An absolute method for the determination of the persistence length of native DNA from electron micrographs

Structure and hydrodynamic properties of plectin molecules

Plectin is a cytoskeletal, high molecular weight protein of widespread and abundant occurrence in cultured cells and tissues. To study its molecular structure, the protein was purified from rat glioma C6 cells and subjected to chemical and biophysical analyses. Plectin's polypeptide chains have an apparent molecular weight of 300,000, as shown by one-dimensional sodium dodecyl sulfate/polyacrylamide electrophoresis. Cross-linking of non-denatured plectin in solution with dimethyl suberimidate and electrophoretic analyses on sodium dodecyl sulfate/agarose gels revealed that the predominant soluble plectin species was a molecule of 1200 X 10(3) Mr consisting of four 300 X 10(3) Mr polypeptide chains. Hydrodynamic properties of plectin in solution were obtained by sedimentation velocity centrifugation and high-pressure liquid chromatography analysis yielding a sedimentation coefficient of 10 S and a Stokes radius of 27 nm. The high f/fmin ratio of 4.0 indicated a very elongated shape of plectin molecules and an axial ratio of about 50. Shadowing and negative staining electron microscopy of plectin molecules revealed multiple domains: a rigid rod of 184 nm in length and 2 nm in diameter, and two globular heads of 9 nm diameter at each end of the rod. Circular dichroism spectra suggested a composition of 30% alpha-helix, 9% beta-structure and 61% random coil or aperiodic structure. The rod-like shape, the alpha-helix content as well as the thermal transition within a midpoint of 45 degrees C and the transition enthalpy (168 kJ/mol) of secondary structure suggested a double-stranded, alpha-helical coiled coil rod domain. Based on the available data, we favor a model of native plectin as a dumb-bell-like association of four 300 X 10(3) Mr polypeptide chains. Electron microscopy and turbidity measurements showed that plectin molecules self-associate into various oligomeric states in solutions of nearly physiological ionic strength. These interactions apparently involved the globular end domains of the molecule. Given its rigidity and elongated shape, and its tendency towards self-association, plectin may well be an interlinking element of the cytoskeleton that may also form a network of its own.

The molecular size and shape of xanthan, xylinan, bronchial mucin, alginate, and amylose as revealed by electron microscopy

Electron microscopy of some selected, vacuum-dried and rotary-shadowed, polyelectrolytic polysaccharides and glycoproteins adsorbed to mica indicates that this technique can yield reliable information about polymer conformation for chains with persistence lengths q exceeding about 10 nm. Statistical analyses of the local polymer tangent-direction yield q = 150 nm for double-stranded xanthan, q = 60 nm for single-stranded xanthan, q = 45 nm for xylinan, q = 16 nm for alginate (90% beta-D-mannuronic acid), and q = 15 nm for human-bronchial mucin. These values are all in adequate agreement with values of q obtained by using other techniques. Amylose, on the other hand, appears as non-randomly aligned chains. The observed contour lengths of amylose indicate a mass per unit length of 1440 dalton/nm, consistent with a pseudo-helical conformation.

Relevance of aggregation properties of tropoelastin to the assembly and structure of elastic fibers

Solutions of tropoelastin incubated under different experimental conditions were examined by electron microscopy after negative staining and after fixation and embedding. Below 37 degrees C only polymorphous structureless elements of variable size could be found. In samples kept for a few minutes at 40 degrees C, flexible, isolated filaments of 5 nm diameter and variable length, together with a few small aggregates of filaments, were seen. No single filaments, but only bundles of filaments were detectable after incubation at 40 degrees C for longer than 5-10 min. Tropoelastin kept at 40 degrees C for longer than 10 hr formed a white precipitate, which, when fixed and embedded as in conventional electron microscopy, consisted of 0.5-2 microns thick, amorphous and branching fibers, identical to those seen in identically processed normal tissues. From these observations a model for the assembly and structure of elastic fibers is proposed.

Packaged DNA. An elastic model

We review and deepen a theory of elastic bending of DNA on a persistence length scale. In a regime of extensive charge neutralization the axis of the double helix is elastically unstable when straight. Its stable bent conformation allows nucleation of DNA toruses and in principle could direct the supercoiled (solenoid) form of a polynucleosome. The Euler theory of elastic instability of macroscopic rods gives a partial description of the intrinsic ability of DNA to form locally stable bends. A different, quasi-Eulerian theory can be based on what is probably the dominant bending mechanism of DNA in solution-flexible kinking at the sites of open base pairs. This predictive theory is in quantitative agreement with the observed value (about 16 nm) for the minimum radius of torus holes. Stability of the inner torus ring is achieved when DNA phosphate groups are about 90% neutralized by trivalent cations, another prediction that is consistent with the observed formation of toruses in these conditions. The predicted stable radius of curvature of charge-neutralized DNA is also equal to the radial dimension of a maximally contracted polynucleosome supercoil as measured by neutron scattering (17 nm), but further experimental investigation of the geometrical disposition of the spacer DNA regions in the solenoid will be necessary to rule out the possibility of accidental agreement for this complex system. We stress again the experimental reality and probable importance of open base pairs in the equilibrium solution conformation of DNA.

Electron microscopic measurement of chain flexibility of poly(dG-dC).poly(dG-dC) modified by cis-diamminedichloroplatinum(II)

The antitumor drug cis-diamminedichloroplatinum (II) (cis-Pt) forms bidentate adducts with guanine residues of poly(dG-dC).poly(dG-dC). The secondary structure of the polymer is altered. In this work, high resolution pictures of naked molecules, obtained by dark field electron microscopy reveal DNA chain distortions with radii as small as 30 A. The extent of distortion increases with the drug/nucleotide ratio (rb). These alterations of the secondary structure are responsible for the apparent shortening of the molecules. Measurements of the persistence lengths of the polymer as well as the end-to-end distances of elementary segments of various lengths, are obtained from digitized electron micrographs. The measurements are used to monitor and quantify the observed modifications of polymer structure upon cis-Pt binding at various rb or incubation times. Poly(dG-m5dC).poly(dG-m5dC) in the B and Z forms have different persistence lengths. In the B form, this polymer is more altered by cis-Pt than in the Z one.

Localization of flexible sites in thread-like molecules from electron micrographs. Comparison of interstitial, basement membrane and intima collagens

A computer method for detecting kinks and flexible sites in thread-like molecules was developed. The method is based on the determination of the local curvature along the digitized electron micrographs of the molecules. The root-mean-square curvature provided a measure for the local flexibility, which is related to the persistence length. The influence of various error sources was assessed using computer-simulated thread molecules. "Flexibility profiles" showing the variation of flexibility along molecules were calculated for interstitial, basement membrane and intima collagens. Approximately uniform stiffness corresponding to a persistence length of 60 nm was found for the triple helices of interstitial and monomeric intima collagen. A highly flexible site in interstitial collagen could be assigned to a non-triple helical segment in the sequence surrounding the linkage site of the N-terminal propeptide. A flexible site in the triple helix of collagen I corresponds to a segment of the sequence lacking proline residues. Flexibility varies strongly along the collagen IV molecule. This is consistent with the fact that a series of non-triple helical interruptions have already been found in the not yet completed amino acid sequence of basement membrane collagen. Most of the detected flexible sites allow random bending about the mean zero, but in one case, at the border of the 7S domain of polymeric collagen IV, a flexible site with a preferential angle of 40 degrees was found.

Electron-microscopical approach to a structural model of intima collagen

Intima collagen was studied by electron microscopy (rotary shadowing and negative staining) and by analytical ultracentrifugation. It was found that the monomeric unit (Mr 170 000) consists of a 105 nm-long triple helix terminated by a small globular domain (Mr about 30 000) at one end and a large globular domain (Mr about 40 000) at the other end. The monomer was produced by selective reduction of interchain disulphide bridges. Before reduction, dimers, tetramers and larger filamentous structures were found. Dimers are lateral staggered aggregates of two monomers aligned in an anti-parallel fashion. This gives rise to an inner 75 nm-long region of two slightly intertwisted triple helices flanked by the large globular domains. The outer triple-helical segments (length 30 nm) with the small globular domains at their ends emerge at both sides of this structure. Interchain disulphide bridges are probably located in the vicinity of the large domains. Only the outer segments could be degraded by bacterial collagenase. In tetramers the outer segments of two dimers are covalently linked, forming a scissors-like structure. In the fibrous forms several tetramers are assembled end-to-end with an overlap between the outer segments. The molecular masses and sedimentation coefficients were calculated for these various forms from the electron-microscopically observed dimensions and agreed with results obtained by ultracentrifugation. The unique structure of intima collagen suggests that it originates from a microfibrillar component and that it can be considered a unique collagenous protein, for which we propose the designation type VI collagen.

Evidence for an increase of DNA contour length at low ionic strength

The polyion chain expansion of DNA was studied by viscometry within the Na+ concentration range c5 = 0.002 M to 0.4 M. The DNA molecular weights M were between 0.5 x 10(6) and 13 x 10(6). The relative change of intrinsic viscosity [eta] is linearly correlated to c5(-1/2) with a slope that increases with increasing M. This behaviour reflects the predominance of helix stiffening in chain expansion. At c5(112) > 0.01(-1/2 M-1/2 (Debye-Hückel screening radius 1/chi > (1/chi)*=3nm) the relative change of [eta] rises with a steeper slope. This effect increases with decreasing M suggesting that helix lengthening contributes to the chain expansion. Our model enables us to interpret other ionic-strength dependent effects known from literature. The start of the significant duplex elongation at (1/chi)* can be correlated to the polyion-charge arrangement. In accordance with our interpretation (1/chi)* is found to be greater for DNA-intercalator complexes.