Salt induced transitions of chromatin core particles studied by tyrosine fluorescence anisotropy

Libertini, Louis J.; Small, Enoch W.

doi:10.1093/nar/8.16.3517

Cited by 99 publications

(77 citation statements)

References 44 publications

(37 reference statements)

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“…The wrapped phase can occur again with a minimum chain length and salt screening parameter (e.g., for fixedZ = 1 and for a mechanically flexible chain, these minimum values are given byL = L/R s = 5.57 andκ = κR s > 1, respectively). The wrapped phase is thus predicted to occur at intermediate salt concentrations or sufficiently large sphere charge in agreement with previous studies [37, 38, 63, 67, 68, 70-72, 78, 95] and also recent experiments [1,3,11,16,17,44,45,[79][80][81][82][83][84][85][86][87].…”

Section: Conclusion and Discussionsupporting

confidence: 89%

“…It was shown that a minimal chain-sphere model for nucleosome core particles [37][38][39][40][41]51] can closely predict the experimentally observed [79][80][81][82][83][84][85][86][87] salt-induced wrapping-unwrapping behavior of these complexes based on an interplay between two competing mechanisms: the electrostatic attraction of DNA (modeled as a negatively charged worm-like chain) with the histone core (modeled as a positively charged nano-sphere), which favors DNA adsorption and wrapping around the sphere, and the mechanical bending stiffness of the DNA and its electrostatic self-repulsion, which favor unwrapping and even dissociation of the DNA from the complex. The experimental stability diagrams [45] also exhibit an association (or complexation) equilibrium between nucleosome core particles and the free DNA and free histones in an electrolyte solution in the regime of moderately large values of core particle and salt concen-tration.…”

Section: Introductionmentioning

confidence: 95%

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Global analysis of the ground-state wrapping conformation of a charged polymer on an oppositely charged nano-sphere

2014

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We investigate the wrapping conformations of a strongly adsorbed polymer chain on an oppositely charged nano-sphere by employing a reduced (dimensionless) representation of a primitive chainsphere model. This enables us to determine the global phase behavior of the chain conformation in a wide range of values for the system parameters including the chain contour length, its linear charge density and persistence length as well as the nano-sphere charge and radius, and also the salt concentration in the bathing solution. The phase behavior of a charged chain-sphere complex can be described in terms of a few distinct conformational symmetry classes (phases) separated by continuous or discontinuous transition lines which are determined by means of appropriately defined (order) parameters. Our results can be applied to a wide class of strongly coupled polymer-sphere complexes including, for instances, complexes that comprise a mechanically flexible or semiflexible polymer chain or an extremely short or long chain and, as a special case, include the previously studied example of DNA-histone complexes.

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Section: Conclusion and Discussionsupporting

confidence: 89%

Section: Introductionmentioning

confidence: 95%

Global analysis of the ground-state wrapping conformation of a charged polymer on an oppositely charged nano-sphere

2014

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Section: Methodsmentioning

confidence: 99%

“…In a few experiments, 10 mM Tris/HCl (pH 7.5) was used; the structures observed in Tris buffer were indistinguishable from those in triethanolamine buffer. When desired, chromatin was stripped of histones H1 and H5 (29).Glutaraldehyde fixation of chromatin in the various salt concentrations was done as described (8,30); the fixed preparations were dialyzed extensively versus triethanolamine buffer and were stored on ice.Scann-ng Force Mkroscopy (SFM) Imain. Fibers were deposited on cover glass cleaned by prebaking for 5 min at 600°C.…”

mentioning

confidence: 99%

Three-dimensional structure of extended chromatin fibers as revealed by tapping-mode scanning force microscopy.

Leuba

Yang

Robert

et al. 1994

Proc. Natl. Acad. Sci. U.S.A.

233

159

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Unfixed chicken erythrocyte chromatin fibers in very low salt have been imaged with a nning force microscope operating in the tapping mode in air at ambient humidity. These images reveal a threedimensional organizaffon of the fibers. The planar "6zig-zag" conformation is rare, and extended "beads-on-a-string" fibers are seen only in chromatin depleted of histes Hi and H5. Glutaraldehyde fixation reveals very similar structures. Fibers fixed in 10 mM salt appear somewhat more compacted. These results, when compared with modeing stude, suggest that chromatin fibers may exist as frregular three-dimensional arrays of nucleosomes even at low ionic strength.The structure of the chromatin fiber in low salt concentrations remains controversial. Electron microscopy (EM) experiments, most of which utilized the Miller spreading technique (1), typically showed extended "beads-on-a-string" or "open zig-zag" structures (refs. 2 and 3; for reviews, see refs. 4-6). At slightly higher ionic strength (-10 mM NaCI), somewhat more compact, "closed" zig-zags of nucleosomes were observed (7-9). Only upon further addition of NaCl to about 100 mM did these extended structures condense to form the so-called 30-nm fiber (8), which resembles structures observed in situ (7, 9, 10). However, there has been concern that strong interactions of the fiber with the EM support surface, and the dehydration produced by the high vacuum conditions, could distort the structure, especially at low ionic strength.Attempts to circumvent these problems used solution studies. The first scattering experiments suggested that the nucleosomes were densely packed in a linear array (11,12 To address this controversy, a study was performed using the three-dimensional imagi capabilities ofa scanning force microscope, which makes it possible to image chromatin fibers under less damaging conditions (22,23). The samples are never vacuum dried and are scanned in air at about 50%o relative humidity. Under these conditions a film of liquid water resides on the support surface (24). The newly developed tapping operation mode (25, 26) was employed, in which a stiff cantilever is oscillated near its resonance frequency with amplitudes typically in the range of 10-20 nm as the sample is scanned laterally. The oscillation amplitude is kept constant via feedback control. This operation has several advantages over the contact mode, in which a tip is pulled across the sample. Tip-sample forces are lighter than in the contact mode. Moreover, since most of the force is perpendicular to the surface, the sample experiences minimal lateral deformation during scanning, thus improving spatial resolution (25, 26). MATERIAL AND METHODSPreparation and Fization of Chromatin. Chicken erythrocyte chromatin was prepared essentially as described (27), with a reduction in the amount of micrococcal nuclease to allow isolation of long fibers (28). Soluble chromatin was dialyzed versus 5 mM triethanolamine/HC1 (pH 7.0), with or without 10 mM NaCl and was stored on ice. In a few experiments...

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“…Chromatin (0.1 mg/ml) in the above buffers, containing 0, 10, or 80 mM NaCl, was fixed with 0.1% (vol/vol) glutaraldehyde overnight at 49C and then dialyzed extensively versus 10 mM Tris/HCI (pH 7.5) and stored on ice. Chromatin depleted ofhistones Hi and H5 was obtained by stripping the linker histones with 0.35 M NaCl in the presence of CM-Sephadex C25 (Pharmacia) (6).…”

Section: Chicken Erythocyte Crmentioning

confidence: 99%

Linker DNA accessibility in chromatin fibers of different conformations: a reevaluation.

Zlatanova

Leuba

Yang

et al. 1994

Proc. Natl. Acad. Sci. U.S.A.

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New studies on chromatin fiber morphology, using the tehque of s ig force microscopy (SFM) Micrococcal nuclease (MNase) has been widely used for the study of chromatin structure. It preferentially attacks the linker regions between nucleosomes to give the well-known "ladder" patterns corresponding to DNA fragments which are of multiples of nucleosomal length (1, 2). Usually, however, the enzymatic digestion has been performed under conditions which led to rapid degradation of the fiber. Under such circumstances, subtle effects of fiber structure on the digestion might be obliterated. In an attempt to look for possible differences in the accessibility of the linker DNA in soluble chromatin fibers of different conformation, we have recently performed a systematic study using extremely mild digestion conditions (3). Long chromatin fibers from chicken erythrocytes were brought to different states of compaction by increasing the concentration of monovalent ions. Digestions were performed with extremely low enzyme concentrations, in the absence of added Ca2+ ions. Under such conditions, the "extended" fiber conformations which exist at low salt were readily digested with both soluble and membrane-immobilized MNase, whereas the compact fiber present at high salt proved to be almost refractory to nucleolytic attack. The results were interpreted in the light of the then-existing models ofchromatin fiber structure in solutions of different ionic strengths: open zig-zag, closed zig-zag, and 30-nm fiber.,

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Salt induced transitions of chromatin core particles studied by tyrosine fluorescence anisotropy

Cited by 99 publications

References 44 publications

Global analysis of the ground-state wrapping conformation of a charged polymer on an oppositely charged nano-sphere

Global analysis of the ground-state wrapping conformation of a charged polymer on an oppositely charged nano-sphere

Three-dimensional structure of extended chromatin fibers as revealed by tapping-mode scanning force microscopy.

Linker DNA accessibility in chromatin fibers of different conformations: a reevaluation.

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