Steady‐state and transient electric birefringence of solutions of bent‐rod macromolecules

Mellado, Pelayo; Torre, José Garcı́a de la

doi:10.1002/bip.360210913

Cited by 32 publications

(27 citation statements)

References 17 publications

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“…Our programs proved to be correct with respect to hydrodynamic, optical and electrical properties by comparison to calculations on models discussed in the literature according to published numerical results (18,20,29,31 ).…”

Section: Coordinate System Optical and Electrical Tensorsmentioning

confidence: 77%

Turn of Promotor DNA by cAMP Receptor Protein Characterized by Bead Model Simulation of Rotational Diffusion

Antosiewicz¹,

Pörschke²

1988

Journal of Biomolecular Structure and Dynamics

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The rotation diffusion of DNA double helices and their complexes with the cAMP receptor protein (CRP) has been simulated by bead models, in order to derive information on their structure in solution by comparison with results obtained from dichroism decay measurements. Straight DNA double helices are simulated by linear, rigid strings of overlapping beads. The radius of the beads and the length of the string are increased simultaneously by the same increments from initial outer dimensions derived from crystallographic data to final values, which are fitted to experimental rotation time constants observed for short DNA fragments (less than 100 bp). The final values reflect the solvated structure with the same 'solvation layer' added in all three dimensions. The protein is simulated by overlapping beads, which are assembled to a structure very similar to that found by x-ray crystallography. Complexes of the protein with DNA are formed with the centres of palindromic DNA sites at the centre of the two helix-turn-helix-motifs of the protein with some overlap of the two components. Simulation of the experimental data obtained for CRP complexes with specific DNA in the presence of cAMP requires strong bending of the double helices. According to our simulation the DNA is almost completely wrapped around the protein both in the complexes with a 62 bp fragment containing the standard CRP site and with a 80 bp fragment containing the second binding site of the lac operon. Simulations of the data obtained for a 203 bp fragment with both binding sites suggest that the two bound CRP proteins are in contact with each other and that the DNA is wrapped around the two protein dimers. A stereochemical model is suggested with a tetrahedral arrangement of the four protein subunits, which provides the advantage that two binding sites of the protein formed by two subunits each are located favorable for tight contacts to two binding sites on bent DNA, provided that the DNA sites are separated by an integer number of helix turns. In summary, the simulations demonstrate strong bending, which can be reflected by an arc radius in the range around 50 A. According to these data the overall bending angle of our longest DNA fragment is approximately 180 degrees, and thus the protruding ends are sufficiently close to each other such that RNA polymerase, for example, could contact both helical segments.

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Section: Coordinate System Optical and Electrical Tensorsmentioning

confidence: 77%

Turn of Promotor DNA by cAMP Receptor Protein Characterized by Bead Model Simulation of Rotational Diffusion

Antosiewicz¹,

Pörschke²

1988

Journal of Biomolecular Structure and Dynamics

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“…[C~(NH,),]~+-induced bending of the 153-bp fragment is also indicated by the decrease in the limit dichroism (Table I) (Table I) demonstrates that the hydrodynamic dimensions of the 153-bp fragment are not affected by the presence of two B-2 junctions. Since the 2-DNA segments at the ends of our 153-bp fragment are relatively long and rotation time constants of rodlike molecules are known to be strongly affected by bending, 19,25 we may conclude that the two B-Z junctions are neither strongly bent nor particularly flexible. The effect of strong bending on rotational diffusion is not expected to be canceled by phasing of two bending sites or by an increased stiffness of Z-DNA, whereas compensation of weak bending effects cannot be excluded.…”

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confidence: 92%

B‐Z DNA junctions are neither highly flexible nor strongly bent

1987

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The biological and chemical properties of the structural junctions between righthanded B-and left-handed Z-helical segments have been the subject of considerable interest.'-" Model building shows that the conformation of at least one base pair at the junction must be different from the standard B or Z att tern.'^-'^ The junction probably involves at least several base pairs (bp),5~7~8,"~'6 which deviate from the standard B or Z double helical structure. B-Z junctions are recognized by S, and BAL 31 n~c l e a s e s '~~-~ as well as osmium-tetraoxide,lo which were originally characterized as agents that preferred single-stranded polynucleotides. However, these studies were interpreted as the recognition of structural aberrations in the double helices rather than unpaired and/or unstacked nucleotides. Also, the accessibility of bases at B-Z junctions to modification by bromoacetaldehyde was relatively low,16 further confirming this notion.More information on the structure of B-Z junctions may be obtained by hydrodynamic measurements on DNA fragments containing B-and Z-helical segments. Changes of the effective hydrodynamic length resulting from an increased flexibility or from a turn of the helix axis may be detected with particularly high sensitivity by measurements of the electric dichroism." The high sensitivity is due to the fact that the rotation diffusion coefficient obtained from the dichroism decay curves decreases approximately with the third power of the length for rodlike fragment^'^ (if the chain length is below the persistence length).This technique was used to analyse the B-Z junctions in a 153-bp DNA fragment,4 containing a central piece of 95-bp DNA derived from the E . coli lac control region with flanking segments of 26 and 32 bp of (CG). The fragment had 4 single-stranded residues at each end, which resulted from the preparation by Bam H1. An analysis of dichroism decay curves under B-form conditions (1 mM NaC1, 1 mM Na cacodylate pH 7.0, 0.2 mM EDTA) revealed two relaxation processes as expected for a fragment of this length?' The slow process with a time constant rr reflects the overall rotation of the DNA, whereas the fast process is attributed to bending. This assignment is based on the fact that the fast process is hardly detected at small field strengths, whereas its amplitude increases to substantial values at high field strengths." Extrapolation of the observed dependence of rr on the field strength E by linear regressiodg to E = 0 provided a value rp = 2.14 ps. The bending process was associated with a time constant rb = 140 ns and the bending amplitude approached a constant relative contribution of -23% at field strengths above 50 kV/cm. The values are in the range expected for our fragment. The stationary dichroism observed as a function of the electric field strength was fitted by the saturating induced dipole model" using the square root approximation.21 According to this model the limit dichroism corresponding to complete orientation is -1.34.

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“…This interpretation is clearly at odds with the crystal structure (Moras et al, 1980) which resembles a bent rod with arms of approximately equal length separated by an angle of -1000 and with the base planes at an angle s20°to the long axis of the arm. Using a recently derived equation (Mellado and Garcia de la Torre, 1982), this model is calculated to have an f value close to that measured (see Materials and methods). This encourages belief in the estimates presented for the plant viruses and shows that they are related to RNA conformation but also makes it clear that detailed interpretation is not possible.…”

Section: Resultsmentioning

confidence: 93%

Internal structural anisotropy of spherical viruses studied with magnetic birefringence.

Torbet

1983

The EMBO Journal

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Six so called spherical viruses (four plant and two animal) are shown to exhibit magnetically induced birefringence in solution. They must therefore be magnetically and optically anisotropic. This is attributed to static structural anisotropy of the interiors as neither natural shape nor field‐induced deformations are likely causes. Thus at least part of these virus cores have a symmetry differing from that of their capsids. An estimate of the average orientation of the RNA bases is given for the plant viruses: turnip yellow mosaic, bromegrass mosaic, tomato bushy stunt and turnip crinkle. The packing geometry of the nucleic acid/protein cores of adenovirus and probably influenza virus are anisotropic but to an extent that cannot be quantified.

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Steady‐state and transient electric birefringence of solutions of bent‐rod macromolecules

Cited by 32 publications

References 17 publications

Turn of Promotor DNA by cAMP Receptor Protein Characterized by Bead Model Simulation of Rotational Diffusion

Turn of Promotor DNA by cAMP Receptor Protein Characterized by Bead Model Simulation of Rotational Diffusion

B‐Z DNA junctions are neither highly flexible nor strongly bent

Internal structural anisotropy of spherical viruses studied with magnetic birefringence.

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