Variation of Type-B DNA X-Ray Fiber Diagrams with Base Composition

Abstract

Eight natural DNAs of widely differing base composition have been studied by x-ray diffraction in fibers at high relative humidity. The resulting type B diffraction diagrams showed that all of the DNAs had a 34-A pitch and 3.4-A interbase pair separation. However, the intensity dlistribution on the inner three layer lines was a strong function of the base content. In diffraction diagrams of very AT-rich DNA, the intensity of the first and third layer line was 2-or 3-times stronger than in the patterns of GC-rich DNA. These high humidity diffraction patterns agree with x-ray scattering from solutions of DNA. The results are interpreted to imply that each AT base pair may have a different cross section than a GC pair. If this is so, it would appreciably alter the currently held ideas concerning DNA recognition.Until recently, it was generally accepted that DNA could exist only in one of three forms, and also that the structure of DNA was independent of the nature of the DNA. The latter conclusion was based on an x-ray fiber diffraction study of only the A forms of various natural DNAs (1). Nevertheless, x-ray fiber diffraction experiments on AT-rich DNAs at intermediate and low relative humidities (r.h.) have shown that the secondary structure under these conditions does depend on the base composition (2, 3) and that there exists at least several new forms for DNA.At high water contents, in fibers and in solution, calfthymus DNA exists in a conformation of the B type (4, 5). However, no extensive x-ray fiber diffraction study of the high-humidity configuration of various DNAs has been reported. [A short preliminary report of three high-humidity patterns has recently been published (6)]. The high-humidity experiments presented here were prompted by the finding that the wide-angle x-ray scattering patterns of natural and synthetic DNAs in solution were, indeed, functions of the nature of the DNA (7). The wide-angle x-ray scattering patterns from all natural DNAs in solution show two intensity maxima near 13 and 10 A. (Other maxima are observed at smaller equivalent Bragg spacings.) To a first approximation,. these maxima correspond to the maximum of the molecular transform of the fiber diffraction pattern on the second and third layer lines, respectively. The x-ray intensity corresponding to the first layer line is mostly obscured by the smallangle scattering of the whole molecule in solution. Nevertheless, the contribution from the first order bessel function term does raise the overall intensity scattered in the neighborhood of 20-30 A, and the relative intensity in this region was observed to be significantly larger for DNA very rich in AT (7). Abbreviation: r.h., relative humidity.It was also noticed that the sharpness of the 13-and 10-A maxima were functions of the base composition, but recenexperiments show that the width of these maxima is also aft fected by the salt content. However, the ratio of the intensity of the 10-maxima to the one at 13 A does not seem to vary, at least over the range 0.05-1 M...

Nucleosome assembly of simian virus 40 DNA in a mammalian cell extract.

“…10,1990 Reic The inhibitory effect of excess histones became more evident when the endogenous histones of the extract were presented with lower DNA concentrations. About 0.05 ,ug of y-32P-labeled, covalently closed relaxed SV40 DNA per ml together with various amounts of unlabeled relaxed DNA were added to an Mg2"-free or Mg2"-containing Glu-extract in the presence of EDTA.…”

“…Samples were analyzed as for Fig. 1 and 2 10,1990 2871 acetylation (4), and poly-ADP-ribosylation (20), have profound effects on chromatin organization and cell cycledependent gene expression. A somatic cell extract will facilitate study of these phenomena under controlled experimental conditions.…”