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dc.contributor.advisorWilliams, Loren D.
dc.contributor.authorGulen, Burak
dc.date.accessioned2016-05-27T13:10:27Z
dc.date.available2016-05-27T13:10:27Z
dc.date.created2015-05
dc.date.issued2015-04-02
dc.date.submittedMay 2015
dc.identifier.urihttp://hdl.handle.net/1853/54884
dc.description.abstractThe ribosome is one of the most universal molecular machinery, synthesizing proteins in all living systems. The small ribosomal subunit plays a crucial role in decoding the messenger RNA during translation. We propose and validate a new architectural model of the ribosomal small subunit, with broad implications for function, biogenesis and evolution. We define an rRNA domain: compact and modular, stabilized by self-consistent molecular interactions, with ability to fold autonomously when it is isolated from surrounding RNA or protein. Each rRNA helix must be allocated uniquely to a single domain. These criteria identify a core domain of small subunit rRNA (domain A), which acts as a hub, linking to all other domains by A-form helical spokes. Experimental characterization of isolated domain A, and mutations and truncations of it, by methods including selective 2’OH acylation analyzed by primer extension and circular dichroism spectroscopy are consistent with autonomous folding, and therefore classification as a domain. We show that the domain concept is applicable and useful for understanding the small ribosomal subunit. Our results support the utility of the concept of the domain as applied to at least some RNAs, the interdependence of the elements of domain A, and its ability to fold autonomously. Moreover, domain A, which exhibits elements of tRNA mimicry, is the essential core of the small ribosomal subunit. Understanding the structure and dynamics of domain A will provide valuable insight into the translational machinery.
dc.format.mimetypeapplication/pdf
dc.language.isoen_US
dc.publisherGeorgia Institute of Technology
dc.subjectRibosome
dc.subjectSmall subunit
dc.subjectCentral pseudoknot
dc.subjectSSU
dc.subjectTranslation
dc.subjecttRNA mimicry
dc.subjectRibosomal evolution
dc.subjectSHAPE
dc.subjectS5
dc.subjectS12
dc.titleArchitecture and core of the small ribosomal subunit
dc.typeDissertation
dc.description.degreePh.D.
dc.contributor.departmentChemistry and Biochemistry
thesis.degree.levelDoctoral
dc.contributor.committeeMemberHud, Nicholas V.
dc.contributor.committeeMemberOyelere, Adegboyega K.
dc.contributor.committeeMemberWartell, Roger M.
dc.contributor.committeeMemberArya, Dev P.
dc.date.updated2016-05-27T13:10:27Z


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