title: Parametric resonance in DNA.
abstract: We consider a simple mesoscopic model of DNA in which the binding of the RNA polymerase enzyme molecule to the promoter sequence of the DNA is included through a substrate energy term modeling the enzymatic interaction with the DNA strands. We focus on the differential system for solitary waves and derive conditions--in terms of the model parameters--for the occurrence of the parametric resonance phenomenon. We find that what truly matters for parametric resonance is not the ratio between the strength of the stacking and the inter-strand forces but the ratio between the substrate and the inter-strands. On the basis of these results, the standard objection that longitudinal motion is negligible because of the second order seems to fail, suggesting that all the studies involving the longitudinal degree of freedom in DNA should be reconsidered when the interaction of the RNA polymerase with the DNA macromolecule is not neglected.
authors: Dipartimento di Ingegneria Elettrica e dell'Informazione, Università degli Studi di Cassino e del Lazio Meridionale, 03043, Cassino, Italy, d.lacitignola@unicas.it.
authors: Deborah
authors: D
authors: Lacitignola
authors: Giuseppe
authors: G
authors: Saccomandi
mesh_terms: D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism; D055641:Mathematical Concepts; D008956:Models, Chemical; D008958:Models, Molecular; D009038:Motion; D009690:Nucleic Acid Conformation; D011401:Promoter Regions, Genetic; D055672:Static Electricity; D013816:Thermodynamics; D014158:Transcription, Genetic
chemical_list: D004247:DNA; D012321:DNA-Directed RNA Polymerases