title: Premeltons in DNA.
abstract: Premeltons are examples of emergent-structures (i.e., structural-solitons) that arise spontaneously in DNA due to the presence of nonlinear-excitations in its structure. They are of two kinds: B-B (or A-A) premeltons form at specific DNA-regions to nucleate site-specific DNA melting. These are stationary and, being globally-nontopological, undergo breather-motions that allow drugs and dyes to intercalate into DNA. B-A (or A-B) premeltons, on the other hand, are mobile, and being globally-topological, act as phase-boundaries transforming B- into A-DNA during the structural phase-transition. They are not expected to undergo breather motions. A key feature of both types of premeltons is the presence of an intermediate structural-form in their central regions (proposed as being a transition-state intermediate in DNA-melting and in the B- to A-transition), which differs from either A- or B-DNA. Called beta-DNA, this is both metastable and hyperflexible--and contains an alternating sugar-puckering pattern along the polymer backbone combined with the partial unstacking (in its lower energy-forms) of every-other base-pair. Beta-DNA is connected to either B- or to A-DNA on either side by boundaries possessing a gradation of nonlinear structural-change, these being called the kink and the antikink regions. The presence of premeltons in DNA leads to a unifying theory to understand much of DNA physical chemistry and molecular biology. In particular, premeltons are predicted to define the 5' and 3' ends of genes in naked-DNA and DNA in active-chromatin, this having important implications for understanding physical aspects of the initiation, elongation and termination of RNA-synthesis during transcription. For these and other reasons, the model will be of broader interest to the general-audience working in these areas. The model explains a wide variety of data, and carries with it a number of experimental predictions--all readily testable--as will be described in this review.
authors.affiliation: Departments of Chemistry and Molecular Biophysics, University of Rochester, Rochester, NY, 14642, USA. sobell@localnet.com.
authors.forename: Henry M
authors.identifier: http://orcid.org/0000-0003-0706-7681
authors.initials: HM
authors.lastname: Sobell
mesh_terms: D001665:Binding Sites; D055598:Chemical Phenomena; D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D044704:DNA, A-Form / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D059371:DNA, B-Form / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D007364:Intercalating Agents / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D008967:Molecular Biology / Q000379:methods; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation
chemical_list: D044704:DNA, A-Form; D059371:DNA, B-Form; D007364:Intercalating Agents; D004247:DNA
keywords: Actinomycin-DNA binding; B- to A- DNA structural phase-transition; DNA transcription; DNA-melting and premelting; Elongation; Ethidium-DNA binding; Gene-regulation; Initiation; Intercalation; Meltons; Premeltons; Protein: DNA allosterism; RNA-polymerase: promoter recognition; Termination of RNA-synthesis