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Biomedical subjects

C J Benham

Publications and source records attributed to C J Benham.

At least 37 records · Page 2Linked to original sources
PubMed1991

Negative supercoiling increases the sensitivity of plasmid DNA to single-strand break induction by X-rays.

Negatively supercoiled topoisomers of the plasmid pIBI 30 were irradiated with 250 kV X-rays and assayed for strand scission by agarose gel electrophoresis. The survival of supercoiled molecules (Form I) decreased exponentially with increasing X-ray exposure and the dose required to reduce the fraction of DNA in Form I to 37% of its value in unirradiated controls (D37) decreased with increasing negative superhelicity. This enhanced radiation sensitivity of underwound DNA is tentatively attributed to the transient denaturation of the double helix that increases the susceptibility of individual strands to free radical attack.

DNA Damage↗
PubMed1987

The influence of tertiary structural restraints on conformational transitions in superhelical DNA.

This paper examines theoretically the effects that restraints on the tertiary structure of a superhelical DNA domain exert on the energetics of linking and the onset of conformational transitions. The most important tertiary constraint arises from the nucleosomal winding of genomic DNA in vivo. Conformational transitions are shown to occur at equilibrium at less extreme superhelicities in DNA whose tertiary structure is restrained than in unrestrained molecules where the residual linking difference alpha res (that part of the superhelical deformation which is not absorbed by transitions) may be freely partitioned between twisting and bending. In the extreme case of a rigidly held tertiary structure, this analysis predicts that the B-Z transition will occur at roughly half the superhelix density needed to drive the same transition in solution, other factors remaining fixed. This suggests that superhelical transitions may occur at more moderate superhelical deformations in vivo than in solution. The influence on transition behavior of the tertiary structural restraints imposed by gel conditions also are discussed.

Base Sequence↗
PubMed1987

Environmental influences on DNA superhelicity. The effect of ionic strength on superhelix conformation in solution.

The techniques of small-angle X-ray scattering and analysis that have been developed by the authors are used to investigate the influence of ionic strength on the superhelical conformation of native COP608 plasmid DNA in solution. For salt concentrations below 0.1 M, the superhelicity is partitioned between twisting (Tw) and writhing (Wr) in the ratio delta Tw/Wr = 2. Near the physiological salt concentration, [Na+] = 0.2 M, a co-operative transition is observed in which the pitch angle of the toroidal superhelix is drastically decreased. This results in an almost complete relaxation of writhe. At salt concentrations in excess of the threshold for this transition, the superhelical partitioning occurs in the ratio delta Tw/Wr greater than 25. Energetic considerations support the suggestion that this transition results from co-operative, superhelical B to Z transconformation reactions at susceptible sites. A method is discussed that will enable the direct measurement of this secondary structural transition by means of X-ray scattering.

DNA, Superhelical↗
PubMed1987

Energetics of superhelicity and of B-Z transitions in superhelical DNA.

The linking difference, alpha, imposed upon a superhelically constrained DNA molecule must be partitioned between twisting and bending deformations. Transitions to alternative secondary structures can occur at susceptible sites, altering the local molecular twist by an amount delta Twtrans. That part of the linking difference not accommodated in this way, the residual linking difference alpha res, must be manifested as smooth torsional and flexural deformations of secondary structure. The competition among the alternative ways of accommodating the imposed linking difference alpha determines a stressed equilibrium state. The superhelical free energy, G(alpha), is the excess free energy of the equilibrium state at linking difference alpha above that of the relaxed state under identical conditions. In this paper a method is described by which the free energies associated both to linking, G(alpha), and to residual linking differences can be determined from data on superhelical conformational transitions. The application of this approach to previously published experimental data on the B-Z transition suggests that the free energy associated with alpha res is about 30% larger at substantial superhelicities than it is near the relaxed state. At the onset of transition the functional form of G(alpha) is shown to change in a manner dependent upon the length of the Z-susceptible site.

DNA, Superhelical↗
PubMed1983

X-ray scattering from the superhelix in circular DNA.

This communication presents measurements, made with a newly constructed position-sensitive detector, of the small-angle x-ray scattering from the first-order superhelix of native COP608 plasmid DNA. This instrument measures intensities free of slit effects and provides good resolution in the region of interest. The reported observations, made both in the presence and in the absence of intercalator, closely fit the scattering patterns calculated for noninterwound helical first-order superhelices. These results are consistent with a toroidal helical structure but not with interwound conformations. The pitch angle alpha and contour length per turn c are reported for the native molecule at several concentrations of the platinum intercalating compound. From these parameters, the best-fitting toroidal helix is constructed and its geometry is investigated. The specific linking difference of the native molecule is estimated to be delta Lk/Lk0 approximately equal to -0.055. If the best-fitting toroidal helix is taken to be the actual structure, the partitioning of superhelicity between twist and writhe occurs in the approximate ratio of 2:1.

DNA, Superhelical↗
PubMed1980

X-ray scattering from randomly oriented superhelices. Circular superhelical DNA.

The scattering functions of randomly oriented filaments of finite length exhibiting two orders of helicity have been calculated. It is shown to a good approximation that each order scatters as if present alone as a first order helix of the same contour length and pitch angle. These results show that the measured scattering pattern from dissolved superhelical DNA molecules is consistent with the scattering pattern calculated for a coiled coil geometry.

DNA, Bacterial↗