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Rad dostupan nakon 2019-02-21
disertacija
31
0
Compaction of nucleic acids
physical mechanisms and biological relevance
Sanjin Marion (2017)
Sveučilište u Zagrebu
Prirodoslovno-matematički fakultet
Fizički odsjek
Za citiranje koristite ovu mrežnu adresu:
https://urn.nsk.hr/urn:nbn:hr:217:999923
Podaci o radu
Naslov
Compaction of nucleic acids : physical mechanisms and biological relevance
Autor
Sanjin Marion
Voditelj/Mentor
Antonio Šiber
Sažetak rada
Packing of nucleic acids inside (naturally occurring) confined spaces presents an intriguing problem of compacting a long and highly charged polymer into a small space possibly crowded with other particles (proteins). For example, viruses have a large amount of genomic information that is encoded in nucleic acids packed in small spaces resulting in high densities of matter. The arising interactions are coupled to the confinement giving a more complex phase diagram than expected in bulk. In this work we study the problem of packing nucleic acids in confined spaces in the context of physical virology. First, we study compacted states of DNA including condensed DNA in cells and confined DNA in bacteriophage capsids. We apply polymer and liquid crystal theory along with mean field approximations for the bending energy to characterize the state of DNA. The resulting framework is used to explain in vivo ejection of DNA from a bacteriophage into a Gram-positive bacteria based only on thermodynamic considerations, without invoking any active cellular mechanisms. The packing mechanism for DNA with condensing proteins in adenoviruses is studied by comparing Langevin dynamics simulations of effective particle models, representing condensing proteins, with experimental data. The DNA is found to act as an effective medium for condensing core protein interactions. A backbone of DNA linking the condensing proteins is not needed to explain the experimental results. To further explain such systems, we construct a full model of packed polymer and condensing proteins inside spherical confinement using Langevin dynamics. Internal organization of condensing particles shows that they tend to cover themselves with the DNA polymer which provides an effective medium for interactions with other condensers, confirming the applicability of our effective model for core particle organization in adenoviruses. Crowding of the viral interior and confinement influences the conformation of the DNA and protein, facilitating more direct contacts between the DNA polymer and the condensing particles, and modifying the interactions between them. Our model is able to explain the general internal organization of adenovirus cores, and provide insight into packing of genetic material in similar systems.
Ključne riječi
physical virology
nucleic acids
confinement
DNA condensation
protein-DNA mixtures
crowding
Naslov na drugom jeziku (hrvatski)
Sažimanje nukleinskih kiselina : fizikalni mehanizmi i biološka relevantnost
Povjerenstvo za obranu
Antonio Šiber
(predsjednik povjerenstva)
Ustanova koja je dodijelila akademski/stručni stupanj
Sveučilište u Zagrebu
Prirodoslovno-matematički fakultet
Ustrojstvena jedinica niže razine
Fizički odsjek
Mjesto
Zagreb
Država obrane
Hrvatska
Znanstveno područje, polje, grana
PRIRODNE ZNANOSTI
Fizika
UDK
53
PRIRODNE ZNANOSTI
Fizika
Vrsta studija
sveučilišni
Stupanj
poslijediplomski doktorski
Naziv studijskog programa
Fizika
Akademski / stručni naziv
doktor/doktorica znanosti, područje prirodnih znanosti, polje fizika
Kratica akademskog / stručnog naziva
dr. sc.
Vrsta rada
disertacija
Jezik
engleski
Datum obrane
2017-02-21
Opseg
123 str.
Verzija
obranjena verzija
Vrsta resursa
tekst
Prava pristupa
Rad dostupan nakon 2019-02-21
Uvjeti korištenja rada
URN:NBN
https://urn.nsk.hr/urn:nbn:hr:217:999923
Pohranio
Iva Čizmin