Life Sciences, Vol. 33, pp. 2049-2060 PerRamon Press Printed in the U.S.A. MINIREVIEW ASPECTS OF THE SECONDARY AND TERTIARY STRUCTURE OF DNA Geoffrey Dougherty Department of Physics, Monash University Clayton, Victoria, Australia 3168 Summary DNA is the primary genetic material of most organisms. A wide variety of naturally occurring duplex DNA's are known to exist as covalently closed circles. This covalent continuity introduces a topologlcal constraint, and consequently these molecules possess aspects of tertiary and even hlgher-order structure. Virtually every physical, chemical and biological property of DNA - its transcription, hydrodynamic behavlour, energetlcs, enzymology and so on - are related to these structural features. We describe the parameters describing the topology and conformation of covalently-closed, duplex DNA's (form I DNA's), the conservation relationship between them and its implications. In duplex DNA, two chains of complementary nucleotides wind around a common helix axis. The number of turns about this common axis is called the number of duplex (or Watson-Crlck) turns and is denoted by the symbol 8. This number depends on the length of the molecule (or more precisely, on the number of base-pairs, N) and on the tightness of the helical winding. The tightness can be characterlsed by the winding angle, 0, which measures the rotation of one base-palr relative to the next when viewed along the helix axis. For DNA fibres at high humidity (viz. in the B conformation), 0 has been shown by X-ray diffraction to be 36*, corresponding to I0 base-palrs per helical repeat. The winding angle fs sensitive to the environment of the DNA. For instance, with fibres at low humidity (the A conformation), 0 is 32.7" corresponding to II base-palrs per helical turn. The value of the helical repeat in solution has proved more difficult to determine, and depends critically on the ionic concentration, temperature and pH of the solution. Low-angle X-ray scattering studies have suggested that the structure should be ll-fold (I). The value will also depend on whether or not the DNA molecule is linear (form III) or covalently closed (form I). Theoretical energy mlnimisation studies (2) have suggested that O for linear DNA in solution may be about 34 ° (lO.6-fold), and for superhellcal DNA in chromatin about 35.5" (lO.3-fold), although the effect of ionic concentration was not considered. Partial DNAse digestion of nucleosomal DNA has suggested a I0-+0.I fold repeat (3). More recently, the distance between successive DNAsel cutting sites on short, stiff pieces of random-sequence DNA Immoblllsed on a flat surface has been found to be 10.6±0.1 bases (4). The relationship between ~ and 0 is given by e (1) 8 - N. ,~rf 0024-3205/83 $3.00 + .00 Copyright (c) 1983 Pergamon Press Ltd.