From owner-biophysics@net.bio.net Sun Apr 18 23:00:00 1999 From: "Clive Delmonte" Newsgroups: bionet.biophysics Subject: DNA Structure: Puzzle #14 (Version 2) Date: Mon, 19 Apr 1999 11:06:40 +0100 X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 NNTP-Posting-Host: 195.7.227.167 Message-ID: <371af251.0@news.netdirect.net.uk> X-Trace: 19 Apr 1999 10:07:29 GMT, 195.7.227.167 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!dispose.news.demon.net!demon!ayres.ftech.net!news.ftech.net!peer.news.nildram.co.uk!news-peer.netdirect.net.uk!news.netdirect.net.uk!195.7.227.167 Lines: 44 The Methylation of Nucleosomal DNA Talking about nucleosomal DNA (Puzzle #13) brings us to McGhee & Felsenfeld (39) who reacted nucleosomal DNA with dimethyl sulphate and recorded their surprise at their results: "We are unable to detect any significant difference between the reactivity of the N7 of guanines in nucleosomal DNA and of that in naked DNA... Contrary to our expectation, there is no detectable periodic modulation of reactivity corresponding to the twist of DNA on the nucleosome surface... Judging from the relative concentration of intact unreacted DNA remaining, the guanines in the nucleosome reacted about 20 - 30% FASTER (their emphasis) than in the isolated DNA... " For a double helix, about half the DNA wrapped around a nucleosome core should lie on the inside in contact with the histone proteins, or up against adjacent turns of the DNA and therefore offer reduced accessibility to methylation. Crucially, the double helix offers no clue as to how the methylation of nucleosomal DNA could be faster than it is for naked DNA. There is a clue in the true side-by-side structure found by Lee et al. (Puzzle #1, ref. 1). With the base pairs linked directly across the sugar-phosphate chains, and stacked upon each other, all the base pairs would be equally exposed to the methylating reagent when wound onto the cores with their rear face in contact with the histones (see attachment to Puzzle#1 taken from (37)). The reaction could be faster when wound onto nucleosomal cores because there would be no folding or twisting of the DNA, which would otherwise obstruct the approach of the reagent. ---------------------------------------------------------------- 39 Reaction of Nucleosomal DNA with Dimethyl Sulfate; J.D. McGhee & G. Felsenfeld; Proc. Nat. Acad. Sci. (USA) Vol 76 (1979) 2133 - 2137 ------------------------------------------------------------ Clive Delmonte .