From owner-biophysics@net.bio.net Mon Jan 25 22:00:00 1999 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!news.gtei.net!newsfeed.berkeley.edu!diablo.theplanet.net!dispose.news.demon.net!demon!news.demon.co.uk!demon!revealer.demon.co.uk!not-for-mail From: "Simon Dobbs" Newsgroups: bionet.biophysics Subject: Re: DNA Structure: Puzzle Number 20 Date: Tue, 26 Jan 1999 23:49:33 +0000 Organization: dobbs research Message-ID: <01HW.B2D4050D0016CFD706F62390@news.demon.co.uk> References: <36a86b4e.0@news.netdirect.net.uk> NNTP-Posting-Host: revealer.demon.co.uk X-NNTP-Posting-Host: revealer.demon.co.uk:158.152.19.25 X-Trace: news.demon.co.uk 917394552 nnrp-06:11995 NO-IDENT revealer.demon.co.uk:158.152.19.25 X-Complaints-To: abuse@demon.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Newsreader: Hogwasher 1.03 (Macintosh) Lines: 72 On Fri, 22 Jan 1999 12:37:25 +0000, Iris Delmonte wrote (in message <36a86b4e.0@news.netdirect.net.uk>): > > > Enhanced Rates of Cleavage of Duplex DNA > > Sakonju & Brown (47) reported on the contacts made by a 40,000 > daltontranscription factor, tf IIIA, which protected its substrate from the > actionof deoxyribonuclease 1 (RMM 31,000) between bases 44 to 90. Within > that protected region, relative to bare duplex DNA, there is strong > enhancement of cleavage at 60 & 61, and marked enhancement also at bases > 74, 75 & 76, that is, 1.5 double helical turns away from 60 & 61. > > Since the two sites enjoy enhanced cleavage rates compared to bare DNA they > must both be more accessible than is bare DNA, even in the middle of > theprotected region, and even though tf III A must have some 2500 C,N,O > atoms and the nuclease must have some 2000 C,N,O atoms. > > > More specifically, site 60 & 61, if facing the nuclease, would leave site > 74-76 on the opposite double helical face away from the nuclease, though > both sites experience enhanced rates of cleavage compared to bare DNA and > are only some 4.5 nm apart. > > Drew & Travers (48) record their frustration with this situation: > > "Many eukaryotic transcription factors, notably tf III A ... , protect up > to 50 bp of DNA from enzymatic cleavage, yet somehow manage to induce > regions of enhanced cleavage within their binding sites..." > > With the true side-by-side model (Puzzle 1, Ref.1) we can discern a > possible explanation of these results. Tf III A may bind largely to the rear > face where phosphates predominate, though, being a substantial protein, > there may be some obstuction of the other face where the base pairs are > stacked upon each other. > > This allows deoxyribonuclease 1 access to the stacked base pairs at both > positions 60 - 61 and 1.5 turns away at 74 - 76, where both sites face way > from tf III A, and the rates of cleavage are enhanced compared to bare DNA > because the DNA bound onto tf III A is immobilised and entirely unfolded > compared to its situation alone with the nuclease. > > No explanation of enhanced rates of cutting within zones of protection has > ever been advanced based upon the double helical model of duplex DNA. > > 47 Contact Points between a Positive Transcription Factor and the > Xenopus 5S RNA Gene; S. Sakonju & D.D. Brown; Cell Vol 31 (1982) 395 - 405 > > 48 DNA Bending and its Relation to Nucleosome Positioning; H.R. Drew > & A.A. Travers; J Mol Biol Vol 186 (1985) 773 - 790 > --------------------------------------------------------------- Clive > Delmonte > > > > surely there is a philosophical difficulty in using our hazily understood model of one situation, viz the interaction of proteins with DNA, to criticise another model, the structure of DNA. Until we understand the former to a much greater degree, it is wrong to use this understanding to form another hypothesis. For instance, why is it not possible for a region of DNA to 'spool out' from the protein complex in such a way that a small region of DNA is accessible to attack- indead much more accesible than the surrounding region which is in intimate contact with the protein; it is therefore subject to enhanced cleavage relative to surrounding regions (it is also constrained in its position and may be strained due to its highly curved topology such that it is readiy cleaved). this 'hypothesis' may well be bunkum, but until considered, can the presence of readily cleaved areas in a DNA-protein complex really be used as evidence for or against a particular model for the structure of DNA? .