From owner-biophysics@net.bio.net Mon Dec 14 22:00:00 1998 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!news.gtei.net!nntp.flash.net!newspeer.monmouth.com!rill.news.pipex.net!pipex!server1.netnews.ja.net!hgmp.mrc.ac.uk!pegasus.csx.cam.ac.uk!taurus.cus.cam.ac.uk!hrp1000 From: Harry Powell Newsgroups: bionet.biophysics,bionet.xtallography Subject: Re: DNA Structure: Puzzle Number 12 Date: Tue, 15 Dec 1998 10:11:53 +0000 Organization: University of Cambridge, England Lines: 64 Message-ID: References: <36760904.0@news.netdirect.net.uk> NNTP-Posting-Host: taurus.cus.cam.ac.uk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII In-Reply-To: <36760904.0@news.netdirect.net.uk> Xref: biosci bionet.biophysics:4654 bionet.xtallography:4522 On Tue, 15 Dec 1998, clive delmonte wrote: > These days, the structure of oligonucleotides is deduced from diffraction > from true crystals and purports to show double helical structures. > true (in part), but... > 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, Tosh. Although "direct methods" as used (and understood) by small molecule crystallographers require data to that resolution, there is a basic flaw to this, namely that you don't need direct methods or molecular replacement to solve oligonucleotide structures. You can use the heavy atom method in one of its modern guises, e.g. MAD. There are several oligonucleotide structures in the literature which have been solved using this method without resorting to molecular replacement and its requirement for a model. check: *>TI: MAD phasing strategies explored with a brominated oligonucleotide crystal at 1.65 angstrom resolution AU: Peterson_MR, Harrop_SJ, McSweeney_SM, Leonard_GA, Thompson_AW, Hunter_WN, Helliwell_JR JN: JOURNAL OF SYNCHROTRON RADIATION, 1996, Vol.3, No.Pt1, pp.24-34 > and the > highest oligonucleotide resolution to date is about 0.15 nm. ->TI: The crystal structure of a parallel-stranded guanine tetraplex at 0.95 angstrom resolution AU: Phillips_K, Dauter_Z, Murchie_AIH, Lilley_DMJ, Luisi_B JN: JOURNAL OF MOLECULAR BIOLOGY, 1997, Vol.273, No.1, pp.171-182 ->TI: The bi-loop, a new general four-stranded DNA motif AU: Salisbury_SA, Wilson_SE, Powell_HR, Kennard_O, Lubini_P, Sheldrick_GM, Escaja_N, Alazzouzi_E, Grandas_A, Pedroso_E JN: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1997, Vol.94, No.11, pp.5515-5518 (this last structure was refined with data to ~1.1A, but had 67% complete date to 0.98A. It was solved with phases derived from the position of an adventitious Ba++, so we didn't even use MAD...) > All the > oligonucleotide studies reported to date involve feeding the double helix, > directly or indirectly, into the computational algorithms along with the raw > data. Most, maybe, but not all. I could be _very_ picky about the term "raw data". I don't know any crystallographers anywhere who use raw, unprocessed, data in their structure solution or refinement, but I'm prepared to be corrected ;-) Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 2QH .