From owner-biophysics@net.bio.net Mon Dec 14 22:00:00 1998 From: "clive delmonte" Newsgroups: bionet.biophysics,bionet.xtallography Subject: DNA Structure: Puzzle Number 12 Date: Tue, 15 Dec 1998 07:28:21 -0000 Lines: 118 X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 NNTP-Posting-Host: 195.7.225.236 Message-ID: <36760904.0@news.netdirect.net.uk> X-Trace: 15 Dec 1998 07:00:20 GMT, 195.7.225.236 Path: biosci!agate!newsfeed.berkeley.edu!newsfeed.wirehub.nl!peer.news.nildram.co.uk!news-peer.netdirect.net.uk!news.netdirect.net.uk!195.7.225.236 Xref: biosci bionet.biophysics:4652 bionet.xtallography:4521 Aaron Klug (18, page 373) has reported that Rosalind Franklin was working on a sugar-phosphate helical diameter of 1.1nm, deduce from her Pattersons, at the time that Watson & Crick formulated their idea of a double helix. Franklin's value of 1.1 nm resonates with the values of 1.2 nm to 1.3 nm outer helical diameters recorded, for example, in Puzzle 1(ref. 1 and other AFM &STM refs.), Puzzle 2 (ref. 2), Puzzle 3 (ref. 4) and Puzzle 4 (ref. 7). Most importantly, and unknown to Franklin at that time,1.1 nm is also the width of the Watson-Crick base pair. Supposing, as a working hypothesis, that base pairs are connected across the two (antiparallel) helices recorded by Lee et al. (Puzzle 1, ref. 1), then the geometry requires each sugar-phosphate helix to adopt the same diameter as the base pair width. This leads us directly to dimensions for the duplex of about 1.2nm x 2.1nm, values deduced already from the experimental results of James & Mazia (Puzzle 3, ref. 4). Wilkins et al. (19) analysed the diffraction pattern of B-DNA: "...The strong equatorial reflection....suggests that the helices have a maximum diameter of approximately 2.0 nm....On the sixth, seventh and eighth layer lines the maxima correspond to a helix of diameter approximately 1.2nm..."; and, further, Wilkins et al. write (20):...In particular, it appears that the helix, when viewed along the fibre axis, may not be quite round in section but elliptical." So Wilkins' group finds a helical diameter of 1.2 nm in an elliptical section of major diameter approximately 2.0 nm, which reinforce closely similar, elliptical values of 1.2 nm and 2.1 nm deduced directly from the 1953 paper by James & Mazia. These days, the structure of oligonucleotides is deduced from diffraction from true crystals and purports to show double helical structures. But there is a slight snag with this process. There are no oligonucleotide structural solutions based upon direct methods on their own, because direct methods require data at a very high resolution, about 0.1 nm, and the highest oligonucleotide resolution to date is about 0.15 nm. All the oligonucleotide studies reported to date involve feeding the double helix, directly or indirectly, into the computational algorithms along with the raw data. Typical examples of this practice, which just happen to lie randomly to hand, would include B-DNA: (21, page 8863): " ...starting with a standard B-form DNA as established from fiber diffraction..." Z-DNA: (22, Note 19): The 3 x 3 matrix, generating the coordinates of the two strands, defines a double helix. B-DNA: (23, page 1374):The initial coordinates of the ....decamer were those of the idealized canonical B-DNA..." A-DNA: (24, page 806): "...a model... was constructed in the A-form using fibre coordinates..." B-DNA: (25, page 1162): "We decided to solve and refine the structure using coordinates from idealized, fibre-diffraction B-DNA..." So, if a double helix is fed into the algorithm, naturally a double helix comes out. The Puzzle for today is this. The true side-by-side structure visualised by Lee et al. (Puzzle 1, ref.1) in their STM research shows identically zero plectonaemic turns over any and all lengths and has a helical diameter of some 1.3 nm for each helix, in accord with results from many independent experiments. If this model is fed as B-DNA into the computational algorithms shall we get out a structure with a comparable crystallographic residual to those resulting from a double helical input ? The whole body of oligonucleotide structures presently deposited at Brookhaven would seem to be compromised by the prior acceptance of a plectonaemic structure for duplex DNA in the A, B and Z forms which even early fibre diffraction studies and other, especially recent, non-crystallographic work does not much support. 18 The Path to the Double Helix; R. Olby: Macmillan 19 Molecular Structure of DNA; M.H.F. Wilkins, A.R. Stokes and H.R. Wilson; Nature Vol 171 (1953) 738 - 740 20 Helical Structure of Crystalline DNA; M.H.F. Wilkins, W.E. Seeds, A.R. Stokes & H.R. Wilson; Narure Vol 172 (1953) 759 - 762 21 The Structure of B-helical CGATCGATCG and Comparison with CCAACGTTGG; K. Grzeskowiak, K. Yanagi, G.G. Prive & R.E. Dickerson; J Biol Chem Vol 266 (1991) 8861 - 8883 22 Left-handed Double Helical DNA: Variations in the Backbone Conformation; A.H.-J. Wang, G.J. Quigley, F.J. Kolpak, G. van der Marel, J.H. van Boom & A. Rich; Science Vol 211 (1981) 171 - 176 23 Interaction of Berenil with the EcoRI Dodecamer (CGCGAATTCGCG) in Solution Studies by NMR; A.N. Lane, T.C. Jenkins, T. Brown & S. Neidle; Biochemistry Vol 30 (1991) 1371 - 1385 24 G.T Base-pairs in a DNA Helix: The Crystal Structure of d(GGGGTCCC); G. Kneale, T. Brown, O. Kennard & D. Rabinovich; J Mol Biol Vol 186 (1985) 805 - 814 25 Molecular Structure of the B-DNA Dodecamer d(CGCAAATTTGCG); K.J. Edwards, D.G. Brown, N. Spink, J.V. Skelly & S. Neidle; J Mol Biol Vol 226 (1992) 1161 - 1173 ------------------------------------------------------------------ Clive Delmonte .