From owner-biophys@hgmp.mrc.ac.uk Sun May 4 08:18:11 2003 Return-Path: X-Original-To: biophys-outgoing Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with SMTP id 45E367D160 for ; Sun, 4 May 2003 08:18:11 +0100 (BST) X-Original-To: biophys-list@hgmp.mrc.ac.uk Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id D73C57D353 for ; Sun, 4 May 2003 08:18:10 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 500D77D160 for ; Sun, 4 May 2003 08:18:09 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.11.6+Sun/8.8.8) id h447I8p06686 for biophys-list@hgmp.mrc.ac.uk; Sun, 4 May 2003 08:18:08 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: "Enzo Di Giulio" X-Newsgroups: bionet.biophysics Subject: Introns Date: Sun, 4 May 2003 08:59:08 +0200 Organization: MC-link SpA InterNetNews site Lines: 93 Message-ID: X-Complaints-To: usenet@newsreader2.mclink.it X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 To: biophys@hgmp.mrc.ac.uk Sender: owner-biophys@hgmp.mrc.ac.uk Precedence: bulk Introns: a hypothesis on their origin, function, elimination. Rather than being molecular junk, introns may have a meaningful role in the structure of DNA. In the following the 'story' of introns is sketched on the basis of the 'theory of electroscalenes' (E.S.T.). This theory investigates on the electrostatic features of the heteroatomic molecules of biochemistry, using the schemata of abstract entities: clusters of linked electric charges (with links capable of rotating around their axis, for flexibility). The name scalene means that for these structures to be interesting, they must be irregular (not symmetrical). A scalene is a sort of electrical skeleton of a molecule, its charges coinciding (approximately) with charge concentrations along the molecular architecture. Natural environments are ionic solutions, therefore electric fields are of the diffuse charge type: the potential (x,y,z) is a solution of the Poisson equation, rather than the Laplace equation that rules common dielectric fields. This leads to a fundamental property: provided parameters satisfy some conditions, the electrical forces acting on the scalene can zero in at a definite point in space and the scalene can sit in equilibrium in this 'address'. Even at the two-dimension level, that is accessible to simple mathematics, a number of properties of natural systems can thus be given reasonable justification. In particular, the theory can account for the specificity of some reactions. Long linear scalenes can simulate natural polymers like polynucleotides and polypeptide. 'Polyscalenes' of orderly structure possess an address in particular fields: they can be used to represent genes. Primitive seawaters contained all sort of soluble molecules, waiting to meet their chemical fate. In times when earthquakes and volcanic eruptions were intense and frequent, strong electric fields accompanied the mutual sliding of rock layers. In the diffuse charge environment of sea waters this gave way to active sites that acted on specific molecules catalyzing chemical conversions. Polymer science knows the way ionic catalysts cen select specific monomers to generate long chain of specific structure. Under the influence of electric fields, it was then possible to collect a great number of monomer units in homo- or co-polymers that dispersed in the seawater environment. The copolymers of particular purins and pyrimidines with short phosphor units and the copolymers of a restricted number of alpha amino acids were so robust to survive degradation for long stretches of time: enough to reach the shelter, as explained below, of lipid bubbles. This chemical selection of nucleic acids and polypeptides following the creation of specific catalytic sites is the origin of the complex process of development of living structures. The peculiar properties of lipids generated hollow spheres that realized the separation of an inside from the outside. The membranes attracted lipo-soluble molecules. The presence of electric charges on their surface generated in the inside an electric field. As can be shown, this field has a zero-intensity zone at the center of the structure: a zone (widely coinciding with the cell nucleus) that can be called a 'crater'. This crater acted as an attractor on charge-carrying polymers. Polynucleotides and polypeptide were sucked in, with negatively charged nucleic acids 'falling' in the crater and rolling up in a compact mass. As ionic polymerization never produces perfect isotactic polymers, the chains contained non-isotactic sequences. Polynucleic chains consisted of orderly sequences with helically disposed monomer triplets, alternating with non-isotactic sequences. In the cellular fields, the first (exons) would lie along lines of force, the second (introns) remained as free-bending linking elements. Is this the beginning of a cell. In a complete cell orderly polynucleotide sequences may be caught up by cellular fields displaying particular patterns (depending on the development stage of the cell). If specifity conditions are met the macromolecules protrude from the central mass, sliding along a line of force till they reach their address. Their linear configuration makes them accessible to replication enzymes. These sequences are the expressed genes (exons). They are linked to the 'next' exon and/or the central mass by strings of flexible introns. In conjunction with the cellular field, variable with the cell stage, they determine the kind of cell that is active at any time. The function of introns is then to connect the regular sequences forming genes into one and the same linear element (chromosome). The problem of a code realizable with chemical means has been solved by nature by this superposition of tasks in a random-access, ribbon-like structure. After replication, the structure must get rid of excess units and send to the ribosomes a sequence of 'genes only'. This comes about spontaneously: on the spot where it is formed, a messenger RNA molecule finds itself in an 'alien' field, and to diminish the moment acting on the molecule it rolls up to a closed curve. ( This can be seen in two dimensions calculating the total moment when the units are bent with an angle of increasing value, till the sequence rolls up to a closed polygon: the moment decreases progressively to become zero in the full 'circle'). Then the end of one exon and the beginning of the next are brought to close proximity (a 'capital omega' effect) and join, while the free intron sequence detaches itself and is quickly demolished. The orderly sequences (RNA-copies of genes) travel along lines of force that, like rails of a railway, pass through the nuclear membrane pores and lead to the ribosome. .