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Statistical Physics of DNA: Melting and Confinement Effects

Reiter-Schad, Michaela LU (2015)
Abstract (Swedish)
Popular Abstract in Swedish

Studier av enstaka makromolekyler gör det möjligt att få insikt i och karakterisera viktiga biologiska processer. DNA, livets molekyl, är av särskilt intresse här. I denna avhandling användar vi metoder från statistisk fysik för att studera olika aspekter av DNA i nanokanaler och dess smältegenskaper. DNA-smältning är inte bara relevant för förståelsen av denna molekyls egenskaper, utan öppnar också upp för tillämpningar såsom grov-kornig identifiering av DNA sekvenser och genotyper, detta genom mätningar av sekvens-känsliga DNA-streckkoder orsakat av lokal DNA-smältning.

I artikel I studerar vi hur fluorescerande cirkulära DNA molekyler i en nanokanal vecklas ut till sina linjära... (More)
Popular Abstract in Swedish

Studier av enstaka makromolekyler gör det möjligt att få insikt i och karakterisera viktiga biologiska processer. DNA, livets molekyl, är av särskilt intresse här. I denna avhandling användar vi metoder från statistisk fysik för att studera olika aspekter av DNA i nanokanaler och dess smältegenskaper. DNA-smältning är inte bara relevant för förståelsen av denna molekyls egenskaper, utan öppnar också upp för tillämpningar såsom grov-kornig identifiering av DNA sekvenser och genotyper, detta genom mätningar av sekvens-känsliga DNA-streckkoder orsakat av lokal DNA-smältning.

I artikel I studerar vi hur fluorescerande cirkulära DNA molekyler i en nanokanal vecklas ut till sina linjära konformationer, samt undersöker dessa molekylers jämviktsegenskaper. Detta är av särskild betydelse för analys av bakterie-DNA, som oftast antar cirkulär form. I artikel II analyserar vi långa linjära DNA i meander-formade nanokanaler. Denna typ av kanaler gör det möjligt att studera hela kromosomer i en enda mikroskop-bild. Med hjälp av våra bildanalysverktyg extraherar vi DNA-streckkoder, en följd av osmält fluorescerande DNA regioner och smält mörka regioner, och anpassar dessa experimentalla DNA-streckkoder till teoretiska lokal smältprofiler. I artikel III introducerar vi en grovkorniga metod för beräkningen av teoretiska streckkoder som bygger på identifiering av ett mest sannolikt tillstånd, DNA-"grundtillstånd". Till skillnad från tidigare metoder, behöver vi därför inte summera över alla möjliga konfigurationer. Vi visar att denna metod signifikant minskar beräkningstid och lagringskrav jämfört med tidigare metoder. Artiklarna IV och V handlar om frågan hur smältegenskaper av DNA förändras p.g.a. instängning i en nanokanal. Vi visar, både för en idealiserad och för mer realistiska modeller, att smältövergången breddas och att smälttemperaturen minskar med minskande kanal-diameter för realistiska värden för kanalstorleken och flexibilitetsparametrar för DNA. (Less)
Abstract
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... (More)
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. (Less)
Please use this url to cite or link to this publication:
author
supervisor
opponent
  • Orlandini, Enzo, Department of Physics, University of Padova
organization
publishing date
type
Thesis
publication status
published
subject
keywords
biopolymers, DNA melting, DNA confinement, random walk, Fysicumarkivet A:2015:Reiter-Scad
pages
119 pages
publisher
Department of Astronomy and Theoretical Physics, Lund University
defense location
lecture hall F, Department of Physics
defense date
2015-05-22 10:15
ISBN
978-91-7623-316-0 (pdf)
978-91-7623-315-3 (print)
language
English
LU publication?
yes
id
070e16b0-a974-424e-be1a-8c032be512b0 (old id 5277541)
date added to LUP
2015-05-06 12:23:19
date last changed
2016-09-19 08:45:14
@misc{070e16b0-a974-424e-be1a-8c032be512b0,
  abstract     = {Investigation of single macromolecules makes it possible to gain insight into and characterize important biological processes. DNA as the molecule of life is<br/><br>
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 <br/><br>
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.<br/><br>
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.},
  author       = {Reiter-Schad, Michaela},
  isbn         = {978-91-7623-316-0 (pdf)},
  keyword      = {biopolymers,DNA melting,DNA confinement,random walk,Fysicumarkivet A:2015:Reiter-Scad},
  language     = {eng},
  pages        = {119},
  publisher    = {ARRAY(0xb07b4d8)},
  title        = {Statistical Physics of DNA: Melting and Confinement Effects},
  year         = {2015},
}