Simulating the aggregation of DNA oligonucleotides

Cristofaro, Silvia (2019) Simulating the aggregation of DNA oligonucleotides. [Laurea magistrale], Università di Bologna, Corso di Studio in Chimica industriale [LM-DM270], Documento ad accesso riservato.
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Abstract

In this work we have studied, by means of Molecular Dynamics simulations, the process of denaturation and self-assembly of short oligonucleotides. Supramolecular ordering of DNA short strands is a promising field which is constantly enriched with new findings. Examples are provided by micellar and fibrils formations and due to the selectivity of DNA bindings, "intelligent" devices have been developed to perform simple logic operations. It is worth to notice that computer simulations of these DNA nanosystems would complement experiments with detailed insight into processes involved in self-assembly. In order to obtain an accurate description of the interactions involved in the complex structure of DNA we used oxDNA, a coarse-grained model developed by Ouldridge. We simulated the melting transition of 4, 6, and 8 base pair sequences. Sequence and length dependence were analyzed, specifically we compared thermodynamic parameters DeltaH, DeltaS and the melting temperature with literature results. Moreover, we have attempted to reproduce liquid crystal ordering of the ultrashort sequence GCCG at relatively high saline concentration, until now only experimentally observed in Bellini's works. We found that our simple model successfully reproduces the experimental phase sequence (isotropic, nematic, columnar) at T= 5 °C as a function of oligonucleotide concentration, and we fully characterized the microscopic structure of the three phases.

Abstract
Tipologia del documento
Tesi di laurea (Laurea magistrale)
Autore della tesi
Cristofaro, Silvia
Relatore della tesi
Correlatore della tesi
Scuola
Corso di studio
Indirizzo
CHIMICA INDUSTRIALE
Ordinamento Cds
DM270
Parole chiave
molecular dynamics DNA coarse-grained simulations self-assembly liquid crystals ordering melting temperatures
Data di discussione della Tesi
25 Ottobre 2019
URI

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