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Dive into the research topics where J. Michael Schurr is active.

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Featured researches published by J. Michael Schurr.


Biophysical Chemistry | 1980

Torsion dynamics and depolarization of fluorescence of linear macromolecules: II. Fluorescence polarization anisotropy measurements on a clean viral φ29 DNA

John C. Thomas; Stuart A. Allison; Carl J. Appellof; J. Michael Schurr

Abstract The decay of the fluorescence polarization anisotropy (FPA) of ethidium bromide bound to DNA has been studied over a range of time-spans from 18 ns to 120 ns with the aid of a picosecond dye laser. These FPA data have been fitted to three different functional forms: (1) the single-exponential-decay-plus-baseline employed by Wahl et al.; (2) the Initial Exponential Decay Zone formula of a recently developed rigid-rod and torsion spring model for the torsion dynamics of DNA; (3) the Intermediate Zone formula of that same model. At any fixed experimental time-span the formulas (2) and (3) provide slightly better fits than formula (1), but cannot be distinguished from each other by reduced chi-squaied values alone. However, only the Intermediate Zone formula fits the data from all different time-spans with the same set of physical parameters. The parameters determined for formulas (1) and (2) vary with the time-span of the experiment in a characteristic manner that can be rationalized in the event that the FPA actually follows the Intermediate Zone curve. The fact that the torsion dynamics for this DNA is well described by the Intermediate Zone formula discounts the possibility of distinct widely spaced torsion joints in such Clean DNAs. We are able to provide the first reliable value for the torsional rigidity of DNA, C = 1.29 ± 0.10 × 10 −19 dyne cm 2 in 0.01 M NaCl at 25° C.


Critical Reviews in Biochemistry and Molecular Biology | 1977

Dynamic Light Scattering Of Biopolymers And Biocolloid

J. Michael Schurr; Victor A. Bloomfield

AbstractOf the physical techniques available for the study of biopolymers and other macromolecular and colloidal systems, dynamic light scattering is, perhaps, the most fascinating. The very idea of extracting useful dynamical and structural information from random fluctuations in the intensity of light scattered from otherwise unperturbed equilibrium solutions1-3 seems, at first glance, almost too good to be true. Indeed, for fragile preparations that are prone to suffer undesirable fates at the slightest change in solution conditions, dynamic light scattering may be the perfect technique. It is nondestructive, relatively rapid, and typically requires only modest amounts of material. In routine applications, even on unfamiliar samples, the dust-removal procedure (either gravity flow Millipore ® filtration or low-speed centrifugation) requires 10 to 20 min, and determination of the translational diffusion coefficient to an accuracy of a few percent, or less, requires 5 min. Verification that the dynamical...


Chemical Physics | 1980

A theory of electrolyte friction on translating polyelectrolytes

J. Michael Schurr

Abstract Enormous increases in friction factors of isolated polyelectrolytes have been observed when the concentration of added monovalent salt is decreased below 10−2M. Electrolyte friction on translating polyions, analogous to dielectric friction on translating small ions, is postulated to account for this effect. A quantitative theory of this electrolyte friction is developed, based on the fluctuating force formulation of Kirkwood and Previous development of the author for the dynamics of smallion concentration fluctuations. By modelling the flexible linear polyelectrolyte as a charged gel sphere of constant radius equal to the measured hydrodynamic radius in 1.0 M NaBr, where electrolyte friction is negligible, and employing the theory of Harris and Rice to determine the net charge on the sphere, remarkably good agreement with the data is obtained using no adjustable parameters. Polyion expansion of only a few percent would make the agreement perfect. Diffusion of polyions at finite concentration is discussed in the light of the present work, and it is suggested that an appropriate reinterpretation of parameters in the existing theories can account for the observed dependence of the measured diffusion coefficients on salt and polyion concentration in the linear range.


Chemical Physics | 1984

Rotational diffusion of deformable macromolecules with mean local cylindrical symmetry

J. Michael Schurr

Abstract A simple diffusion equation is derived for the rotational brownian motions of a single rod element in a deformable macromolecule with mean local cylindrical symmetry. The effective diffusion coefficients for rotations about the local symmetry and transverse axes are expressed in terms of the time-dependent mean-squared angular displacements about those body-fixed axes. The Greens function of the diffusion operator and the correlation functions of the Wigner rotation matrix elements are likewise evaluated in terms of those same quantities. A simple general expression is presented for the fluorescence polarization anisotropy of any macromolecule with parallel absorption and emission dipoles, and its relation to the correlation functions measured in other incoherent, and coherent experiments, including transient photodichroism, is discussed. The fluorescence polarization anisotropy of macromolecules with mean local cylindrical symmetry is expressed in terms of its twisting, tumbling, and internal correlation functions. The anisotropy formula of Barkley and Zimm is shown to be incorrect unless either the helix axis is immobile, or the time is very small and the transition dipole lies along the helix axis. The internal and twisting correlation functions are formulated in a computationally practical way for models of uniform filaments of arbitrary length and uniform rigidity. Both empirical and theoretical approaches to the tumbling correlation function are also described. The twisting correlation function for a filament constrained to girdle the equator of a sphere is presented in a computationally practical form.


Biophysical Journal | 1970

The Role of Diffusion in Bimolecular Solution Kinetics

J. Michael Schurr

An appropriate boundary condition is derived which permits both the bimolecular association and dissociation steps to be simultaneously treated within the framework of the theory of Smoluchowski, Debye, and Collins, and Kimball. Kinetic theory expressions are derived for the intrinsic rate constants. The transient case of the suddenly switched-on reaction is considered as well as the suddenly perturbed equilibrium, but only the time dependence of the rate constants is obtained. The frequency response spectrum for a diffusion-controlled reaction is obtained in the linear approximation and compared with the corresponding Debye relaxation spectrum.


Biopolymers | 1997

The question of long‐range allosteric transitions in DNA

J. Michael Schurr; Jeffrey J. Delrow; Bryant S. Fujimoto; A. Steven Benight

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.


Biophysical Chemistry | 1991

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

Peng Guang Wu; Bryant S. Fujimoto; Lu Song; J. Michael Schurr

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.


Journal of Molecular Biology | 1990

Evidence for allosteric transitions in secondary structure induced by superhelical stress

Lu Song; Bryant S. Fujimoto; Pengguang Wu; John C. Thomas; John H. Shibata; J. Michael Schurr

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)


Journal of Chemical Physics | 1983

Electrophoretic light scattering studies of poly(L‐lysine) in the ordinary and extraordinary phase. Effects of salt, molecular weight, and polyion concentration

Jess Wilcoxon; J. Michael Schurr

Electrophoretic light scattering (ELS) is employed to determine the electrophoretic mobilities μE and apparent diffusion coefficients DELS obtained from ELS linewidths for three samples of poly(L‐lysine)HBr (PLL) of degree of polymerization n=406, n=946, and n=2273 as a function of salt (Cs) and polyion (Cp) concentration. Dynamic light scattering (DLS) is used to determine apparent diffusion coefficients Dapp of these same PLL samples in the absence of the applied field. The polyelectrolyte system exhibits an ordinary to extraordinary phase transition at low salt concentrations that is manifested by a more than 50‐fold decrease in Dapp as well as a twofold decrease in scattered intensity. In the extraordinary phase, the DELS values are typically very small, though still somewhat (frequently twofold) larger than Dapp. When the salt concentration is raised to enter the ordinary phase DELS remains small, less than one tenth of Dapp, in the low‐salt end of the ordinary phase, but increases with increasing Cs...


Time-Resolved Laser Spectroscopy in Biochemistry IV | 1994

Fluorescence and photobleaching studies of methylene blue binding to DNA

Bryant S. Fujimoto; James B. Clendenning; Jeffrey J. Delrow; Patrick J. Heath; J. Michael Schurr

Complexes of methylene blue with DNA are characterized by time- resolved fluorescence spectroscopy and transient photobleaching methods. At least four, and probably five, spectroscopically distinct binding sites have been identified. Three of these (components 1, 2, and 3B) dominate the fluorescence decay at low ionic strength and have fluorescence lifetimes significantly different from that of the free dye. With increasing ionic strength a fourth component (3A) appears at the expense of components 1 and 3B. Component 3A exhibits two subcomponents with different degrees of shielding from O2 quenching of its triplet state. The relative amplitudes of the components at low ionic strength are strongly dependent on the composition of the DNA, and independent of superhelix density. Hence, it is inferred that components 1, 2, and 3B represent binding to different base pair steps, and that all of these components represent intercalation sites that unwind the DNA to the same degree. Component 3A is apparently not intercalated. From plots of the relative photobleach amplitudes versus the relative fluorescence intensities, we infer that the triplet yield and photobleach amplitude are dominated by components 3A and/or 3B under nearly all conditions. Our results are used to discuss the suitability of methylene blue as the extrinsic probe in transient photodichroism experiments.

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Lu Song

University of Washington

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Jeffrey J. Delrow

Fred Hutchinson Cancer Research Center

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John A. Gebe

Benaroya Research Institute

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