Single molecule studies of processes involved in genome maintenance

Preserving the integrity of a genome is essential for life. A given cell has a multitude of maintenance mechanisms which allow it to respond to environmental demands. During my PhD, I used single-molecule optical trapping to identify biophysical features of helicase regulation, DNA secondary structure formation, and phase-separation, all crucial to maintain the genome and prevent disease. Helicases are biomolecular motors that unwind nucleic acids and are involved in all aspects of DNA metabolism. Uncontrolled helicase unwinding is detrimental; therefore, helicase activity must be attuned to a cellular context. The detailed mechanisms that regulate unwinding are not well understood. I studied mechanisms that regulate a helicase called Rep, which is involved in DNA repair and replication restart in E. coli. I focused on quantifying the effects of removal and light-induced rotation of an auto-inhibitory subdomain, duplex stability and geometry, and interaction with accessory proteins. I found that the helicase unwinds longer stretches of DNA and at higher speed without the 2B subdomain or when the 2B subdomain is rotated with light. The helicase processivity and speed increase as the duplex is destabilized with force. Regulation by an accessory protein PriC does not involve the 2B subdomain. The presence of PriC has a minor role on unwinding processivity and does not change the speed of unwinding. The primary role of PriC is to stabilize Rep on DNA and to recruit a Rep dimer onto a DNA fork. The secondary role of PriC is to assist Rep in the removal of DNA-bound protein SSB. The final role of PriC is to enhance Rep unwinding with a specificity to a forked/double-tailed DNA. My findings establish a dynamical model of fork remodeling where PriC recruits Rep to the front of an SSB-bound replication fork, allowing Rep to open enough DNA to reload the replicative helicase and restart replication. Self-assembly of nucleic acids provides another layer of regulation around the genome. Guanine-rich regions within the DNA can self-organize into planar structures that stack on top of each other forming a guanine-quadruplex (GQ). GQs vary in structure, and their mechanical stabilities under physiological levels of tension are not known. Based on the unfolding force of individual GQs, I determined that there at least six unique conformations, which form stochastically from an unfolded state. Lastly, nucleic acids and proteins can self-organize into a membranelles compartments many of which regulate the dynamics of DNA processes. Fused in sarcoma (FUS) is a nucleic-acid binding protein with many disease-linked mutations. I determined that a glycine mutation impedes FUS-condensate fusion with itself and with wild type.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Molecular & Integrative Physi

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2022

Author dc:creator

• Makurath, Monika A

Contributors dc:contributor

• Chemla, Yann R
• Grosman, Claudio
• Selvin, Paul R
• Golding, Ido

• single molecule
• molecular motors

Statement dc:rights

• Copyright 2022 Monika Makurath

Language dc:language

en, eng

Handle dc:identifier

https://hdl.handle.net/2142/122081

OAI record oai:identifier

https://www.ideals.illinois.edu/oai-pmh?verb=GetRecord&metadataPrefix=etdms&identifier=oai%3Awww.ideals.illinois.edu%3A2142%2F122081