Statistical Physics of DNA: Melting and Confinement Effects

Sammanfattning: Investigation of single macromolecules makes it possible to gain insight into and characterize important biological processes. DNA as the molecule of life is of special interest here. In this thesis tools from statistical physics are used to study different aspects of DNA confined to nanochannels, with particular regard to its denaturation properties. The study of DNA melting from the theoretical point of view is not only relevant for the understanding of the properties of that macromolecule, but also opens up for promising applications, notably for sequence and genotype identification through measurements of local melting probabilities. In paper I, we study both experimentally and theoretically the unfolding of fluorescently labelled circular DNA confined in a nanochannel to its linear configuration and its equilibrium conformational statistics. This is of special relevance for the analysis of bacterial DNA, which is mostly found in a circular form. In paper II, we introduce long linear DNA in newly designed meandering nanochannels that make it possible to study entire chromosomes in a single frame of the microscope. Using our new image analysis tools we extract barcodes, a succession of unmelted fluorescent DNA regions and melted dark regions, and successfully align it to a theoretical local melting profile. In paper III, we introduce a coarse-grained model for the calculation of theoretical barcodes by looking at the ground state instead of equilibrium probabilities with all possible states. We show that this model significantly reduces computational speed and storage requirements. Papers IV and V address the question on how the melting properties of DNA change upon confinement. We show for idealized and for more realistic models that the melting transition broadens and that the melting temperature decreases with increasing confinement for realistic values for the channel size and flexibility parameters of the DNA.