From owner-biophysics@net.bio.net Fri Jan 08 22:00:00 1999 From: "clive delmonte" Newsgroups: bionet.biophysics Subject: DNA Structure: Puzzle Number 18 Date: Fri, 8 Jan 1999 19:35:00 -0000 Lines: 56 X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 NNTP-Posting-Host: 195.7.225.221 Message-ID: <369733f6.0@news.netdirect.net.uk> X-Trace: 9 Jan 1999 10:48:22 GMT, 195.7.225.221 Path: biosci!news.alaska.edu!newsfeed.acns.nwu.edu!newsfeed.berkeley.edu!btnet-peer!btnet-feed2!btnet!news-peer.netdirect.net.uk!news.netdirect.net.uk!195.7.225.221 The Diameter of Tetraplexes under AFM Vesenka and colleagues have measured the strand height of DNA tetraplexes. Their guanine-rich tetraplexes were found to have a strand height, i.e., diameter of 2.1 to 2.5nm (40). Curiously enough, this is the height which should be recorded for the DNA double helix under AFM and STM, but no-one has ever found these values, or anything approaching them, for duplex DNA. It seems that this situation has caused Vesenka to reflect on the meaning of the height measurements for duplex and tetraplex DNA (41). Determined readers of these Puzzles will discern a different explanation (42). If two of the true side-by-side DNA duplexes caught on STM by Lee et al. (Puzzle 1, ref. 1, Figure 3b (duplex height = 1.3 nm)) are laid one upon the other, et voila! we have a true side-by-side tetraplex with a height around 2.5 nm. The implied pairing of base pairs into tetrads was described by Loewdin long ago (43). Equally important, and in accord with the structure of Lee et al., using AFM, Vesenka's group reports "...no significant differences in duplex and quadruplex DNA width." (44) 40 A new DNA nanostructure, the G-wire, imaged by scanning probe microscopy; T.C. Marsh, J. Vesenka & E. Henderson; Nucl Acids Res Vol 23 (1995) 696 - 700 41 Atomic Force Microscopy of Duplex DNA Diameter Paradox; J. Vesenka; Scanning Vol 18 (1996) 133 - 134 42 Advances in AFM & STM Applied to the Nucleic Acids; Clive Delmonte (1997); ISBN 0 9512276 2 9; Chapter 8, Figure 8.1 43 Electronic Aspects of Biochemistry, Chapter by P.-O. Loewdin, Editor: B. Pullman; Academic Press (1963) 44 The morphology of duplex and quadruplex DNA on mica; Tera Muir et al.; Draft paper kindly supplied by James Vesenka prior to publication in J Vac Sci & Tech. (1996) -------------------------------------------------------------- Clive Delmonte .