From owner-biophysics@net.bio.net Sun Nov 29 22:00:00 1998 From: "clive delmonte" Newsgroups: bionet.biophysics,bionet.xtallography Subject: DNA Structure: Puzzle Number 4 Date: Mon, 30 Nov 1998 09:25:53 -0000 Lines: 63 X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 NNTP-Posting-Host: 195.7.227.190 Message-ID: <36625bf2.0@news.netdirect.net.uk> X-Trace: 30 Nov 1998 08:48:50 GMT, 195.7.227.190 Path: biosci!agate!newsfeed.berkeley.edu!btnet-peer!btnet-feed2!btnet!news-peer.netdirect.net.uk!news.netdirect.net.uk!195.7.227.190 Xref: biosci bionet.biophysics:4602 bionet.xtallography:4496 Marvin et al. (5) drew fibres of the lithium salt of C-DNA in both hexagonal and orthorhombic lattices. In a hexagonal lattice of side 3.5nm., systematic absences followed (-h+k) =/=3n for l=0, and (-h+k)=3n when l=1 or 2. Streaks were found on several layer lines and could be explained by molecules having a random axial translation of c/2, without using the systematic absences, according to Marvin et al. Fuller et al. (6) state that such a pattern of systematic absence allows the choice of a hexagonal unit cell of side reduced by root 3. Marvin et al. chose a unit cell large enough to accommodate a double helix. If we elect to reduce the unit cell size, a double helix cannot be accommodated, and we find that the maximum, outer helix diameter is (3.5nm/root 3) x sin60 x 2/3 = 1.2 nm In an orthorhombic lattice, where Marvin et al. found a=3.22nm and b=2.02nm, large enough to accommodate a double hlix, they report that systematic equatorial absences follow h+k=2n+1. This pattern of absence is reported by Langridge et al. (7) to allow the halving of the long side to form a new reduced unit cell. In an orthorhombic cell with a=2.02nm and b=1.61nm, a double helix cannot be accommodated, and we find that the maximum outer diameter of a helix is now 1.3nm. Again, the observed streaks in the orthogonal pattern could result from a random axial displacement of duplexes of c/2, according to Marvin et al. If we elect to explore the implications of a random axial translation of c/2, utilising the layer line streaks as evidence, we are able to use the systematic absences in both lattices to choose a smaller unit cell in each case. Applying Stokes' equation to the helical cross of Li DNA in the Langridge paper, we find delta = 41 degrees and the helical diameter to be 1.22nm. A DNA helical diameter of 1.2 to 1.3 nm is therefore deducible directly from the STM work of Lee et al. (Puzzle 1, ref. 1) (and many other AFM &STM studies), or by applying Stokes' equation to Franklin's B-DNA diffraction pa ttern (Puzzle 2, ref. 2) and to diffraction from Li DNA in the C form (7), or from James and Mazia's surface film of B-DNA (Puzzle 3, ref. 4). A very wide range of entirely separate experiments suggests that the helical diameter of the major diffractors (the sugar-phosphate chains) is 1.2 to 1.3 nm. 5 The Molecular Configuration of Deoxyribonucleic Acid. III. X-ray Diffraction Study of the C form of the Lithium Salt; D.A. Marvin, M. Spencer, M.H.F. Wilkins & L.D. Hamilton; J Mol Biol Vol 3 (1961) 547 - 565 6 Molecular and Crystal Structures of Double-helical RNA; W. Fuller, F. Hutchinson, M. Spencer & M.H.F. Wilkins; J Mol Biol Vol 27 (1967) 507 - 524 7 The Molecular Configuration of Deoxyribonucleic Acid. I.; R. Langridge, H.R. Wilson, C.W. Hooper, M.H.F. Wilkins & L.D. Hamilton; J Mol Biol Vol 2 (1960) 19 - 37 ---------------------------------------------------------------------------- Clive Delmonte .