From owner-biophysics@net.bio.net Thu Dec 10 22:00:00 1998 From: "clive delmonte" Newsgroups: bionet.biophysics Subject: DNA Structure:Puzzle Number 10 Date: Thu, 10 Dec 1998 07:07:54 -0000 Lines: 40 X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 NNTP-Posting-Host: 195.7.225.242 Message-ID: <367128e1.0@news.netdirect.net.uk> X-Trace: 11 Dec 1998 14:14:57 GMT, 195.7.225.242 Path: biosci!agate!newsfeed.berkeley.edu!btnet-peer!btnet-feed2!btnet!news-peer.netdirect.net.uk!news.netdirect.net.uk!195.7.225.242 Lohr et al. (17) equilibrated histone cores onto DNA, cleaved the complexes with deoxyribonuclease 1 and resolved the resulting fragments of DNA up to a maximum of some 300 bp. They reported that: "Since the average size of the nucleosomal repeat in yeast is 160 bp...the presence of discrete, regularly spaced bands between 160 and 300 bases shows that ... there is structural regularity extending over regions much larger than one nucleosomal repeat unit. Even when digestion produces fragments so large that they must have arisen from cleavages within two different nucleosomes, the fragments are still of discrete sizes, spaced at intervals of 10 bases.....The extended ladder is extremely clear and background free." How would deoxyribonuclease 1, cleaving a cylindrically symmetrical double helical DNA within both the linker regions and within the nucleosomal core DNA, always produce fragments related as multiples of 10 bp, in an extended ladder which is extremely clear and free of fragments of any intermediate differences in length ? The true side-by-side duplex DNA found by Lee et al. (Puzzle 1, ref. 1) is not cylindrically symmetrical, but the stacked base pairs are only accessible from one face of the duplex. Cleavage with deoxyribonuclease 1 can only take place in a regular manner producing fragments which are integer multiples of the pitch. Intermediate lengths and cutting at a range of azimuthal angles is not possible with the true side-by-side of Lee et al. 17 On the Occurrence of Nucleosome Phasing in Chromatin; D. Lohr, K. Tatchell & K.E. van Holde; Cell Vol 12 (1977) 829 - 836 -------------------------------------------------------------------------- Clive Delmonte .