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Generation of Superhelical Torsion by ATP-Dependent Chromatin Remodeling Activities [PDF]
Cell, 2000 ATP-dependent chromatin remodeling activities participate in the alteration of chromatin structure during gene regulation. All have DNA- or chromatin-stimulated ATPase activity and many can alter the structure of chromatin; however, the means by which ...
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Internal Dynamics of Superhelical DNA
Physical Review Letters, 2008We present the first data on the temporal kinetics of monomer mean square displacements in DNA circles with defined degrees of superhelicity. The segmental dynamics of specifically labeled DNA plasmids with superhelical densities between 0 and -0.016 was assessed by fluorescence correlation spectroscopy.
Roman, Shusterman +2 more
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Surface-Induced DNA Superhelicity
Biomacromolecules, 2000Certain biopolymers, such as DNA, have a double-stranded twisted structure and frequently exhibit a supercoiled conformation. Over the past decade, extensive conformational analyses of different biopolymers have been performed using atomic force microscopy.
Y S, Velichko +2 more
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Replication of Superhelical DNAs in Vitro
1986Publisher Summary This chapter discusses purified systems that can replicate closed-circular, double-stranded superhelical (form I) DNAs in vitro . It also discusses problems unique to the replication of DNAs under topological constraint. Studies on the reconstituted pBR322 DNA replication system are used as a guide in the chapter. Recent studies on
K J, Marians, J S, Minden, C, Parada
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Prokaryotic DNA Ligases Unwind Superhelical DNA
Biochemical and Biophysical Research Communications, 1996We have studied the effect on DNA topology of binding of prokaryotic DNA ligases (T4 and E. coli) to superhelical or nicked circular DNA. Performing topoisomerase I-mediated relaxation in the presence of increasing amounts of T4 ligase led to a shift in the topoisomer distribution to increasingly more negative values.
M, Ivanchenko +2 more
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Electrostatic effects in short superhelical DNA
Biophysical Chemistry, 1994We present Monte Carlo simulations of the equilibrium configurations of short closed circular DNA that obeys a combined elastic, hard-sphere, and electrostatic energy potential. We employ a B-spline representation to model chain configuration and simulate the effects of salt on chain folding by varying the Debye screening parameter.
M O, Fenley +3 more
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Energetics of superhelicity and of B-Z transitions in superhelical DNA
Cell Biophysics, 1987The 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.
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Effect of DNA superhelicity on transcription termination
Molecular and General Genetics MGG, 1987Restriction fragments containing either leut (a rho-independent transcription termination site) and/or leut' (a rho-dependent transcription termination site) were cloned into plasmid pOL4. Treatment of plasmid-containing Escherichia coli strains with coumermycin resulted in loss of in vivo plasmid superhelicity 10 min after antibiotic addition ...
E R, Rosenthal, J M, Calvo
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Superhelicity and DNA Radiation Sensitivity
SAE Technical Paper Series, 1990<div class="htmlview paragraph">Several underwound families of topoisomers of the plasmid pIB130 were irradiated with fission neutrons at 28 C in TE buffer. Form I DNA followed the expected exponential dependence on dose, and was greater for those DNA molecules characterized by larger linking numbers.
Charles E. Swenberg +2 more
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Geometry and mechanics of DNA superhelicity
Biopolymers, 1983AbstractThis paper analyzes the elastic equilibrium conformations of duplex DNA constrained by the constancy of its molecular linking number, Lk. The DNA is regarded as having the mechanical properties of a homogeneous, linearly elastic substance with symmetric cross section.
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