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  • 1
    Electronic Resource
    Electronic Resource
    Springer
    Journal of statistical physics 1 (1969), S. 41-55 
    ISSN: 1572-9613
    Keywords: DNA ; helical molecule ; computer simulation ; biopolymers ; Langevin equation ; bead-spring macromolecule ; polymer dynamics ; unwinding of DNA ; tensile relaxation ; Rouse-Bueche model
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Abstract This paper investigates the use of a high-speed computer to simulate the unwinding of DNA. A Langevin equation of motion for the well-known bead-spring statistical macromolecule is written in difference form. An appropriate set of boundary conditions is developed to simulate a helical molecule and the resulting set of rules for the motion of the chain elements is used to produce the strand unwinding. The unwinding appears to proceed via initial end-unwinding followed by progressive unwinding inward. The latter process appears to occur by diffusion of twist outward from the central portion of the macromolecule. A computer simulation, using the Langevin equation, of linear tensile relaxation is compared with the appropriate analytical solution via the Rouse treatment of polymer dynamics, good agreement being obtained. The helical results are compared both with tensile relaxation and with Crothers' (1964) analytical treatment of the unwinding problem, which is analogous to the well-known temperature diffusion problem. The tensile results and Crothers' results are identical in form, and agree quantitatively remarkably closely with the computer-simulated helical unwinding, although the helical unwinding is somewhat slower.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 7 (1969), S. 475-493 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The kinetics of denaturation of DNA have been studied by relaxation techniques. Examination of the terminal relaxation times for a variety of DNA's under a variety of conditions has shown that DNA denaturation is principally a hydrodynamically limited process. Measurements within the helix-coil transition have demonstrated that the experimentally measured terminal relaxation times are a function of the following: (1) position in the helix-coil transition; (2) ionic strength of the solvent; (3) solvent viscosity; (4) DNA concentration; (5) molecular weight; (6) number and position of single-strand breaks. The dependence of the terminal relaxation time on the above mentioned factors can be attributed to hydrodynamic effects. Thus a hydrodynamic model for DNA unwinding is required. The model which best fits the data involves the assumption of a rotational frictional coefficient independent of molecular weight. This assumption is suggested by the fact that the relaxation time is proportional to the first power of the molecular weight.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 12 (1973), S. 857-867 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A simple model is introduced to investigate the stability of a sedimenting entanglement. The sedimenting entanglement is represented by a sedimenting sieve. Solvent can pass through it, but single-chain molecules that flow into it become entangled and their flow decreases or, if permanent entanglements form, ceases entirely. With this model we are able to find the conditions under which the mass of a sedimenting entanglement remains constant, grows or decays to a stable value, grows beyond limit, or decays to the mass of a single chain. The theory is applied to the sedimentation of small concentrations of large chain molecules in solutions of small chain molecules in solutions of small chain molecules for the case in which the entanglements are long-lived. Equations are derived which, (1) give the stable entanglement mass as a function of rotor speed and concentration and, (2) for a given concentration predict the rotor speed at which the entanglement mass grows without limit. Numerical results for small concentrations of T2 DNA sedimenting in solutions of T7 DNA are presented.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 21 (1982), S. 2315-2316 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 1333-1335 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 1481-1502 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A Monte Carlo analysis is presented which establishes a relationship between the rotational diffusion coefficients and the flexibility (persistence length, P) of short, wormlike chains. The results of this analysis are presented in terms of experimentally observable quantities; namely, the rotational relaxation times for the field-free decay of optical anisotropy. The pertinent theoretical quantity is R, defined as the ratio of the longest rotational relaxation time of a wormlike chain to the transverse rotational relaxation time of a rigid cylinder having the same axial length (L) and segmental volume. R, so defined, is essentially independent of the axial ratio of the cylinder for any value of L/P within the range of validity of the present analysis (axial ratio 〉 20; 0.1 〈 L/P 〈 5). It is pointed out that P can be determined with reasonable accuracy even in the absence of a precise knowledge of the local hydrodynamic radius of the chain.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 271-285 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We report a calculation of the distribution of small ions around a charged cylinder representing a polyelectrolyte molecule in solution. The Monte Carlo method of Metropolis, Rosenbluth, and Teller was used to avoid the inaccuracies known to be associated with the Poisson-Boltzmann equation. The systems examined contained a long polyelectrolyte cylinder with charge parameter, χ, equal to 4.2, corresponding approximately to a DNA molecule. In one model, the cylinder had charges on its axis and an exclusion radius to the center of the small ions equal to 10 Å, while the small ions had various radii in the range from 1 to 10 Å and one or two protonic charges. Various systems were studied; some had one species of small ion alone, others had mixtures of different types. The results showed good agreement with the solution of the Poisson-Boltzmann equation when only the species with 1-Å radius was present, but considerable discrepancies appeared with larger ions as a result of excluded volume interactions between the latter. Deviations from the Poisson-Boltzmann equation also appeared when both positive and negative small ions were present; the deviations were in the direction of a higher concentration of both counter- and co-ions, but particularly co-ions, close to the polyelectrolyte. In another model, the charges were arranged along two helices on the surface of the cylinder; the resulting radial distribution of small ions was not much different from that found when the charges were situated on the axis. In all cases there was a striking accumulation of counterions in a layer of concentration exceeding 1 mol/L at the surface of the polyion.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 24 (1985), S. 1573-1593 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A theory of the electrophoresis of DNA through gels with large interfiber spacing, such as dilute agarose, is presented. We assume that the DNA molecule moves along its axis through a “tube” in a neutral gel under the influence of the electric field. The tube is random except for possible bias due to the effects of the field. When the field is small, we easily recover the inverse-length dependence of the mobility found previously by de Gennes and by Doi and Edwards. At higher fields, a new effect appears; the tube becomes oriented because the field biases the direction of the leading end of the chain as it moves to form an extension of the tube. This leads to an increase of the mobility with increasing field by adding a field-dependent but length-independent term to the mobility expression. In agreement with experiment, we find that the field effect can be important at fields as low as 1 V/cm and that the effect can seriously decrease the sensitivity of the mobility to chain length. We also examine the fluctuation of the migration distance, the degree of orientation induced by the field, and the transient effects occurring when the feld direction is rotated by a right angle.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
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  • 9
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A statistical thermodynamic treatment of thermally induced helix-coil transitions is formulated with the matrix method for an (ensemble) of system(s) in which one strand of a double helix consists of a homopolymeric polynucleotide and the other strand comprises a number of complementary oligonucleotides. Each oligonucleotide is considered to be completely bound to the longer chain when in the helical configuration and completely free from it when in the randomly coiled configuration. The case of partial binding; i.e., “dangling,” is treated in a later paper. Taken into account in both cases are intrachain “stacking” interactions between nearest neighbor residues and interchain hydrogen bonding.An approximate treatment of the characteristic equation of the formulation indicates that the reciprocal of the transition temperature (1/T0) is a linear function of the reciprocal of the degree of polymerization (D.P.) of the oligonucleotides. In the same approximation, 1/T0 is also a linear function of the negative logarithm of the absolute activity of the oligonucleotides. Transition curves obtained by exact calculation on a computer are presented for various degrees of polymerization of both the oligo- and polynucleotides. These curves show a sharpening of the transition with increasing D.P. of the long chain and the aforementioned reciprocal D.P. dependence of 1/T0.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 12 (1973), S. 869-876 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Zones of T2 DNA were sedimented through uniform solutions of T7 DNA to determine if the smaller DNA molecules would become entangled in the larger. No entanglement could be demonstrated even at high DNA concentrations. It is suggested that molecular entanglement is not responsible for the sudden loss of DNA from solution which occurs in high centrifugal fields. This communication also includes observations on the effects of rotor speed on the sedimentation behavior of DNA in high centrifugal fields, distortion of zone shape at high concentrations, and hydrodynamic interactions between DNA and MS2 bacteriophage particles.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
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