From owner-biophysics@net.bio.net Mon Jan 25 22:00:00 1999 From: "Clive Delmonte" Newsgroups: bionet.biophysics,bionet.xtallography Subject: DNA Structure: An Age of Refinement Part 2 of 6 Date: Tue, 26 Jan 1999 13:15:02 -0000 Lines: 78 X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 NNTP-Posting-Host: 195.7.227.228 Message-ID: <36adba4d.0@news.netdirect.net.uk> X-Trace: 26 Jan 1999 12:51:25 GMT, 195.7.227.228 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!btnet-peer!btnet!news.netkonect.net!peer.news.nildram.co.uk!news-peer.netdirect.net.uk!news.netdirect.net.uk!195.7.227.228 Xref: biosci bionet.biophysics:4741 bionet.xtallography:4564 DNA Structure Refinement using Constrained & Restrained Least Squares (CORELS) We saw that in Part 1 that a natural desire to maximise the information that could be extracted from sparse diffraction data from DNA and oligonucleotide studies inevitably has led to the incorporation of double-helical features into the LALS algorithm. Structures refined using this algorithm have informed the subsequent work in very many studies, often being used as models based upon which new structures are refined. A similar rationale seems to underpin the mode of application of the CORELS approach to nucleic acid structure refinement (62, 63): "We have used this method for idealizing a nucleic acid model..." (62, page 801), and "The structure of this fragment (d(GGTATACC)) of DNA was determined ... It incorporated..... calculations assuming models of both B and A types of DNA." (63, page 229) It was this structure which was then refined with CORELS. We also see in this latter quotation, as in the work of other research groups, the assumption that the crystallisation of short oligonucleotides gives rise to the same structure in vitro as that formed by proteins when they synthesise and assemble high polymer DNA in vivo, even though this proposition has never been proved. In the years since 1953, a growing body of experimental results, illustrated by the twenty DNA Structure Puzzles I selected for citation recently in these newsgroups, has become impossible to explain using the DNA double helical paradigm. These days biophysics and molecular biology is increasingly constrained by a model of duplex DNA which no longer offers helpful structural insights in a wide range of situations and many researchers find themselves reporting results in the literature without being able to offer any structural or mechanistic insights to explain those results. A wide-ranging review of such literature reports up to 1990 has been published (64). We find ourselves increasingly in a situation which calls to mind a remark of Sir Lawrence Bragg: "The important thing in Science is not so much to obtain new facts, as to obtain new ways of thinking about them." Oligonucleotide structures deduced by assuming duplex DNA to double helical at any stage in the process are therefore likely to be compromised and can only be used with caution, if at all, to explain experimental results in the wider field outside oligonucleotide crystallography. An entirely new possibility for duplex DNA has been described (64) and visualised experimentally in STM (65, Figure 3b) In An Age of Refinement Part 3 we shall consider the algorithm NUCLSQ. ------------------------------------------------------------------------- 62 A Structure-Factor Least-Squares Refinement Procedure for Macromolecular Structures using Constrained and Restrained Parameters; J.L. Sussman, S.R. Holbrook, G.M. Church & Sung-Hou Kim; Acta Cryst. A33 (1977) 800-804 63 APPLICATION OF REFINEMENT CONSTRAINTS AND RESTRAINTS TO PROTEINS AND NUCLEIC ACIDS; J.L. Sussman; pages 206-237 in Methods & applications in crystallographic computing; Ed. S.R. Hall & T. Ashida; Clarendon Press, Oxford, 1984 (ISBN 0-19-855190-8) 64 "Towards a New Structural Molecular Biology" by Clive Delmonte, ISBN 0 9512276 0 2 (1991) 65 Scanning Tunnelling Microscopy of Nucleic Acids: G. Lee et al.; SCIENCE Vol 244 (1989) 475 - 477 ------------------------------------------------------------------------- Clive Delmonte .