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Dissertations / Theses on the topic 'Single Stranded DNA Binding Protein (SSBb)'

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Published: 6 September 2023

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1

Bain, Amanda Louise. "Investigation of the Physiological Role of Ssb1 using an in-vivo Targeted Mouse Model." Thesis, Griffith University, 2013. http://hdl.handle.net/10072/366937.

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Single-stranded DNA binding proteins (SSBs) are critical for binding, protecting and sequestering single-stranded DNA intermediates during multiple cellular transactions, including DNA replication, repair and transcription. The canonical SSB in eukaryotes, Replication Protein A (RPA), is a heterotrimeric protein essential for numerous cellular processes, including DNA repair by homologous recombination (HR). Recently, Richard et al. (2008) identified a novel human SSB, designated human Single-Stranded DNA Binding protein 1 (hSSB1), critical to DNA repair and the maintenance of genomic stabilit

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2

Jordan, Christian. "Helicase-SSB Interactions In Recombination-Dependent DNA Repair and Replication." ScholarWorks @ UVM, 2014. http://scholarworks.uvm.edu/graddis/270.

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Dda, one of three helicases encoded by bacteriophage T4, has been well- characterized biochemically but its biological role remains unclear. It is thought to be involved in origin-dependent replication, recombination-dependent replication, anti- recombination, recombination repair, as well as in replication fork progression past template-bound nucleosomes and RNA polymerase. One of the proteins that most strongly interacts with Dda, Gp32, is the only single-stranded DNA binding protein (SSB) encoded by T4, is essential for DNA replication, recombination, and repair. Previous studies have shown

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3

In, Junghoon Erie Dorothy A. "Structure-function studies of late stages of E. Coli MMR interaction of DNA helicase II with single-stranded DNA binding protein SSB and MutL /." Chapel Hill, N.C. : University of North Carolina at Chapel Hill, 2008. http://dc.lib.unc.edu/u?/etd,2053.

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Thesis (Ph. D.)--University of North Carolina at Chapel Hill, 2008.<br>Title from electronic title page (viewed Feb. 17, 2009). "... in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Curriculum in Applied and Material Sciences." Discipline: Applied and Materials Sciences; Department/School: Applied and Materials Sciences.

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4

Nag, Purba. "Delineating the overlapping roles of the single-stranded DNA binding proteins Ssb1 and Ssb2 in the maintenance of genomic stability and intestinal homeostasis." Thesis, Griffith University, 2019. http://hdl.handle.net/10072/384796.

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Single stranded DNA (ssDNA) binding proteins (SSBPs), are known key players of DNA damage response (DDR) pathway and play an essential role in stabilising fragile ssDNA generated during DNA replication, transcription and repair. The canonical SSBP is the heterotrimeric Replication Protein A (RPA) which is involved in a number of key cellular processes including replication and repair via Homologous Recombination (HR) in the course of DNA damage. Our lab recently described two new SSBPs, termed SSB1 and SSB2 (also known as NABP2/OBFC2B/SOSS-B1 and NABP1/OBFC2A/SOSSB-2, respectively) which form

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5

Johnson, Vinu. "Structural and Biophysical Studies of Single-Stranded DNA Binding Proteins and dnaB Helicases, Proteins Involved in DNA Replication and Repair." University of Toledo / OhioLINK, 2007. http://rave.ohiolink.edu/etdc/view?acc_num=toledo1198939056.

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6

Howland, Christopher James. "The single-stranded DNA-binding protein gene of plasmid Colib-P9." Thesis, University of Leicester, 1989. http://hdl.handle.net/2381/34428.

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The Incil plasmid Colib-P9 was found to carry a single-stranded DNA-binding protein gene (ssb), and the cloned gene was able to suppress the UV and temperature-sensitivity of an ssb-l strain of Escherichia coli K-12. Determination of the nucleotide sequence of Colib ssb demonstrated that the gene shows considerable homology to the ssb gene of plasmid F. In contrast, Southern hybridization techniques indicated that the IncP plasmid RP4 lacks a gene with any extensive homology to F ssb. It was shown that the direction of transfer of Colib-P9 is such that the Colib ssb gene, which lies approximat

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7

Stroud, A. L. "Genetic analysis of RPA single-stranded DNA binding protein in Haloferax volcanii." Thesis, University of Nottingham, 2012. http://eprints.nottingham.ac.uk/12623/.

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Replication protein A (RPA) is a single-stranded DNA-binding protein that is present in all three domains of life. The roles of RPA include stabilising and protecting single- stranded DNA from nuclease degradation during DNA replication and repair. To achieve this, RPA uses an oligosaccharide-binding fold (OB fold) to bind single- stranded DNA. Haloferax volcanii encodes three RPAs – RPA1, RPA2 and RPA3, of which rpa1 and rpa3 are in operons with genes encoding associated proteins (APs). The APs belong to the COG3390 group of proteins found in Euryarchaeota and feature an OB fold. Genetic anal

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8

Morten, Michael J. "Developing novel single molecule analyses of the single-stranded DNA binding protein from Sulfolobus solfataricus." Thesis, University of St Andrews, 2015. http://hdl.handle.net/10023/7568.

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Single-stranded DNA binding proteins (SSB) bind to single-stranded DNA (ssDNA) that is generated by molecular machines such as helicases and polymerases. SSBs play crucial roles in DNA translation, replication and repair and their importance is demonstrated by their inclusion across all domains of life. The homotetrameric E. coli SSB and the heterotrimeric human RPA demonstrate how SSBs can vary structurally, but all fulfil their roles by employing oligonucleotide/oligosaccharide binding (OB) folds. Nucleofilaments of SSB proteins bound to ssDNA sequester the ssDNA strands, and in doing so pro

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9

Dodd, Isabel. "Characterisation of the single-stranded DNA binding protein encoded by Kaposi's sarcoma herpesvirus." Thesis, Cranfield University, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.421241.

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10

Ashton, Nicholas W. "Characterisation of human single-stranded DNA-binding protein 1 (hSSB1) regulation by post-translational modifications." Thesis, Queensland University of Technology, 2016. https://eprints.qut.edu.au/98660/1/Nicholas_Ashton_Thesis.pdf.

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Human single-stranded DNA-binding protein 1 (hSSB1) is required for the timely repair of double-strand DNA breaks, as well as the stabilisation and restart of stalled replication forks. In this work, evidence is provided that cellular survival in response to replication stress is promoted by dynamic phosphorylation of hSSB1 by the DNA-dependent protein kinase (DNA-PK) and PPP-family protein phosphatases. These data provide insight into the functional regulation of hSSB1 following replication fork disruption.

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11

Boutemy, Laurence S. "Analysis of the Interactions between the 5' to 3' Exonuclease and the Single-Stranded DNA-Binding Protein from Bacteriophage T4 and Related Phages." Connect to full text in OhioLINK ETD Center, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=toledo1223979052.

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Thesis (Ph. D.)--University of Toledo, 2008.<br>Typescript. "Submitted as partial fulfillment of the requirements for the Doctor of Philosophy in Chemistry." Includes bibliographical references (leaves 305-309).

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12

Jaffary, Syed Ali Naqi Raza. "The human single-stranded DNA binding protein 2 (HSSB2) and its novel role in the base excision repair pathway." Thesis, Queensland University of Technology, 2018. https://eprints.qut.edu.au/119175/1/Syed%20Ali%20Naqi%20Raza_Jaffary_Thesis.pdf.

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Genetic instability is the driver of cancer initiation and progression. The human single stranded DNA binding protein 2 is known to be involved in the prevention of such genetic instability. This project has highlighted how human single stranded DNA binding protein 2 is involved in a particular DNA repair pathway called, base excision repair. The researcher identified the role of human single stranded DNA binding protein 2 in the removal of uracils that have been added by mistake to the human genome. This project details the mechanism by which uracils are removed from the genome, shedding ligh

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13

Fisher, Mark. "Intra and extracellular responses to DNA damage." Thesis, Queensland University of Technology, 2021. https://eprints.qut.edu.au/214106/1/Mark_Fisher_Thesis.pdf.

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14

Senger, Anne Benedict. "A Study of DNA Replication and Repair Proteins from Bacteriophage T4 and a Related Phage." University of Toledo / OhioLINK, 2004. http://rave.ohiolink.edu/etdc/view?acc_num=toledo1104776177.

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15

Bonne-Andrea, Catherine. "Contribution à l'étude des propriétés et du rôle biologique de la protéine non-histone HMG1." Paris 6, 1986. http://www.theses.fr/1986PA066451.

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16

Cordonnier, Agnès. "Etude des mecanismes moleculaires de la replication de l'adn mitochondrial de xenopus laevis." Paris 6, 1987. http://www.theses.fr/1987PA066156.

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17

Gharizadeh, Baback. "Method development and applications of Pyrosequencing technology." Doctoral thesis, KTH, Biotechnology, 2003. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-3645.

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<p>The ability to determine nucleic acid sequences is one ofthe most important platforms for the detailed study ofbiological systems. Pyrosequencing technology is a relativelynovel DNA sequencing technique with multifaceted uniquecharacteristics, adjustable to different strategies, formatsand instrumentations. The aims of this thesis were to improvethe chemistry of the Pyrosequencing technique for increasedread-length, enhance the general sequence quality and improvethe sequencing performance for challenging templates. Improvedchemistry would enable Pyrosequencing technique to be used fornumer

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18

Kaushal, Prem Singh. "Structural Studies Of Mycobacterial Uracil-DNA Glycosylase (Ung) And Single-Stranded DNA Binding Protein (SSB)." Thesis, 2010. https://etd.iisc.ac.in/handle/2005/1432.

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For survival and successful propagation, every organism has to maintain the genomic integrity of the cell. The information content, in the form of nucleotide bases, is constantly threatened by endogenous agents and environmental pollutants. In particular, pathogenic mycobacteria are constantly exposed to DNA-damaging assaults such as reactive oxygen species (ROS) and reactive nitrogen intermediate (RNI), in their habitat which is inside host macrophage. In addition, the genome of Mycobacterium tuberculosis makes it more susceptible for guanine oxidation and cytosine deamination as it is G-C ri

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19

Kaushal, Prem Singh. "Structural Studies Of Mycobacterial Uracil-DNA Glycosylase (Ung) And Single-Stranded DNA Binding Protein (SSB)." Thesis, 2010. http://etd.iisc.ernet.in/handle/2005/1432.

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For survival and successful propagation, every organism has to maintain the genomic integrity of the cell. The information content, in the form of nucleotide bases, is constantly threatened by endogenous agents and environmental pollutants. In particular, pathogenic mycobacteria are constantly exposed to DNA-damaging assaults such as reactive oxygen species (ROS) and reactive nitrogen intermediate (RNI), in their habitat which is inside host macrophage. In addition, the genome of Mycobacterium tuberculosis makes it more susceptible for guanine oxidation and cytosine deamination as it is G-C ri

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20

Huang, Wen Hsin, and 黃文昕. "Molecular Cloning and Functional Characterization of single-stranded DNA binding protein (SSB, HP1245) from Helicobacter pylori." Thesis, 2005. http://ndltd.ncl.edu.tw/handle/90698822259257219099.

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碩士<br>國立清華大學<br>生物科技研究所<br>93<br>Single strand DNA binding protein (SSB) plays essential roles in many processes related to DNA metabolism such as DNA replication, repair, and homologous genetic recombination. The HP1245 gene was annotated as SSB in Helicobacter pylori strain 26695. However, there are no functional or structured studies for this SSB up to now. The full length (179 residues), three different C-terminal truncated species (106, 122 and 134 residues) and four different site directed mutants (F37A, F50A, F56A and W84A) were individually sub-cloned into pQE30 vector and expressed

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21

Singh, Amandeep. "Exploration of the Recombination Repair Pathway in Mycobacteria : Identification and Characterization of New Proteins." Thesis, 2018. https://etd.iisc.ac.in/handle/2005/4259.

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Genomic integrity is a fundamental requisite for survival and proliferation of all organisms. The genetic material is continuously threatened by a multitude of extrinsic and intrinsic factors. Consequently, the presence of strong DNA repair systems is essential to aid errorfree transmission of genetic material to successive generations. In prokaryotes, repair by homologous recombination (HR) provides a major means to reinstate the genetic information lost in DNA damage. Pathogenic bacteria, such as Mycobacterium tuberculosis, face an additional threat of DNA damage due to antibiotic treatmen

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22

Padmakar, Purnapatre Kedar. "Uracil DNA Glycosylase From Mycobacteria And Escherichia coli : Mechanism Of Uracil Excision From Synthetic Substrates And Differential Interaction With Uracil DNA Glycosylase Inhibitor (Ugi) And Single Stranded DNA Binding Proteins (SSBs)." Thesis, 1999. https://etd.iisc.ac.in/handle/2005/1567.

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23

Padmakar, Purnapatre Kedar. "Uracil DNA Glycosylase From Mycobacteria And Escherichia coli : Mechanism Of Uracil Excision From Synthetic Substrates And Differential Interaction With Uracil DNA Glycosylase Inhibitor (Ugi) And Single Stranded DNA Binding Proteins (SSBs)." Thesis, 1999. http://etd.iisc.ernet.in/handle/2005/1567.

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24

Saikrishnan, K. "Structural Studies On Mycobacterial Proteins." Thesis, 2005. https://etd.iisc.ac.in/handle/2005/1496.

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25

Saikrishnan, K. "Structural Studies On Mycobacterial Proteins." Thesis, 2005. http://etd.iisc.ernet.in/handle/2005/1496.

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26

Eggington, Julie M. "Deinococcus radiodurans single stranded DNA binding protein." 2006. http://www.library.wisc.edu/databases/connect/dissertations.html.

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27

Lee, Yi-Juan, and 李易撰. "The ssDNA Binding Mode of Single-stranded DNA binding Protein from Helicobacter pylori." Thesis, 2008. http://ndltd.ncl.edu.tw/handle/34606420981705800849.

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28

Dombek, Priscilla Emily. "Functional domains of Agrobacterium tumefaciens single-stranded DNA binding protein VirE2." Thesis, 1996. http://hdl.handle.net/1957/34220.

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Agrobacterium tumefaciens is a gram-negative soil bacterium that causes crown gall tumors on dicotyledenous plants. The transferred DNA (T-DNA) portion of the A. tumefaciens tumor-inducing (Ti) plasmid enters infected plant cells and integrates into plant nuclear DNA. The T-DNA is accompanied into plant cells by the VirD2 endonuclease covalently attached to its 5' end. VirE2, a cooperative, single-stranded DNA-binding protein is also transported into plant cells during infection by A. tumefaciens. VirD2 and VirE2 contain nuclear localization signals (NLSs) and are transported into the plant ce

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29

Chan, Kun-Wei, and 詹坤衛. "Structural Studies of Single-Stranded DNA Binding Protein from Helicobacter pylori." Thesis, 2007. http://ndltd.ncl.edu.tw/handle/94826272919650941118.

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碩士<br>國立清華大學<br>生物資訊與結構生物研究所<br>95<br>Abstract Single-stranded DNA binding protein (SSB) plays an important role in DNA metabolism, such as DNA replication, repair and recombination. The N-terminal domain of SSB forms an oligonucleotides/oligosaccharides binding (OB) fold, which function as single-stranded DNA (ssDNA) binding domain. The C-terminal conserved tail is supposed to participate in the protein-protein interaction. The crystal structure of C-terminal truncated SSB from Helicobacter pylori (residues 1-134, HpSSB134) bound to two dT(pT)34 [HpSSB134-dT(pT)34] was determined by mole

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30

Landt, Stephen George. "Arginine-rich motif peptides as tools for understanding single-stranded DNA recognition /." 2004. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3136068.

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31

Chia-Hung, Wang. "Crystallographic Structural Studies of Single-Stranded DNA Binding Protein from Helicobacter pylori." 2006. http://www.cetd.com.tw/ec/thesisdetail.aspx?etdun=U0016-1303200709300493.

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32

Wang, Chia-Hung, and 王嘉宏. "Crystallographic Structural Studies of Single-Stranded DNA Binding Protein from Helicobacter pylori." Thesis, 2006. http://ndltd.ncl.edu.tw/handle/98529896469303152233.

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碩士<br>國立清華大學<br>生物資訊與結構生物研究所<br>94<br>Single-stranded DNA binding protein (SSB) plays an important role in DNA metabolism, such as DNA replication, repair, and recombination. SSB of Helicobacter pylori (HpSSB) is encoded by the ssb gene and contains 179 residues. The crystal structure of truncated HpSSB protein (residue 1-134) complexed with dT(pT)34 was determined at 3.1  resolution by X-ray crystallographic method. HpSSB exists as a tetramer in both crystal and solution states. The N-terminal domain (residue 1-115) contains an OB-fold (oligonucleotides binding fold), which is similar w

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33

Szap, Matthew C. "Identification and characterization of a human single-stranded telomeric DNA binding protein /." Diss., 1997. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:9814991.

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34

Kariawasam, Ruvini. "Determining the structural mechanism of how single-stranded DNA binding proteins bind DNA." Thesis, 2017. http://hdl.handle.net/1959.7/uws:47195.

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Single stranded DNA binding proteins (SSB) play a major role in cellular DNA processing events such as replication, recombination and repair and are central to maintaining the integrity of our genome. These processes require the DNA double helix to unwind, exposing less stable and highly vulnerable regions of single stranded DNA (ssDNA). SSB proteins bind ssDNA via a highly conserved oligonucleotide-binding (OB) domain and function to temporarily bind and protect exposed ssDNA generated during these events. The vital role of SSBs is evident from their ubiquitous presence in all forms of life.

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35

Webb, John R. "Cloning and characterization of a single-stranded DNA-binding protein of Leishmania major." Thesis, 1993. http://hdl.handle.net/2429/1899.

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Protozoan parasites of the genus Leishmania are the etiologic agents of a spectrum of important human diseases collectively referred to as leishmaniasis. The major surface protein on all species of Leishmania is a highly abundant 63 kDa glycoprotein referred to as GP63. GP63 has been characterized as a cell surface protease, however, its exact role in the Leishmania life cycle is not clear. The genes encoding GP63 are arranged in the Leishmania genome as a species-specific combination of direct head to tail tandem repeats and single dispersed gene copies. In the present study, a single repeat

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36

Sun, Siyang. "Biochemical and crystallographic studies of bacteriophage RB69 DNA polymerase and single-stranded DNA binding protein interactions." Thesis, 2006. http://hdl.handle.net/1911/18982.

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The organization and proper assembly of proteins to the primer-template junction during DNA replication is essential for accurate and processive DNA synthesis. The DNA replication process in RB69 (a T4-like bacteriophage) is similar to the processes in eukaryotes and archaea and has been a prototype for studies on DNA replication and assembly of the functional replisome. In order to examine protein-protein interactions at the DNA replication fork, solution conditions have been established for the formation of a discrete and homogeneous complex of RB69 DNA polymerase (gp43), primer-template DNA

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37

Touma, Christine. "Defining the mechanistic role of hSSB1 : a novel single-stranded DNA binding protein essential for DNA repair." Thesis, 2016. http://hdl.handle.net/1959.7/uws:41175.

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DNA is under constant attack from the external and internal environment. It is imperative to repair and maintain the vital genetic information of DNA. Otherwise it leads to an accumulation of mutations that alters the normal function of DNA and in turn causes a disorder in cellular metabolism. During repair, DNA unwinds into single-stranded DNA (ssDNA) and is even more vulnerable to damage. This is where human single-strand DNA binding protein 1 (hSSB1) binds and protects ssDNA. It is known that hSSB1 exists both as part of the MRN (MRE11, RAD50, NBS1) repair complex and the SOSS1 complex (mad

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38

黃禮堃. "Functional characterization of wild type and mutant single stranded DNA binding protein (HP1245) from H. pylori." Thesis, 2009. http://ndltd.ncl.edu.tw/handle/74535860768245069895.

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碩士<br>國立清華大學<br>生物科技研究所<br>97<br>Single stranded DNA (ssDNA) binding protein (SSB) plays essential roles in many processes related to DNA metabolism such as DNA replication, repair, and homologous genetic recombination. The HP1245 gene was annotated as SSB in Helicobacter pylori strain 26695. However, there are no functional or structured studies for this SSB up to now. The full length (179 residues) HP1245, a C-terminal truncated HP1245 containing 134 resides (tmHP1245 (1~134)), and four HP1245 mutants each containing 134 residues with a specific site mutant (F37A, F50A, F56A and W84A) wer

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39

Eggler, Aimee Laura. "Dissecting the inhibitory and stimulating effects of single-stranded DNA binding proteins on the activities of saccharomyces cerevisiae Rad51 protein and escherichia coli RecA protein." 2002. http://www.library.wisc.edu/databases/connect/dissertations.html.

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40

Barrientos, KS, MF Kendellen, BD Freibaum, BN Armbruster, KT Etheridge, and CM Counter. "Distinct functions of POT1 at telomeres." Thesis, 2008. http://hdl.handle.net/10161/1343.

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The mammalian protein POT1 binds to telomeric single-stranded DNA (ssDNA), protecting chromosome ends from being detected as sites of DNA damage. POT1 is composed of an N-terminal ssDNA-binding domain and a C-terminal protein interaction domain. With regard to the latter, POT1 heterodimerizes with the protein TPP1 to foster binding to telomeric ssDNA in vitro and binds the telomeric double-stranded-DNA-binding protein TRF2. We sought to determine which of these functions-ssDNA, TPP1, or TRF2 binding-was required to protect chromosome ends from being detected as DNA damage. Using separation-of-

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41

Cappadocia, Laurent. "Étude structurale du mode de liaison des protéines Whirly de plantes à l’ADN monocaténaire." Thèse, 2010. http://hdl.handle.net/1866/4957.

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Les plantes doivent assurer la protection de trois génomes localisés dans le noyau, les chloroplastes et les mitochondries. Si les mécanismes assurant la réparation de l’ADN nucléaire sont relativement bien compris, il n’en va pas de même pour celui des chloroplastes et des mitochondries. Or il est important de bien comprendre ces mécanismes puisque des dommages à l’ADN non ou mal réparés peuvent entraîner des réarrangements dans les génomes. Chez les plantes, de tels réarrangements dans l’ADN mitochondrial ou dans l’ADN chloroplastique peuvent conduire à une perte de vigueur ou à un ralentiss

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