Linear dichroism studies of nucleic acids. II. Calculation of reduced dichroism curves of A‐and B‐form DNA

Matsuoka, Yukio; Nordén, Bengt

doi:10.1002/bip.360211208

Cited by 69 publications

(51 citation statements)

References 32 publications

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“…(1) would correspond to a = 86". 47 Observations that certain dyes in association with DNA give a more negative LD' than the DNA tran~itions'~Jl@ could indicate that the fiber structure is invalid for solution (e.g., a = 76' has been discussedll); however, the difference can also be explained by a decreased flexibility of DNA (increased S ) in regions with associated dye.12 On the basis of the limiting value of electric dichroism, it has been proposed that the bases should be twisted as much as 17" from the plane perpendicular to the helix a~i s . 4~ However, such a large twist would, according to the calc~lations,4~ give a considerable variation of LD' with wavelength, in contradiction to the constant LD' between 245 and 285 nm observed for B-form DNA in aqueous solution and humid films (for A-form DNA, with a base tilt of 19", LD' is found to vary by some 10% over this wavelength region).5O As mentioned earlier, ( cos2a) may deviate from zero, as a result of base oscillations, even if the equilibrium structure corresponds to ( a ) = 90"; however, in the crude model represented by Eq.…”

Section: Discussionmentioning

confidence: 99%

Structure of methylene blue–DNA complexes studied by linear and circular dichroism spectroscopy

1982

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SynopsisBradley et al. [(1972) Biopolyrners 11,645-6521 used electro-optical measurements to show that methylene blue (MB), like acridine orange, in its DNA complex is oriented more or less perpendicular to the helix axis as expected if intercalated. High-precision flow linear dichroism (LD) here confirms that MB is coplanar with the DNA bases at low dyeDNA binding ratios and low ionic strengths. CD shows two origins of induced optical activity for the transition of lowest energy (polarized parallel to the long-axis of the dye molecule): a t low binding ratios (r < 0.05), a weak monomeric CD with the same shape as the absorption curve is observed, while at higher binding ratios, a strong exciton CD dominates due to interaction between pairs of MB ligands. The monomeric CD spectrum shows a remarkable dependence on ionic strength: it is negative in the absence of extra salt, but changes sign (at ca 20 mM NaCl or 0.15 mM MgC12) and becomes essentially the positive mirror-image spectrum at high ionic strengths (>300 mM Na+ or >0.4 mM Mg2+). Nondegenerate coupled-oscillator theory can explain the CD in terms of interactions of transition moments of the dye and the nearest nucleotide bases and indicates a change between two intercalation geometries: a Lerman type of mode, denoted y-, and an orthogonal mode, denoted y+. This rotation of MB in the base-pair pocket is accomplished at Na+ and Mg2+ concentrations when the phosphates are effectively screened and the result suggests a more localized bonding of Mg2+ than is expected from simple polyelectrolyte models. The exciton effect at high binding ratios, observed both in CD and in LD, can be interpreted in terms of an interaction between an intercalated and a nonintercalated MB. The geometry of this "accidental" dimer is consistent with a location of the nonintercalated MB in the minor groove, bridging the strands by the positively charged amino groups directed towards phosphate groups. The dihedral angle of the MB pairs, corresponding to a left-handed helix, is opposite to that with acridine orange and proflavine on DNA, indicating that the latter ligands bind t o DNA in a different way.

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Section: Discussionmentioning

confidence: 99%

Structure of methylene blue–DNA complexes studied by linear and circular dichroism spectroscopy

1982

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“…The linker and chromatosome tilts compatible with ELD, FLD as well as x-ray scattering data is represented by the remaining (white) area. and f is the fraction of bases in the linker segments (about 0.11 for Ehrlich ascites chromatin (54)), Sis the flow orientation factor which by our assignment is always positive, a is the base tilt relative to the local DNA helix axis (effective value 86°, see ref 55). ~ is the pitch angle (85°) of the chromatosomal DNA(7,56), 90° -y is the chromatosomal tilt and 8 is the linker tilt (Figure 3).…”

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Reinterpretation of Linear Dichroism of Chromatin Supports a Perpendicular Linker Orientation in the Folded State

Kubista

Hagmar

Nielsen³

et al. 1990

Journal of Biomolecular Structure and Dynamics

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We present a reinterpretation of linear dichroism data for the salt induced condensation of chromatin. A conflict between electric and flow linear dichroism data for identical chromatin samples, studied at varying degrees of Mg2+ induced folding, can be solved if the orientation in electric fields is mainly determined through the polarization of counter ions along the linker parts, whereas the orientation in flow is governed by the hydrodynamical response of the entire chromatin fiber. The orientation of a chromatin fiber in an electric field would then depend on the linker tilt angle so that at an angle larger than 55 degrees the fiber would tend to orient perpendicular to the applied field. The different orientation distributions obtained with the two methods of alignment may in this way provide extra information about the structure and folding of chromatin.

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“…Flow linear dichroism measurements were performed as described previously [12,13,161 at a flow gradient, G, of 1800 s-'. Circular dichroism was measured on a Jasco 5-500 spectropolarimeter.…”

Section: Methodsmentioning

confidence: 99%

Stepwise unfolding of chromatin by urea

Nielsen

Matsuoka

Nordén

1985

European Journal of Biochemistry

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The unfolding of chromatin by urea (0 -7 M) was studied by means of flow linear dichroism, photoaffinity labeling and nuclease digestion. The linear dichroism results indicate that the unfolding of the DNA is accomplished through two distinct transitions at 1 -2 M urea and 6 -8 M urea, respectively. The photoaffinity labeling studies indicate that an opening of the nucleosome histone core occurs above 2 M urea, accompanied by general loosening of the structure. Based on the results a model for the unfolding of chromatin fibers by urea is proposed, which includes a stretching of the linker DNA (0-2 M urea) followed by a "loosening" of the nucleosome core, possibly to a one-loop DNA conformation (2 -6 M urea), and finally resulting in an almost total stretching of the DNA (> 6 M urea).The nucleosomal chromatin structure (for reviews [I, 21) is heavily perturbed by urea as revealed by several studies employing a variety of techniques. These include hydrodynamic [3,4], spectroscopic (in particular circular dichroism) [5, 61 and electron microscopic [7, 81 as well as enzymatic (nuclease digestion) [9, 101 analyses. Increasing concentrations of urea result in a gradual increase of the intrinsic viscosity of the DNA-histone complex [7], a decrease of the sedimentation coefficient [4] as well as a loss of the beaded appearance on electron micrographs [7], which is otherwise characteristic for native nucleosomal chromatin. Furthermore, even high concentrations of urea (8 M) do not result in histone-DNA dissociation [6,7, 111, but rather causes a denaturation of individual histones and a weakening and eventually disruption of intra-nucleosomal histone-histone interactions [7]. However, regardless of the urea concentration limit-digestion with micrococcal nuclease still results in distinct DNA fragments of about 70-200 base pairs [6], and the characteristic ten-base-pair repeats upon digestion with DNase I are analogously retained in 5 M urea [S].Employing two new techniques, i.e. flow linear dichroism, by which information concerning the conformation and orientation of the DNA helix may be obtained [12, 131, and photoaffinity labeling, reflecting changes in protein-DNA interactions [14, 151, we now report results on the influence of urea on chromatin structure. Our data indicate that the unfolding as a function of the urea concentration is a stepwise process in terms of the DNA conformation, showing distinct transitions at 1-2 M urea and 6-8 M urea. Furthermore, on the basis of accumulated results we propose a model for the unfolding process which involves: a stretching of the linker DNA (0 -2 M urea) followed by a "loosening" of the nucleosome histone-core structure, probably resulting in a one-loop Abbreviation. LD,, reduced linear dichroism DNA conformation (2-6 M urea), which is finally also unfolded, resulting in a structure where the DNA is almost totally extended (8 M urea) but still covered with histones. MATERIALS AND METHODSWhole chromatin containing all histones (HI, H2A, H2B, H3 and H4) was isolated from mo...

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Linear dichroism studies of nucleic acids. II. Calculation of reduced dichroism curves of A‐and B‐form DNA

Cited by 69 publications

References 32 publications

Structure of methylene blue–DNA complexes studied by linear and circular dichroism spectroscopy

Structure of methylene blue–DNA complexes studied by linear and circular dichroism spectroscopy

Reinterpretation of Linear Dichroism of Chromatin Supports a Perpendicular Linker Orientation in the Folded State

Stepwise unfolding of chromatin by urea

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