Conformational changes associated with f-1 histone-deoxyribonucleic acid complexes. Circular dichroism studies

Fasman, Gerald D.; Schaffhausen, Brian; Goldsmith, Lisa B.; Adler, Alice J.

doi:10.1021/bi00816a010

Cited by 189 publications

(118 citation statements)

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“…A single negative band at 275 nm, such as that found here in the calculated difference spectra, has previously been observed for DNA under several conditions. Examples are I DNA (36), DNA-H1 complexes (23), and DNA-poly(L-lysine) complexes (37). In each-of these cases, the secondary structure of the DNA remains of the B type (32,37), but the DNA is condensed into a compact, possibly microcrystalline, arrangement.…”

Section: Resultsmentioning

confidence: 99%

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Circular dichroism analysis of mononucleosome DNA conformation.

Cowman¹,

Fasman²

1978

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

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Mononucleosomes were isolated from micrococcal nuclease digests of chicken erythrocyte nuclei. The circular dichroism properties of mononucleosome preparations, differing in average DNA length and in Hi and H5 content, demonstrate that the spectrum of chromatin is due only to the complete structure of its repeating subunits. The nucleoprotein spectra are all altered relative to rotein-free DNA by the emergence of a single negative band at 275 nm, similar to the band observed for * DNA. The intensity of the +-type band depends on the prop rtion of DNA condensed in a specific manner. The *-type and is proposed to be due to the compact DNA tertiary structure; i.e., the manner in which the DNA is wound around the histone core allowing interactions between adjacent turns of the superhelix. This interpretation attributes changes and variability in nucleoprotein circular dichroism spectra under different experimental conditions to alterations in DNA tertiary structure rather than secondary structure. Evidence has been accumulated that indicates that the folding of DNA in chromatin involves several levels of organization. First, DNA is condensed by a histone octamer into compact subunits, or nucleosome cores. The cores contain approximately 140 base pairs of DNA and two each of the histones H2A, H2B, H3, and H4 (for reviews see refs. 1 and 2). The cores are connected by "linker" DNA regions, the lengths of which are variable and with which the very lysine-rich histone H1 (and H5 in avian erythrocytes) interacts. This level of DNA organization corresponds to the "beads-on-a-string" structure (3). The second level of organization is the 100-A nucleofilament, in which adjacent nucleosome cores are presumably in contact, and the linker DNA is condensed (3-5). The third level of organization is the 250 to 300-A diameter chromatin fiber, proposed to be a solenoidal arrangement of the 100-A nucleofilament (4-7). The second and third organizational levels depend on the presence of H1 and/or salts (4-6).We have been interested in the possibility that the circular dichroism (CD) spectrum of DNA is sensitive not only to changes in secondary structure (base tilt, twist, etc.), but also to the higher levels of DNA organization in chromatin (8,9). In the latter case, the DNA secondary structure could remain within the B family of conformations, but the change in tertiary structure might result in an altered CD spectrum. The CD spectrum of DNA in chromatin is substantially reduced in intensity relative to protein-free DNA. There is some variability in the reported extent of this alteration (7, 10-13). For isolated core particle mononucleosomes, reports agree that the CD spectrum shows a maximum ellipticity which is less than onefourth that of protein-free DNA (8,14,15). The overall reductions in ellipticity measured for both chromatin and mononucleosome core particles are accompanied by subtle changes in band shape and wavelength in the spectra.We have examined the CD properties of mononucleosomes having varying linker DNA le...

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Section: Resultsmentioning

confidence: 99%

“…Absorption measurements were made with a Cary 14 spectrophotometer. CD spectra were recorded at 23°C with a Cary 60 and the 6001 circular dichroism accessory, as described (23).…”

Section: Methodsmentioning

confidence: 99%

Circular dichroism analysis of mononucleosome DNA conformation.

Cowman¹,

Fasman²

1978

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

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“…Circular dichroism (CD) studies, although at one time devoted to simple molecules (1, 2), have recently been focused upon a variety of complex biological macrostructures. Much promising CD work has been contributed on the molecular conformation of DNA in chromosomes (3), chromatin (4-12), and related material, such as reconstituted nucleohistone (13)(14)(15)(16)(17)(18)(19) (25-27, 29, 30, 32, 33, 35), other concentration-obscuring effects (30, 32, 33), and differential light scattering (25,26,29,(31)(32)(33). It is the last of these with which we are concerned.…”

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confidence: 99%

Experimental Differential Light-Scattering Correction to the Circular Dichroism of Bacteriophage T2

Dorman

Maestre

1973

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

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Experimental techniques are presented that can be used to assay and correct for differential light scattering effects in circular dichroism spectra of biological macrostructures. The assay is based upon use of variable detector geometries that collect light over large solid angles. Disrupted T2 virus suspensions and purified T2 phage DNA exhibit geometry-independent spectra; the spectrum of intact T2 virus is highly sensitive to detection geometry. On the basis of spectra obtained after light-scattering correction, the structure of T2 DNA in the phage particle is assigned to the C form. We conclude that: (i) The measured circular dichroism of a light-scattering specimen may be highly sensitive to light-detection geometry of the instrument. This effect is indicative of differential scattering intensity for left and right circularly polarized light. (ii) Some optically active particles, although they scatter light intensely, exhibit circular dichroism that is independent of detection geometry and, therefore, apparently uninfluenced by differential light scattering. We infer that whether differential light scattering arises may depend upon the presence or absence of ordered asymmetry in the organization of the scattering particle. (iii) The circular dichroism of any light-scattering specimen should be measured again in apparatus designed for differential light-scattering correction as a prerequisite to meaningful structural conclusions. (iv) Differential scattering effects in circular dichroism may be potentially useful as a probe for large-order organization of the scattering particle. Circular dichroism (CD) studies, although at one time devoted to simple molecules (1, 2), have recently been focused upon a variety of complex biological macrostructures. Much promising CD work has been contributed on the molecular conformation of DNA in chromosomes (3), chromatin (4-12), and related material, such as reconstituted nucleohistone (13)(14)(15)(16)(17)(18)(19) (25-27, 29, 30, 32, 33, 35), other concentration-obscuring effects (30, 32, 33), and differential light scattering (25,26,29,(31)(32)(33). It is the last of these with which we are concerned. (35)(36)(37)(38)(39) have appeared, and some experimental work has been presented (25,26,29,31,32) or proposed (37, 38) for particular applications.We now report a quite general experimental approach to assay the presence of differential light scattering and to correct for its effects on measurements in a circular dichrograph.The proposed assay involves determination of whether the observed CD spectrum varies with changes in the light-collection geometry of the spectropolarimeter. The collection geometry may be described in terms of the position, size, and shape of the light-detection element relative to the incident measuring beam and the sample cell.As a basis for later discussion, we consider first the measurement of normal, unpolarized light absorption spectra.For a photomultiplier tube (PMT) detector located on the optical axis, and with a sufficiently collim...

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“…A structural transition on decreasing the ionic strength of the medium was also observed with complexes reconstituted from DNA and from the lysine-rich fraction F1 [4,5]. This histone fraction appears to be very interesting since it differs significantly in its properties from other fractions [6] and some authors assume that it substantially affects the structure of chromosomes [7].…”

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Complexes of Histone F1 with DNA in 0.15 M NaCl

Šponar

Šormová

1972

European Journal of Biochemistry

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Aggregated complexes of histone F1 with DNA of different composition and origin were prepared by gradual dialysis from a high salt concentration to 0.15M NaCl. Analysis of the DNA composition both in the supernatant and in the precipitate showed that in equilibrium complexes in this medium, histone Fl selectively prefers sequences of native DNA rich in adenine and thymine. The mechanism of the selective binding is discussed.Study of complexes reconstituted from isolated DNA and from histone fractions represents one of the possible approaches to the investigation of the structure of chromatin and of chromosomes. Progress in this field appears t o be essential for a better understanding of the mechanism of genetic processes in higher organisms. It was pointed out before [1,2] that the hydrodynamic and the optical properties of native and reconstituted complexes in their soluble form tally. It is an advantage of the reconstitution procedure that one can independently alter the character of the components of the complex, to study their interaction and the effect on the final structure of the complex.Recently the view was advanced [3] that native nucleohistone molecularly dispersed at Iow ionic strength partly loses the assumed superhelix structure. A structural transition on decreasing the ionic strength of the medium was also observed with complexes reconstituted from DNA and from the lysine-rich fraction F1 [4,5]. This histone fraction appears to be very interesting since it differs significantly in its properties from other fractions [6] and some authors assume that it substantially affects the structure of chromosomes [7].In the present paper we studied the interaction of histone F1 with DNA of different composition and origin in a medium of approximately physiological ionic strength (0.15M NaC1). It was intended to contribute to the elucidation of the origin of specific complexes of histone F1 * DNA under conditions resembling those in vivo and hence to contribute to determining the biological function of this histone fraction. A similar problem was examined in a greater number of papers [S] and some of their results indicate that a certain specificity of the binding of Abbreviation. CD, circular dichroism. 7.histones to DNA exists [9,10]. It was of interest in this context to note the interactions of DNA with synthetic polypeptides [S, 111. Still, the binding of histones to DNA is generally considered to be rather nonspecific, perhaps also because most of the studies conducted on reconstituted complexes as well as on native nucleohistones were done with soluble nucleohistones, i.e. under conditions rather different from physiological. The results of analysis of DNA composition both in the supernatant and in the aggregated phase presented here indicate that histone F1 in aggregated complexes prepared by the equilibrium method selectively prefers sequences of native DNA rich in adenine plus thymine.

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Conformational changes associated with f-1 histone-deoxyribonucleic acid complexes. Circular dichroism studies

Cited by 189 publications

References 58 publications

Circular dichroism analysis of mononucleosome DNA conformation.

Circular dichroism analysis of mononucleosome DNA conformation.

Experimental Differential Light-Scattering Correction to the Circular Dichroism of Bacteriophage T2

Complexes of Histone F1 with DNA in 0.15 M NaCl

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