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

Abstract

SynopsisInformation on spatial correlation in the tangent direction along electron microscope images of filamentous molecule is shown to be obtainable by the analysis of statistical fluctuations in curvature, yielding an absolute measure of the persistence parameter a,i ,,,.The relationship of amicro, a local, microscopic parameter, to the persistence length introduced by Kratky and Porod is discussed. The hypotheses underlying the assumed theoretical model concern (1) the shape of the angle distribution, assumed to be Gaussian; (2) the passage from a three-to a two-dimensional situation, which is supposed to occur by deformation of the flexible chain in a manner that preserves the memory of the spatial correlation in orientation (except for the blocking of one degree of freedom); and (3) the adsorption conditions, which should meet the equilibrium requirement as closely as possible. The analytical method has been checked on computer simulated "Gaussian" molecules: the study of the simulated sample was essential in solving the problems connected with minimum statistics requirements and the effect of the reading error. Experimental images obtained for T2 DNA fragments a t different ionic strengths by Kleinschmidt's adsorption technique have been analyzed by means of an automatic flying spot digitizer, the "Precision Encoder and Pattern Recognition." The results show that adsorbed molecules do in fact "remember" the rigidity they possessed in solution and that the Gaussian hypothesis is well verified. Consequently, the slopes of log a ( 1 ) or @ ( l ) may be used indifferently in the estimate of amicro The dependence of this parameter on ionic strength in the range explored shows the expected behavior.

Microscopic persistence length of native DNA: Its relation to average molecular dimensions

“…We will try to answer the questions formulated above by verifying the predictions of these equations when we take for a the values of amicro determined in Ref. 1 and use the contour data to evaluate the mean-square end-to-end distance and mean-square radius of gyration. We recall that the data consist of point coordinates read along the electron microscope image of DNA fragments, visualized by the Kleinschmidt technique in the adsorption version.…”

“…To this end we will assume, as in Ref. 1, that we can apply the above equations not only to the fragments as a whole, hut also to all subarcs of given length 1. We denote the square of the chord length by r2 and the square of the radius of gyration by sz to distinguish them from the R 2 and S2 of the whole fragment.…”

Neutral and charged polymers at interfaces

“…Biopolymers with a more complex structure on the molecular level tend to be stiffer than simple synthetic polymers. Some typical persistence lengths encountered in biological systems are ℓ 0 ≈ 5 mm for tubulin [16], ℓ 0 ≈ 20 µm for actin [17,18], and ℓ 0 ≈ 50 nm for double-stranded DNA [19]. Because some of these biopolymer are charged, we will discuss in Sec.…”

“…Keeping in mind that γ 1 < 0 for depletion, the solution of the same profile equation (7.9), with the appropriate boundary condition results in 19) which is schematically plotted in Fig. 18b.…”

Pseudomonas aeruginosa AmrZ Binds to Four Sites in the algD Promoter, Inducing DNA-AmrZ Complex Formation and Transcriptional Activation

“…In most DNA looping examples, the distances between two operator sites are typically Ͼ100 bp (45,46). Additionally, DNA duplexes of ϳ50 bp are best modeled as rigid rod-like structures, and the force required to bend such a substrate greatly exceeds the capacity of a protein-protein interaction (47). We therefore constructed a PalgD DNA fragment with a 105-bp (10 DNA turns) truncation (bp Ϫ250 to bp Ϫ146) (Fig.…”