Speculations about alternative DNA structures

An alternative model to the Watson & Crick (W&C) double DNA-spiral and the Pauling & Corey (P&C) triple spiral is presented. In this model: (1) the rotation axis of the polynucleotide chain is in the ribose ring; (2) there is a -H- bond or direct covalent bond between the O2 (PO4 and C2' (in ribose) which makes the nucleic acid strands 'stiff'; (3) when there is a covalent bond between O2 and C2% the unit of the DNA is the ribonucleoside 2', 3'-cyclic monophosphate, an intermediate form between DNA and RNA; (4) the bases point outwards from the rotation axis and may interact with each other to connect 2-4 strands together through complementary base pairs; (5) two strands may, but do not necessarily, form a helical structure and if they do, the interacting strands do not turn around each other. The architecture of this model, termed the Homulus DNA model is open (in contrast to the inverted W&C model) and using it might help us to understand the nature of some specific DNA-protein interactions, ordered chromatin formation (coiling and de-coiling), specific gene-to-gene interaction (gene targeting). It is possible that a small portion of the total DNA, the transcribed, 'working DNA', might be built by this way. (C) 2003 Elsevier Science Ltd. All rights reserved.