Title: Thermodynamics of DNA Hybridization: Theory and Applications
Other Titles: Thermodynamica van DNA-Hybridisatie: Theorie en Toepassingen
Authors: Hadiwikarta, Wahyu; R0266847
Issue Date: 7-Nov-2014
Abstract: In this thesis we discuss the thermodynamic properties of DNA hybridization, which is the recombination of two separate strands to form a double helical structure. In particular we focus on the analysis of hybridization in DNA microarrays, which are devices used in biotechnology to investigate the abundance and composition of DNA sequences in a given biological sample. In microarrays, hybridization takes place between the sample sequences in solution and some sequences covalently bond at a solid surface. Hybridization reactions in a bulk solution have been characterized using the so-called nearest-neighbor model, which provides an estimatefor the free energy ΔG of the hybridization process. The nearest-neighbor model relies upon the additivity principle, which states that the ΔG for a sequence of DNA is given by a sum of dinucleotide terms accounting for hydrogen bonding and stacking interactions between pairs of nucleotides.
Our work can be divided into two parts. In the first part of the thesis we focused on the fundamental properties ofhybridization in DNA microarrays. We analyzed a set of controlled experiments and tested the validity of the nearest-neighbor and Langmuir models. We devoted quite some effort to explore the limitations of the additivity principle. To this purpose we designed experiments in which a single sequence is placed in a solution at a given concentration, while a large number of different sequences (typically 10
Publication status: published
KU Leuven publication type: TH
Appears in Collections:Theoretical Physics Section

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