Photon correlation spectroscopy, total intensity light scattering with laser radiation, and hydrodynamic studies of a well fractionated DNA sample

The Statistical Segment Length of DNA: Opportunities for Biomechanical Modeling in Polymer Physics and Next-Generation Genomics

The development of bright bisintercalating dyes for deoxyribonucleic acid (DNA) in the 1990s, most notably YOYO-1, revolutionized the field of polymer physics in the ensuing years. These dyes, in conjunction with modern molecular biology techniques, permit the facile observation of polymer dynamics via fluorescence microscopy and thus direct tests of different theories of polymer dynamics. At the same time, they have played a key role in advancing an emerging next-generation method known as genome mapping in nanochannels. The effect of intercalation on the bending energy of DNA as embodied by a change in its statistical segment length (or, alternatively, its persistence length) has been the subject of significant controversy. The precise value of the statistical segment length is critical for the proper interpretation of polymer physics experiments and controls the phenomena underlying the aforementioned genomics technology. In this perspective, we briefly review the model of DNA as a wormlike chain and a trio of methods (light scattering, optical or magnetic tweezers, and atomic force microscopy (AFM)) that have been used to determine the statistical segment length of DNA. We then outline the disagreement in the literature over the role of bisintercalation on the bending energy of DNA, and how a multiscale biomechanical approach could provide an important model for this scientifically and technologically relevant problem.

Is DNA a Good Model Polymer?

The details surrounding the cross-over from wormlike-specific to universal polymeric behavior has been the subject of debate and confusion even for the simple case of a dilute, unconfined wormlike chain. We have directly computed the polymer size, form factor, free energy and Kirkwood diffusivity for unconfined wormlike chains as a function of molecular weight, focusing on persistence lengths and effective widths that represent single-stranded and double-stranded DNA in a high ionic strength buffer. To do so, we use a chain-growth Monte Carlo algorithm, the Pruned-Enriched Rosenbluth Method (PERM), which allows us to estimate equilibrium and near-equilibrium dynamic properties of wormlike chains over an extremely large range of contour lengths. From our calculations, we find that very large DNA chains (≈ 1,000,000 base pairs depending on the choice of size metric) are required to reach flexible, swollen non-draining coils. Furthermore, our results indicate that the commonly used model polymer λ-DNA (48,500 base pairs) does not exhibit "ideal" scaling, but exists in the middle of the transition to long-chain behavior. We subsequently conclude that typical DNA used in experiments are too short to serve as an accurate model of long-chain, universal polymer behavior.

Expanded-size bases in naturally sized DNA: evaluation of steric effects in Watson-Crick pairing

We describe physicochemical properties in DNA of altered-size nucleobases that retain Watson-Crick analogous hydrogen-bonding ability. Size-expanded analogues of adenine and thymine (xA and xT, respectively, which are expanded by benzo-fusion) were incorporated into natural DNA oligonucleotides, and their effects on helix stability were measured. Base stacking studies revealed that the two stretched analogues stack much more strongly than do their naturally sized counterparts. In contrast to this, pairing studies showed that single substitutions of the new bases are destabilizing to the natural helix as compared to A or T in standard A-T pairs in the same context, unless multiple adjacent substitutions are used. Interestingly, the size-expanded bases displayed selective recognition of the hydrogen-bonding complementary partners, suggesting that Watson-Crick analogous pairs were still formed despite local backbone strain. In an attempt to compensate for the added size of the expanded adenine, we tested a formamide deoxynucleoside, which Leonard proposed as a shortened thymine analogue (F(o)). Data showed, however, that this compound adopts a conformation unfavorable for pairing. On the basis of the combined thermodynamic data, we estimate the energetic cost of the 2.4 A stretching of an isolated base pair in DNA at ca. +1 to 2 kcal/mol. Notably, during the pairing studies, the two size-expanded nucleobases were found to display significant changes in fluorescence on formation of stacked versus unstacked structures, suggesting possible applications in probing nucleic acid structures and biochemical mechanisms.

Light scattering studies of supercoiled and nicked DNA

Static and dynamic light scattering measurements were made of solutions of pGem1a plasmids (3730 base pairs) in the relaxed circular (nicked) and supercoiled forms. The static structure factor and the spectrum of decay modes in the autocorrelation function were examined in order to determine the salient differences between the behaviors of nicked DNA and supercoiled DNA. The concentrations studied are within the dilute regime, which is to say that the structure and dynamics of an isolated DNA molecule were probed. Static light scattering measurements yielded estimates for the molecular weight M, second virial coefficient A2, and radius of gyration RG. For the nicked DNA, M = (2.8 +/- 0.4) x 10(6) g/mol, A2 = (0.9 +/- 0.2) x 10(-3) mol cm3/g2, and RG = 90 +/- 3 nm were obtained. For the supercoiled DNA, M = (2.5 +/- 0.4) x 10(6) g/mol, A2 = (1.2 +/- 0.2) x 10(-3) mol cm3/g2, and RG = 82 +/- 2.5 nm were obtained. The static structure factors for the nicked and supercoiled DNA were found to superpose when they were scaled by the radius of gyration. The intrinsic stiffness of DNA was evident in the static light scattering data. Homodyne intensity autocorrelation functions were collected for both DNAs at several angles, or scattering vectors. At the smallest scattering vectors the probe size was comparable to the longest intramolecular distance, while at the largest scattering vectors the probe size was smaller than the persistence length of the DNA. Values of the self-diffusion coefficients D were obtained from the low-angle data. For the DNA, D = (2.9 +/- 0.3) x 10(-8) cm2/s, and for the supercoiled DNA, D = (4.11 +/- 0.21) x 10(-8) cm2/s. The contribution to the correlation function from the internal dynamics of the DNA was seen to result in a strictly bimodal decay function. The rates of the faster mode gamma int, reached plateau values at low angles. For the nicked DNA, gamma int = 2500 +/- 500 s-1, and for the supercoiled DNA, gamma int = 5000 +/- 500 s-1. These rates correspond to the slowest internal relaxation modes of the DNAs. The dependence of the relaxation rates on scattering vector was monitored with the aid of cumulants analysis and compared with theoretical predictions for the semiflexible ring molecule. The internal mode rates and the dependence of the cumulants moments reflected the difference between the nicked DNA and the supercoiled DNA dynamical behavior. The supercoiled DNA behavior seen here indicates that conformational dynamics might play a larger role in DNA behavior than is suggested by the notion of a branched interwound structure.

The flexibility of A-form DNA

We have determined the rise per base pair and persistence length of A-form DNA in trifluoroethanol solutions for fragments 350-900 base pairs in length that best describe rotational diffusion coefficients determined by transient electric birefringence. The 2.6 A spacing between base pairs found in crystal and fiber A-form structures is preserved in solution. The persistence length is about 1500 A, or about three times longer than for B-form DNA. There is no apparent electrostatic contribution to the persistence length in the salt concentration range 0.2-2.0 mM Na cacodylate. This suggests an even closer association between DNA and its neutralizing counterions than predicted by condensation theory, perhaps due to a sheath of trifluoroethanol excluded water surrounding the A-form helix.

Internal dynamics of linear and superhelical DNA as studied by photon correlation spectroscopy

Photon correlation spectroscopy has been used to study the translational (D0) and internal dynamics of monodisperse linear and polydisperse superhelical plasmid-DNAs. Scattering vector dependent correlation functions were measured and analyzed with the inverse Laplace transform CONTIN written by S. Provencher. For scattering vectors (q) lower than 1.3 X 10(5) cm-1, D0 can be separated from internal dynamics. Using the measured D0 value, the q dependence of internal modes was determined. Extrapolation of the internal relaxation times for q----0 yields the longest internal relaxation time t1. This time can be connected to the persistence length in terms of the Berg-Soda model, which describes the molecule as a semiflexible circular polymer with hydrodynamic interactions. The calculated length of 76 nm for DNA, I = 0.15 mol/L, is a little higher than the one obtained from static light scattering data without excluded volume corrections. A comparison of experimental and simulated correlation functions for the Berg-Soda model shows that the model gives a fairly good description of the dynamics of the linear molecule, whereas large discrepancies between model and experimental functions are observed for the superhelical DNA. Small differences between model and experimental functions are mainly attributed to the neglect of the torsional modes that may be coupled to bending and flexing modes. For the superhelical DNA the agreement is improved if the calculation is carried out with a linear molecule, with shorter contour length and increased diameter. Both quantities can be derived from the known superhelix tilt angle.

Miniature laser light scattering instrumentation for particle size analysis

We describe the design, construction, and testing of a miniature, all-solid state laser light scattering instrument for determination of particle sizes and distributions using photon correlation spectroscopy techniques (i.e., quasielastic or dynamic light scattering). Detailed comparative tests with standard photon correlation spectroscopy equipment are presented.

Birefringence of macromolecules. Wiener's theory revisited, with applications to DNA and tobacco mosaic virus

We summarize Wiener's theory of the dielectric constant of heterogeneous systems and extend its application to suspensions of particles with corrugated surfaces and interstitial solvent. We retain a simple geometrical shape for the particles and account specifically for the solvent associated with the particles. We calculate the birefringence of the rodshaped Tobacco Mosaic Virus (TMV) particle and of DNA and find excellent agreement between our numerical results and experimental values from the literature.

Size and structure of antigen-antibody complexes. Electron microscopy and light scattering studies

Size parameters of model antigen-antibody (Ag-Ab) complexes formed by the interaction of bovine serum albumin (BSA) and pairs of monoclonal anti-BSA antibodies (mAb) were evaluated by quasielastic light scattering, classical light scattering, and electron microscopy (EM). Mean values for the hydrodynamic radius, radius of gyration, and molecular weight were determined by light scattering. Detailed information regarding the molecular weight distribution and the presence of cycles or open chains was obtained with EM. Average molecular weights were calculated from the EM data, and the Porod-Kratky wormlike chain theory was used to model the conformational behavior of the Ag-mAb complexes. Ag-mAb complexes prepared from three different mAb pairs displayed significantly different properties as assessed by each of the techniques employed. Observations and size parameter calculations from EM photomicrographs were consistent with the results from light scattering. The differences observed between the mab pairs would not have been predicted by idealized thermodynamic models. These results suggest that the geometric constraints imposed by the individual epitope environment and/or the relative epitope location are important in determining the average size of complexes and the ratio of linear to cyclic complexes.

Electric linear dichroism and birefringence of biological polyelectrolytes

The phenomenon of electro-optic orientation was discovered by John Kerr in 1875 and has been used extensively for determining the optical polarizability anisotropy of small molecules and for high-speed transmission of optical signals. Measurements on biopolymers have been made at least since 1950, but only in the last decade have these yielded definitive structural and physical information. In the course of this review, it should become obvious that among the reasons for this late development is the inherent difficulty of analysing optical data that depend simultaneously on intrinsic optical-structural properties of the molecules, and on their degree of orientation under the conditions of the experiment. The problem has been particularly difficult far biopolymers such as the nucleic acids, whose polarization in an electric field is dependent on their special polyelectrolyte properties. These unique electrostatic properties are an important feature in the interpretation of the experimental observations.

Computer modelling of DNA structures involved in chromosome maintenance

Sequence-dependent DNA bending of synthetic and natural molecules was studied by computer analysis. Modelling of synthetic oligonucleotides and of 107 kb of natural sequences gave results which closely resembled published electrophoretic data, demonstrating the powerful predictive capacity of the procedure. The analysis was extended to the study of DNA structures involved in chromosome maintenance. Centromeric DNAs from yeast were found to have sequences in their functional elements which cause them to be unusually straight. Autonomous replicating sequences were found to have two structural domains, one consisting of unusually straight sequences surrounding the consensus and the other of bending elements in flanking DNA. In addition to a structural homology, centromeric and autonomous replicating sequences share common sequence elements. These observations show that computer modelling of natural sequences is a viable approach to the study of the biological implications of alternative DNA structures.

Solution structure of a short DNA fragment studied by neutron scattering

The solution structure of a DNA fragment of 130 base pairs and known sequence has been investigated by neutron small-angle scattering. In 0.1 M NaCl, the overall structure of the DNA fragment which contains the strong promoter A1 of the Escherichia coli phage T7 agrees with that expected for B-DNA. The neutron scattering curve is well fitted by that of a rigid rod with a length of 44 nm and a diameter of 2 nm. The results were confirmed by quasi-elastic light scattering and analytical centrifugation. The neutron measurements in H2O and D2O buffer reveal a cross-sectional inhomogeneity not detected by X-ray small-angle scattering. This inhomogeneity is caused by the hydration layer around the DNA core and not by the helical structure. The primary solvent shell has a density increased by at least 4-9% compared to bulk water.

Macromolecular assemblies of myosin

The self-assembly of myosin into filamentous structures is a highly cooperative and rapid process. Nevertheless, the presence of nonequivalent bonding interactions within the filament permits differential stabilization of several macromolecular assemblies of myosin under well-controlled ionic conditions in citrate/Tris buffer at pH 8.0. We have detected and characterized bipolar myosin minifilaments, myosin octamers, and tetramers by using light scattering, analytical ultracentrifugation, and viscosity techniques. These structures have molecular weights of 8.0 X 10(6), 3.9 X 10(6) g/mol, sedimentation coefficients of 32S, 22S, and 18S, and radii of gyration of 990 A, 890 A and 790, A, respectively. The similar radii of gyration indicate similar bipolar geometry for all these particles. The 32S minifilaments in 10 mM citrate/Tris buffer (pH 8.0) are the most stable species. The smaller 18S and 22S assemblies in 2 mM and 5 mM citrate/Tris, pH 8.0, are readily affected by low concentrations of KCl and fuse into the minifilament particles. The instability of the 18S and 22S forms of myosin assembly is also revealed by their titration with ATP. These structures are dissociated at lower ATP concentrations than the minifilaments and do not show the cooperative dissociation transitions characteristic of filaments and minifilaments. Sedimentation velocity analysis of the 18S and 22S species in the presence of ATP reveals the involvement of 10S myosin dimer in the dissociation of assembled myosin. The different forms of assembled myosin are discussed in the context of formation of myosin minifilaments.

Effects of DNA sequence and conformation on nucleosome formation

A simple theoretical analysis of the free energy balance controlling nucleosome formation shows that the specific effects of different DNA sequences and/or conformations observed in vitro are mainly due to their different elastic properties. A calculation of the elastic free energy required to fold DNA on histone octamers yields quantitative results rationalizing the experimental findings provided that: (i) the average helical repeat of DNA on nucleosomes is greater than 10.2 bp per turn, and (ii) poly[dG.dC] adopts an A-type conformation.

Dynamic light-scattering studies on thermal motions of native DNAs in solution

The basic character of dynamic light-scattering properties of native DNA was investigated on two DNA samples. The degree of non-single exponentiality of photocount correlation functions, C(t), and its dependence on K are quantitatively characterized by two methods. The spectral linewidth, Ts, determined from C(t) exhibits a K dependence near to but significantly different from the prediction for Rouse-Zimm (RZ) chains by Dubois-Violette and De Gennes: It is inferred from data on lambda-DNA that the exponent in the K dependence of the spectral linewidth for native DNA takes a value larger than 3 in the K region corresponding to the 'K3' region for RZ chains. These results are in good agreement with the prediction from the dynamic theory of semiflexible chains presented by one of us (K.S.). The apparent diffusion coefficients are fairly insensitive to DNA concentration and ionic strength at large K. On the other hand, it is indicated that the stiffness of native DNA may vary with temperature even in a temperature range substantially lower than that of melting.

Interaction of chromatin with NaCl and MgCl2. Solubility and binding studies, transition to and characterization of the higher-order structure

Chicken erythrocyte chromatin containing histones H1 and H5 was carefully separated into a number of well-characterized fractions. A distinction could be made between chromatin insoluble in NaCl above about 80 mM, and chromatin soluble at all NaCl concentrations. Both chromatin forms were indistinguishable electrophoretically and both underwent the transition from the low salt "10 nm" coil to the "30 nm" higher-order structure solenoid by either raising the MgCl2 concentration to about 0.3 mM or the NaCl concentration to about 75 mM. The transitions were examined in detail by elastic light-scattering procedures. It could be shown that the 10 nm form is a flexible coil. For the 30 nm solenoid, the assumption of a rigid cylindrical structure was in good agreement with 5.7 nucleosomes per helical turn. However, disagreement of calculated frictional parameters with values derived from quasielastic light-scattering and sedimentation introduced the possibility that the higher-order structure, under these conditions, is more extended, flexible, or perhaps a mixture of structures. Values for density and refractive index increments of chromatin are also given. To understand the interaction of chromatin with NaCl and with MgCl2, a number of experiments were undertaken to study solubility, precipitation, conformational transitions and binding of ions over a wide range of experimental conditions, including chromatin concentration.

Dynamics of Z-form DNA

The torsional and bending rigidities of Z-form DNA have been studied by nanosecond fluorescence anisotropy measurements of intercalated ethidium. The results suggested that Z-form DNA was considerably more flexible than B-form DNA. We have investigated the temperature dependence of the rigidity of B- and Z-form DNA and found that the temperature dependence of the torsional rigidity of Z-form DNA was remarkably lower than that of B-form DNA.

Hydrodynamic properties of human cervical-mucus glycoproteins in 6M-guanidinium chloride

Cervical mucins and fragments thereof were studied by sedimentation-velocity, rotatory viscometry and laser light-scattering performed as photon-correlation spectroscopy as well as low-angle total-intensity measurements. The Mr of the whole mucins is 10 X 10(6)-15 X 10(6), whereas fragments obtained after reduction of disulphide bonds ('subunits') have Mr 2.1 X 10(6)-2.9 X 10(6), depending on the method used. Subsequent trypsin digestion of subunits afforded glycopeptides with Mr approx. 0.4 X 10(6). The high frictional ratio for the whole mucins is interpreted as a large degree of expansion. The Stokes radius calculated from the diffusion coefficient is approx. 110nm for the whole mucins, which is in agreement with that estimated from the radius of gyration (130nm) by using the concept of the equivalent hydrodynamic sphere. The ratio of the concentration-dependence parameter for the reciprocal sedimentation coefficient (Ks) to the intrinsic viscosity ( [eta] ) for the whole mucins is 1.42, suggesting that the individual macromolecule occupies a spheroidal domain in solution. The relationship between [eta] and Mr for whole mucins, subunits and T-domains suggests that they are linear flexible macromolecules behaving as somewhat 'stiff' random coils. This conclusion is supported by the relationships between the sedimentation coefficients, the diffusion coefficients and the Mr. The hydrodynamic behaviour of the mucins is thus close to that expected for coiling macromolecules entrapping a lot of solvent, which is consistent with the postulated polymeric structure.

Polymeric structure of a high-molecular-weight glycoprotein from bovine cervical mucus

A 16 X 10(6)-Mr glycoprotein isolated from bovine oestrus cervical mucus when reduced under conditions where disulphide-bond cleavage is essentially quantitative produces chains whose Mr from light-scattering and from sedimentation and diffusion data is some 4 X 10(6)-5 X 10(6). Pronase digestion of the chains indicates that glycosylated sequences of Mr 0.3 X 10(6)-0.5 X 10(6) are interspersed with enzyme-susceptible non-glycosylated peptide sequences.

Chain flexibility and hydrodynamics of the B and Z forms of poly(dG-dC).poly(dG-dC)

The solution properties of the B and Z forms of poly(dG-dC).poly(dG-dC) have been measured by static and dynamic laser light scattering. The radius of gyration, persistence length, translational and segmental diffusion coefficients, and the Rouse-Zimm parameters have been evaluated. The persistence length of the Z form determined at 3 M NaCl is about 200 nm compared to 84 and 61 nm respectively for the B forms of poly(dG-dC).poly(dG-dC), and calf thymus DNA, both determined at 0.1 M NaCl. The data on persistence length, diffusion coefficients and the Rouse-Zimm parameters indicate a large increase in the chain stiffness of Z DNA compared to the B form. These results are opposite to the ionic strength effects on random sequence native DNAs, for which the flexibility increases with ionic strength and levels off at about 1 M NaCl.

The mechanism of thermal degradation of a high-molecular-weight glycoprotein complex from bovine cervical mucus

Gel-like oestrus bovine cervical mucus can be brought to the point of dissolution by thermal treatment. The glycoprotein complex so produced was isolated on CsCl density gradients, and found to be of a size comparable with that of a complex purified from mucus that had been brought to the point of dissolution by mild mechanical stirring. The latter material (GP-S) had a mol.wt. of 15.9 X 10(6) and was used to study further the effect of thermal treatment. Time and temperature lead to a gradual breakdown of GP-S, which is characterized by a single activation energy of 93.3 kJ/mol (22.3 kcal/mol) over the temperature range of 21-99 degrees C. The process responsible is thermal hydrolysis of peptide bonds, particularly next to aspartic acid residues. This conclusion is consistent with the appearance of aspartic acid as a new N-terminal amino acid and the activation energy of the process. After thermal degradation there is an increase in the buoyant density of GP-S and a change in the amino acid composition. These findings were found to be consistent with the loss of the naked peptide region and the preponderance of aspartic acid residues in this region. Thermal degradation therefore does not involve dispersion of non-covalent bonds, and indeed GP-S is quite unaffected by media commonly used to disperse such bonds.

Tissue structure and macromolecular diffusion in umbilical cord. Immobilization of endogenous hyaluronic acid

Diffusion of endogenous hyaluronic acid and 125I-labelled albumin, monitored by desorption from umbilical cord (Wharton's jelly) slices, was studied in relation to tissue structure. Diffusion of hyaluronic acid was Fickian and some two orders of magnitude slower than that in free solution. After treatment of tissue with trypsin which removes proteoglycan(s) and degrades glycoprotein microfibrils, hyaluronic acid mobility through the collagen fibril network that remains is increased by an order of magnitude. These findings indicate that the mobility of hyaluronic acid in tissue is reduced both by the collagen network and by the presence of proteoglycan(s) and/or microfibrils. Estimates of the reduction in mobility due to physical entanglements with the fibrillar networks show that these play a major role. The mobility of hyaluronic acid found for intact tissue is sufficient for it to permeate the extracellular space within its metabolic turnover time. Labelled albumin diffusion is intact tissue, on the other hand, is reduced by only some 30% relative to free solution. This is consistent with the approximate 10% reduction found for the polysaccharide-free tissue (given by the excluded volume fraction) and the approximate 20% reduction expected for the polysaccharides in the interstitial fluid. Similar effects appear to be involved in the mobility of endogenous diffusible proteins in tissue.

Solution scattering studies of dimeric and tetrameric spectrin

The structure of spectrin dimers and tetramers in solution has been examined by light, low-angle X-ray and neutron scattering. The results show a good correspondence between the solution dimensions of these molecules and their appearance in the electron microscope after shadowing. The scattering profiles are not compatible with an extended rod-like character, but reflect the presence of a considerable degree of bending. The radii of gyration of the dimer and tetramer were determined to be 170 and 375 A and the cross-section radii of gyration 14 and 12.3 A, respectively. Both are thus long, thin, rather bent molecules, and the tetramer is twice the length of the dimer.

Cross-correlation laser scattering

Cross-correlation between two detectors was applied to analyze laser light-scattering fluctuations. Laser scattering from random concentration fluctuations is spatially coherent over small angular areas that are inversely proportional in size to the dimension of the scattering volume. By cross-correlating scattering intensity fluctuations in different angles, the correlation due to relaxation of concentration fluctuations is practically eliminated, and correlations reflecting changes in the scattering from the individual particles can be enhanced. Rotational diffusion of assymetric particles, conformational relaxation of random coils, and association-dissociation dynamics are determined here using the above approach.

Molecular motion of DNA as measured by triplet anisotropy decay

We have used triplet anisotropy decay techniques to measure the internal flexibility and overall rotational motion of DNA, covering a time range from 15 ns to 200 mus. Nearly monodisperse DNA fragments 65--600 base pairs long were studied by using the intercalating dye methylene blue as a triplet probe. We found that the slow end-over-end tumbling of short DNA fragments (less than or equal to 165 base pairs) is as predicted for a rigid rod. As expected, a longer DNA fragment (600 base pairs) experiences slow segmental motion of its helix axis. We found that, at the earliest times, anisotropy decays more rapidly than expected for a rigid rod, suggesting that, when bound, methylene blue monitors fast internal motion of the helix. Since the rod-like end-over-end tumbling of short fragments rules out fast bending motions, we conclude that the fast components of DNA anisotropy decay are due to twisting motion of the helix, occurring with a time constant near 50 ns.