end-to-end vector around any transverse axis is much less than 1.0 radian. With geometrical parameters appropriate for the M13 virus, the intensity autocorrelation function G(2) (K,t) = 1 + magnitude of S(K,t)/S(K,0)2 is calculated over a range of times and scattering vectors K for selected values of the persistence length P. The calculated G(2) (K,t) are fitted to a single exponential with unit baseline over the same range of times as the experimental photon correlation functions, and the apparent diffusion coefficients Dapp (K) are obtained from the best-fit relaxation times. For the sake of completeness, an exact expression is derived for the apparent diffusion coefficient obtained from the initial slope of the dynamic structure factor. However, this does not reduce to the known correct result in the rigid rod limit. To obtain the correct result, the limit of infinite bending rigidity must be taken before the limit of zero time. For this and other reasons, the initial slope value of Dapp (K) is not useful for weakly bending rods. Photon correlation functions are measured for the M13 virus, which is virtually identical to the often-studied fd virus. The experimental photon correlation functions are fitted over 8 relaxation times to a single-exponential plus baseline, and the Dapp (K) are calculated from the best-fit relaxation times. Theoretical curves of Dapp (K) vs K2 for selected values of P are compared with the experimental data, which are satisfactorily reproduced when P = 22000 +/- 2000 A. This dynamic value is close to the static value, P = 20000 +/- 2000 A, reported for the very similar fd virus. The most recent theories of Maeda and Fujime and their dynamic light scattering studies of fd virus are compared with the present results in some detail. Their optimum value of P is in surprisingly good agreement with the present value.

Evidence for allosteric transitions in secondary structure induced by superhelical stress

Previous studies suggest that the global secondary structures of native supercoiled and equilibrium linear DNAs may differ somewhat. Recent evidence also indicates that metastable secondary structure commonly persists following complete relaxation of the superhelical stress by intercalating dyes or by the action of topoisomerase I. In this work, the torsion constants (alpha) of pBR322, pUC8 and M13mp7 (replicative form) DNAs are determined by time-resolved fluorescence polarization anisotropy at various times subsequent to linearization. In all three cases, the torsion constants are relatively low immediately after linearization, and evolve for eight to ten weeks before reaching their apparent equilibrium values. It is shown in detail how the persistence of metastable secondary structure, subsequent to relaxation of superhelical stress, necessarily implies that one or more transitions in equilibrium secondary structure are induced as the superhelix density is varied from zero to native, or vice versa. Samples of pUC8 dimer (5434 base-pairs) with different superhelix densities are prepared by the action of topoisomerase I in the presence of various amounts of ethidium. Their median linking number differences are determined by standard band counting methods. The translational diffusion coefficient (Do) and the plateau diffusion coefficient (Dplat) characterizing internal motions over short distances (225 A) are determined by dynamic light-scattering. The torsion constant (alpha) between base-pairs and the circular dichroism spectrum are also measured for each sample. Curves of Dplat, Do, alpha and molar ellipticity ([theta]) (at the minimum near 250 nm) versus superhelix density (sigma) are constructed. The curve of Do versus sigma is very similar to that for sedimentation coefficient versus sigma for simian virus 40 (SV40) and polyoma DNAs. The curves of Dplat, Do, alpha and [theta] versus sigma show that, with increasing negative superhelix density, a structural transition occurs near sigma = -0.020 to an intermediate state with low torsion constant, and a second structural transition occurs near sigma = -0.035 to a state that exhibits more normal properties by sigma = -0.048. These data are consistent with the hypothesis that supercoiling induces two successive allosteric transitions to alternative global secondary structures. The data are much less consistent with the hypothesis that supercoiling induces some radical secondary structure at one or a few sites of small extent at sigma = -0.020, and at other sites at sigma = -0.035, or with hypotheses based on changes in tertiary structure alone.(ABSTRACT TRUNCATED AT 400 WORDS)

Physical studies of DNA premelting equilibria in duplexes with and without homo dA.dT tracts: correlations with DNA bending

We have employed a variety of physical methods to study the equilibrium melting and temperature-dependent conformational dynamics of dA.dT tracts in fractionated synthetic DNA polymers and in well-defined fragments of kinetoplast DNA (kDNA). Using circular dichroism (CD), we have detected a temperature-dependent, "premelting" event in poly(dA).poly(dT) which exhibits a midpoint near 37 degrees C. Significantly, we also detect this CD "premelting" behavior in a fragment of kDNA. By contrast, we do not observe this "premelting" behavior in the temperature-dependent CD spectra of poly[d(AT)].poly[d(AT)], poly(dG).poly(dC), poly[d(GC)].poly[d(GC)], or calf thymus DNA. Thus, poly(dA).poly(dT) and kDNA exhibit a common CD-detected "premelting" event which is absent in the other duplex systems studied in this work. Furthermore, we find that the anomalous electrophoretic retardation of the kDNA fragments we have investigated disappears at temperatures above approximately 37 degrees C. We also observe that the rotational dynamics of poly(dA).poly(dT) and kDNA as assessed by singlet depletion anisotropy decay (SDAD) and electric birefringence decay (EBD) also display a discontinuity near 37 degrees C, which is not observed for the other duplex systems studied. Thus, in the aggregate, our static and dynamic measurements suggest that the homo dA.dT sequence element [common to both poly(dA).poly(dT) and kDNA] is capable of a temperature-dependent equilibrium between at least two helical states in a temperature range well below that required to induce global melting of the host duplex. We suggest that this "preglobal" melting event may correspond to the thermally induced "disruption" of "bent" DNA.

Reduced DNA flexibility in complexes with a type II DNA binding protein

We studied internal molecular motions in Bacillus subtilis phage SPO1 DNA using the time-resolved fluorescence polarization anisotropy (FPA) of intercalated ethidium. The torsional flexibility of this (hydroxymethyl)uracil-containing DNA is very similar to that of naturally occurring thymine-containing DNAs, as judged from fits of the time-resolved FPA decay to an elastic DNA model. Binding of transcription factor 1 (TF1), a type II procaryotic DNA binding protein encoded by the phage SPO1, enhances the FPA, indicating a substantial decrease in the average DNA torsional flexibility in the DNA-TF1 complex. The FPA increase is correlated with a reduced ethidium binding affinity. The effects can be noticed at TF1 binding ratios less than 1 TF1 dimer/500 DNA base pairs, and the measured torsional rigidity at high TF1 binding ratios (1 TF1 dimer/15-20 DNA base pairs) is about 7 times greater than in the absence of TF1. On the basis of a discussion of various mechanisms for the observed effect we argue that it is due to protein-induced DNA bending at low binding densities although other explanations are also possible. This interpretation might have implications for understanding the biological function of TF1.

Effects of chloroquine on the torsional dynamics and rigidities of linear and supercoiled DNAs at low ionic strength

The magnitude and uniformity of the torsion elastic constant (alpha) of linear and supercoiled pBR322 DNAs are measured in 3 mM Tris as a function of added chloroquine/basepair ratio (chl/bp) by studying the fluorescence polarization anisotropy of intercalated ethidium dye. The time-resolved FPA is measured using a picosecond dye-laser for excitation and time-correlated single-photon counting detection. For both linear and supercoiled DNAs, alpha remains uniform except at the very highest chl/bp ratio examined. For the linear DNA, alpha decreases from 5.0 x 10(-12) dyne-cm at chl/bp = 0 to about 3.5 x 10(-12) dyne-cm at chl/bp = 0.5, and remains at that value up to chl/bp = 5, whereupon it increases back up to its original value. For the supercoiled DNA, alpha remains constant at about 5.2 x 10(-12) dyne-cm from chl/bp = 0 up to chl/bp = 5, whereupon it increases in parallel with the linear DNA. The effect of chloroquine on the secondary structure, torsion constant, and torsional dynamics evidently differs substantially between linear and supercoiled DNAs, even under conditions where the supercoiled DNA is completely relaxed and both DNAs bind the same amount of dye. This strongly contradicts any notion that the local structures of linear and relaxed supercoiled DNA/dye complexes with the same binding ratio are identical. The increase in apparent alpha at chl/bp = 5 for both DNAs may be due to stacking of the chloroquine in the major groove and consequent stiffening of the filament.

Harmonic dynamics of a DNA hexamer in the absence and presence of the intercalator ethidium

Vibrational normal mode calculations are presented for a DNA hexanucleoside pentaphosphate, d(CpGpCpGpCpG)2, and for its complex with the cationic intercalator ethidium. Two intercalation sites are modeled that differ in DNA backbone torsion angles. Normal mode frequencies for the DNA fragment itself are significantly lower than those reported earlier using different force fields, but an analysis of "effective" frequencies suggests that somewhat higher frequencies are more appropriate. Intercalation leads to significant lowering of mobility for the base pairs adjacent to the drug; in this sequence, the ethidium binding affects the guanosine atoms more strongly than the cytosine atoms. Motions of the bases and the intercalator are analyzed in terms of "twist" about the local helix axis and a "tilt" angle relative to this axis, and the results are compared to fluorescence studies of ethidium-DNA complexes.

Interaction of chloroquine with linear and supercoiled DNAs. Effect on the torsional dynamics, rigidity, and twist energy parameter

The magnitude and uniformity of the torsion elastic constant (alpha) of linear pBR322 DNA and supercoiled pBR322 DNAs with high-twist (sigma = -0.083) and normal-twist (sigma = -0.48) are measured in 0.1 M NaCl as a function of added chloroquine/base-pair ratio (chl/bp) by studying the fluorescence polarization anisotrophy (FPA) of intercalated ethidium dye. The time-resolved FPA is measured by using a picosecond dye laser for excitation and time-correlated single-photon counting detection. A general theory is developed for the binding of ligands that unwind superhelical DNAs, and the simultaneous binding of two different intercalators is treated in detail. The equilibrium constant (K) for binding chloroquine to linear pBR322 DNA and the number (r) of bound chloroquines per base pair are determined from the relative amplitude ratio of the slow (normally intercalated) and fast (free) components in the decay of the (probe) ethidium fluorescence intensity as a function of chl/bp. For chloroquine binding to supercoiled pBR322 DNAs, the intrinsic binding constant is assumed to be the same as for the linear DNA, but the twist energy parameter ET (N times the free energy to change the linking number from 0 to 1 in units of kBT) is regarded as adjustable. Using the best-fit ET, the binding ratios r are calculated for each chl/bp ratio. Twist energy parameters are also determined for ethidium binding to these supercoiled DNAs by competitive dialysis. For chloroquine binding, we obtain ET = 360 and 460 respectively for the normal-twist and high-twist supercoiled DNAs. For ethidium binding the corresponding values are ET = 280 +/- 70 and 347 +/- 50. Like other dye-binding values, these are substantially lower than those obtained by ligation methods. In the absence of chloroquine, the torsion constants of all three DNAs are virtually identical, alpha = (5.0 +/- 0.4) x 10(-12) dyn.cm. For linear pBR322 DNA, the magnitude and uniformity of alpha remain unaltered by intercalated chloroquine up to r = 0.19. This finding argues that the FPA is not significantly relaxed by diffusion of any kinks or solitons. If alpha d denotes the torsion constant between a dye and a base pair and alpha 0 that between two base pairs, then our data imply that alpha d/alpha 0 lies in the range 0.65-1.64, with a most probable value of 1.0.(ABSTRACT TRUNCATED AT 400 WORDS)