Interaction of Proliferating Cell Nuclear Antigen With DNA at the Single Molecule Level

Handle URI:
http://hdl.handle.net/10754/609052
Title:
Interaction of Proliferating Cell Nuclear Antigen With DNA at the Single Molecule Level
Authors:
Raducanu, Vlad-Stefan ( 0000-0001-6722-9262 )
Abstract:
Proliferating cell nuclear antigen (PCNA) is a key factor involved in Eukaryotic DNA replication and repair, as well as other cellular pathways. Its importance comes mainly from two aspects: the large numbers of interacting partners and the mechanism of facilitated diffusion along the DNA. The large numbers of interacting partners makes PCNA a necessary factor to consider when studying DNA replication, either in vitro or in vivo. The mechanism of facilitated diffusion along the DNA, i.e. sliding along the duplex, reduces the six degrees of freedom of the molecule, three degrees of freedom of translation and three degrees of freedom of rotation, to only two, translation along the duplex and rotational tracking of the helix. Through this mechanism PCNA can recruit its partner proteins and localize them to the right spot on the DNA, maybe in the right spatial orientation, more effectively and in coordination with other proteins. Passive loading of the closed PCNA ring on the DNA without free ends is a topologically forbidden process. Replication factor C (RFC) uses energy of ATP hydrolysis to mechanically open the PCNA ring and load it on the dsDNA. The first half of the introduction gives overview of PCNA and RFC and the loading mechanism of PCNA on dsDNA. The second half is dedicated to a diffusion model and to an algorithm for analyzing PCNA sliding. PCNA and RFC were successfully purified, simulations and a mean squared displacement analysis algorithm were run and showed good stability and experimental PCNA sliding data was analyzed and led to parameters similar to the ones in literature.
Advisors:
Hamdan, Samir
Committee Member:
Habuchi, Satoshi ( 0000-0002-6663-2807 ) ; Liberale, Carlo ( 0000-0002-5653-199X )
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division; Bioscience
Program:
Bioscience
Issue Date:
May-2016
Type:
Thesis
Appears in Collections:
Theses; Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.advisorHamdan, Samiren
dc.contributor.authorRaducanu, Vlad-Stefanen
dc.date.accessioned2016-05-11T13:22:36Zen
dc.date.available2016-05-11T13:22:36Zen
dc.date.issued2016-05en
dc.identifier.urihttp://hdl.handle.net/10754/609052en
dc.description.abstractProliferating cell nuclear antigen (PCNA) is a key factor involved in Eukaryotic DNA replication and repair, as well as other cellular pathways. Its importance comes mainly from two aspects: the large numbers of interacting partners and the mechanism of facilitated diffusion along the DNA. The large numbers of interacting partners makes PCNA a necessary factor to consider when studying DNA replication, either in vitro or in vivo. The mechanism of facilitated diffusion along the DNA, i.e. sliding along the duplex, reduces the six degrees of freedom of the molecule, three degrees of freedom of translation and three degrees of freedom of rotation, to only two, translation along the duplex and rotational tracking of the helix. Through this mechanism PCNA can recruit its partner proteins and localize them to the right spot on the DNA, maybe in the right spatial orientation, more effectively and in coordination with other proteins. Passive loading of the closed PCNA ring on the DNA without free ends is a topologically forbidden process. Replication factor C (RFC) uses energy of ATP hydrolysis to mechanically open the PCNA ring and load it on the dsDNA. The first half of the introduction gives overview of PCNA and RFC and the loading mechanism of PCNA on dsDNA. The second half is dedicated to a diffusion model and to an algorithm for analyzing PCNA sliding. PCNA and RFC were successfully purified, simulations and a mean squared displacement analysis algorithm were run and showed good stability and experimental PCNA sliding data was analyzed and led to parameters similar to the ones in literature.en
dc.language.isoenen
dc.subjectPCNAen
dc.subjectRFCen
dc.subjectDNAen
dc.subjectSlidingen
dc.subjectMSDen
dc.subjectDiffusionen
dc.titleInteraction of Proliferating Cell Nuclear Antigen With DNA at the Single Molecule Levelen
dc.typeThesisen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentBioscienceen
thesis.degree.grantorKing Abdullah University of Science and Technologyen_GB
dc.contributor.committeememberHabuchi, Satoshien
dc.contributor.committeememberLiberale, Carloen
thesis.degree.disciplineBioscienceen
thesis.degree.nameMaster of Scienceen
dc.person.id133289en
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