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Dissertations / Theses on the topic 'RNA structure'

Author: Grafiati

Published: 4 June 2021

Last updated: 26 July 2025

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1

Lai, Daniel. "Computational analysis of ribonucleic acid basepairs in RNA structure and RNA-RNA interactions." Thesis, University of British Columbia, 2016. http://hdl.handle.net/2429/57538.

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Ribonucleic acids (RNA), are an essential part of cellular function, transcribed from DNA and translated into protein. Rather than a passive informational medium, RNA can also be highly functional and regulatory. Certain RNAs fold into specific structures giving it enzymatic properties, while others bind to specific targets to guide regulatory processes. With the advent of next-generation sequencing, a large number of novel non-coding RNAs have been discovered through whole-transcriptome sequencing. Many efforts have been made to study the structure and binding partners of these novel RNAs, in

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2

Sarver, Michael. "STRUCTURE-BASED MULTIPLE RNA SEQUENCE ALIGNMENT AND FINDING RNA MOTIFS." Bowling Green State University / OhioLINK, 2006. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1151076710.

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3

Zhou, Yu. "Application of RNA Bioinformatics in decoding RNA structure and regulation." Paris 11, 2008. http://www.theses.fr/2008PA112234.

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Ma thèse porte sur le développement de méthodologies informatiques et bioinformatiques pour résoudre des problèmes provenant de questions biologiques liées à l’ARN, telles que la prédiction de structures, l’identification de structures communes, la découverte de cibles des micro-ARN, la prédiction de la régulation de l’épissage, et le design (ou repliement inverse) d'ARN. Le premier chapitre concerne la mise en place d’une méthode itérative pour la prédiction des structures secondaires des introns de groupes 1, incluant les pseudo-nœuds, et la développement d’une base de données complète sur l

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4

Freyhult, Eva. "New techniques for analysing RNA structure /." Uppsala, 2004. http://www.math.uu.se/research/pub/Freyhult1.pdf.

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5

Turnbull, Carly. "Sequence and structure requirements of Y RNA-derived small RNA biogenesis." Thesis, University of East Anglia, 2014. https://ueaeprints.uea.ac.uk/49478/.

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Numerous small non-coding RNAs have been identified in mammalian cells, including microRNAs and piwi-interacting RNAs. The patterns of gene expression within cells can be altered in response to cellular stress. To examine the effects of cellular stress on all small RNA types, a number of human cell lines were treated with Poly(I:C), a mimic of viral infection, and the levels of small RNAs were examined by next generation sequencing. Surprisingly, we did not find many differentially expressed microRNAs, but we discovered a new class of small RNAs that were 30-35 nucleotides and showed up-regula

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6

Hengrung, Narin. "Structure of the RNA-dependent RNA polymerase from influenza C virus." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:694e16a6-f94e-4375-a1f9-7e250aea7343.

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The influenza virus causes a disease that kills approximately 500,000 people worldwide each year. Influenza is a negative-sense RNA virus that encodes its own RNA-dependent RNA polymerase. This protein (FluPol) carries out both genome replication and viral transcription. Therefore, like the L-proteins of non-segmented negative-sense RNA (nsRNA) viruses, FluPol also contains mRNA capping and polyadenylation functionality. In FluPol, capping is achieved by snatching cap structures from cellular mRNAs, so requiring cap-binding and endonuclease activities. This makes FluPol a substantial machine.

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7

Anderson, James William Justin. "Probabilistic models of RNA secondary structure." Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:3e58e9d9-c58d-4616-8e88-4082d1ca0e2a.

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This thesis develops probabilistic models of RNA secondary structure. The first chapter introduces RNA secondary structure prediction, in particular stochastic context-free grammars (SCFGs), and considers a novel method for automated design of SCFGs. Many SCFGs are found with a similar predictive quality as those commonly used for RNA secondary structure prediction. The second chapter discusses the effect alignment quality, evolutionary distance between sequences, and number of sequences in an alignment have on RNA secondary structure prediction. By combining statistical alignment and SCFG mod

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8

Dinda, Stephen B. "Predicting RNA Mutation Using 3D Structure." Bowling Green State University / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1321280932.

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9

Piskol, Robert. "Structural and population genetic determinants of RNA secondary structure evolution." Diss., lmu, 2011. http://nbn-resolving.de/urn:nbn:de:bvb:19-130532.

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10

Bhattacharjee, Puranjoy. "Correlation Between Computed Equilibrium Secondary Structure Free Energy and siRNA Efficiency." Thesis, Virginia Tech, 2009. http://hdl.handle.net/10919/34643.

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We have explored correlations between the measured efficiency of the RNAi process and several computed signatures that characterize equilibrium secondary structure of the partic- ipating mRNA, siRNA, and their complexes. A previously published data set of 609 exper- imental points was used for the analysis. While virtually no correlation with the computed structural signatures are observed for individual data points, several clear trends emerge when the data is averaged over 10 bins of N â ¼ 60 data points per bin.<p> The strongest trend is a positive linear (r 2 = 0.87) correlation between ln

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11

Childs, Liam, Zoran Nikoloski, Patrick May, and Dirk Walther. "Identification and classification of ncRNA molecules using graph properties." Universität Potsdam, 2009. http://opus.kobv.de/ubp/volltexte/2010/4519/.

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The study of non-coding RNA genes has received increased attention in recent years fuelled by accumulating evidence that larger portions of genomes than previously acknowledged are transcribed into RNA molecules of mostly unknown function, as well as the discovery of novel non-coding RNA types and functional RNA elements. Here, we demonstrate that specific properties of graphs that represent the predicted RNA secondary structure reflect functional information. We introduce a computational algorithm and an associated web-based tool (GraPPLE) for classifying non-coding RNA molecules as functiona

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12

Komatsu, Richard Kaoru. "RNA structure-wide discovery of functional interactions with multiplexed RNA motif library." Doctoral thesis, Kyoto University, 2021. http://hdl.handle.net/2433/263573.

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13

Singh, Jaswinder. "RNA Structure Prediction using Deep Neural Network Architectures and Improved Evolutionary Profiles." Thesis, Griffith University, 2022. http://hdl.handle.net/10072/414924.

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RNAs are important biological macro-molecules that play critical roles in many biological processes. The functionality of RNA depends on its three-dimensional (3D) structure, which further depends on its primary structure, i.e. the order of sequence of nucleotides in the RNA chain. Direct prediction of the 3D structure of an RNA from its sequence is a challenging task. Therefore, the 3D structure is further divided into two-dimensional (2D) properties such as secondary structure, contact maps and one-dimensional (1D) properties such as torsion angles and solvent accessibility. An accurate pred

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14

Upton, John H. "The role of RNA secondary structure in replication of Nodamura virus RNA2." To access this resource online via ProQuest Dissertations and Theses @ UTEP, 2009. http://0-proquest.umi.com.lib.utep.edu/login?COPT=REJTPTU0YmImSU5UPTAmVkVSPTI=&clientId=2515.

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15

Voss, Björn. "Advanced tools for RNA secondary structure analysis." [S.l. : s.n.], 2004. http://deposit.ddb.de/cgi-bin/dokserv?idn=97446547X.

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16

Lehmann, Elisabeth. "Structure-function analysis of RNA polymerase II." Diss., lmu, 2011. http://nbn-resolving.de/urn:nbn:de:bvb:19-140132.

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17

Hosna, Hosna. "RNA secondary structure prediction using hierarchical folding." Thesis, University of British Columbia, 2007. http://hdl.handle.net/2429/32001.

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Algorithms for prediction of RNA secondary structure— the set of base pairs that form when an RNA molecule folds— are valuable to biologists who aim to understand RNA structure and function. Improving the accuracy and efficiency of prediction methods'is an ongoing challenge, particularly for pseudoknotted secondary structures, in which base pairs overlap. This challenge is biologically important, since pseudoknotted structures play essential roles in functions of many RNA molecules, such as splicing and ribosomal frameshifting. State-of-the- art methods, which are based on free energy minimiz

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18

Yang, Qian 1973. "RNA sequence alignment and secondary structure prediction." Thesis, McGill University, 2005. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=82453.

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Functional RNA sequences typically have structural elements that are highly conserved during evolution. Here we present an algorithmic method for multiple alignment of RNAs, taking into consideration both structural similarity and sequence identity. Furthermore, we performed a comparative analysis on pairing probability matrices of a set of aligned orthologous sequences and predicted the conserved secondary structure. Our alignment method outperforms the most widely used multiple alignment tool - Clustal W, and the structure prediction approach we proposed can generate a more accurate s

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19

Engel, Christoph. "RNA polymerase I structure and transcription regulation." Diss., Ludwig-Maximilians-Universität München, 2014. http://nbn-resolving.de/urn:nbn:de:bvb:19-173904.

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20

Stombaugh, Jesse. "Predicting the Structure of RNA 3D Motifs." Bowling Green State University / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1225391806.

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21

Mokdad, Ali G. "DEVELOPING TOOLS FOR RNA STRUCTURAL ALIGNMENT." Bowling Green State University / OhioLINK, 2006. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1143320655.

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22

Leeper, Thomas. "The novel ugagau hexaloop RNA structure, dipolar coupling refinement, and transactivation /." free to MU campus, to others for purchase, 2001. http://wwwlib.umi.com/cr/mo/fullcit?p3036840.

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23

Zhu, Jian. "The stabilities of RNA and DNA structural elements." Diss., Georgia Institute of Technology, 1998. http://hdl.handle.net/1853/25194.

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24

Martin, Itziar Serna. "Study of the structure and function of the influenza virus RNA-dependent RNA polymerase." Thesis, University of Oxford, 2017. https://ora.ox.ac.uk/objects/uuid:b1f808d4-4ad4-4eb4-bbe8-c2019263d45a.

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Influenza viruses are segmented, negative-sense RNA viruses responsible for influenza disease. Unlike other negative-sense RNA viruses, influenza virus genome replication occurs in the nucleus of infected cells. The virus encodes a heterotrimeric RNA-dependent RNA polymerase (FluPol) that is responsible for transcribing and replicating the viral genome. In order to transcribe, the FluPol generates capped RNA primers by a process termed 'cap-snatching'. In it, the polymerase binds host capped RNAs and cleaves them 10-13 nucleotides downstream of the cap structure. The catalytic core of FluPol i

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25

Uroda, Tina. "Caractérisation structurale et fonctionnelle de l’ARN long non codant MEG3." Thesis, Université Grenoble Alpes (ComUE), 2019. http://www.theses.fr/2019GREAV014.

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Les ARNs long non codants (ARNlnc) jouent un rôle clé dans les processus cellulaires vitaux, notamment le remodelage de la chromatine, la réparation de l'ADN et la traduction. Cependant, la taille et la complexité des ARNlnc présentent des défis sans précédent pour les études moléculaires mécanistiques, de sorte qu'il s'est avéré difficile jusqu'à présent de relier l'information structurelle à la fonction biologique pour les ARNlnc.Le gène 3 humain exprimé maternellement (de l’anglais "maternally expressed gene 3", MEG3), est un ARNlnc abondant, soumis à empreinte parentale et épissé alternati

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26

Geiger, Sebastian. "Structure and function of RNA polymerase I subunits." Diss., lmu, 2010. http://nbn-resolving.de/urn:nbn:de:bvb:19-126665.

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27

WILLIAMS, DANIEL. "ANALYSIS OF RNase P RNA STRUCTURE AND FUNCTION." NCSU, 2001. http://www.lib.ncsu.edu/theses/available/etd-20010821-140212.

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<p>ABSTRACTWILLIAMS, DANIEL. Analysis of RNase P Structure and Function. (Under the direction of James W. Brown.) The diversity of Archaea in municipal wastewater sludge was investigated by amplification of rRNA sequences from sludge DNA using archaeal-specific primers. The most common sequences were extreme halophiles; also found were sequence members of environmental euryarchaeal and crenarchaeal groups. Only distant relatives of Methanosarcina among the Methanomicrobiales were found.A detailed comparative analysis of archaeal RNase P RNA structure and a comparison of the resulting structura

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28

Legassie, Jason Donald Jarstfer Michael B. "Structure and function of Tetrahymena thermophila telomerase RNA." Chapel Hill, N.C. : University of North Carolina at Chapel Hill, 2007. http://dc.lib.unc.edu/u?/etd,1376.

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Thesis (Ph. D.)--University of North Carolina at Chapel Hill, 2007.<br>Title from electronic title page (viewed Apr. 25, 2008). "... in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the School of Pharmacy Pharmaceutical Sciences." Discipline: Pharmaceutical Sciences; Department/School: Pharmacy.

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29

Chen, Yuanyuan. "Characterizing RNA Structure and synthesis by Raman Microscopy." Case Western Reserve University School of Graduate Studies / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=case1277761094.

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30

MERONI, ALICE. "RNA IN DNA: FROM STRUCTURE TO GENOME INSTABILITY." Doctoral thesis, Università degli Studi di Milano, 2018. http://hdl.handle.net/2434/570097.

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The presence of RNA in the genome of living cells is one of the emerging topics of the last two decades and has been implicated in many biological processes. I focused my attention on ribonucleotides (rNMPs) embedded into DNA during genome duplication, as a threat to its integrity. In fact, rNMPs have been classified as the most frequent non-canonical nucleotides introduced during genome duplication by DNA polymerases. Such high incorporation frequency has been related to a physiological role in mismatch repair, but it can be easily turned into a source of genomic instability if rNMPs are not

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31

Saaidi, Afaf. "Multi-dimensional probing for RNA secondary structure(s) prediction." Thesis, Université Paris-Saclay (ComUE), 2018. http://www.theses.fr/2018SACLX067/document.

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En bioinformatique structurale, la prédiction de la (des) structure(s) secondaire(s) des acides ribonucléiques (ARNs) constitue une direction de recherche majeure pour comprendre les mécanismes cellulaires. Une approche classique pour la prédiction de la structure postule qu'à l'équilibre thermodynamique, l'ARN adopte plusieurs conformations, caractérisées par leur énergie libre, dans l’ensemble de Boltzmann. Les approches modernes privilégient donc une considération des conformations dominantes. Ces approches voient leur précision limitées par l'imprécision des modèles d'énergie et les restri

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32

Selega, Alina. "Computational methods for RNA integrative biology." Thesis, University of Edinburgh, 2018. http://hdl.handle.net/1842/29630.

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Ribonucleic acid (RNA) is an essential molecule, which carries out a wide variety of functions within the cell, from its crucial involvement in protein synthesis to catalysing biochemical reactions and regulating gene expression. Such diverse functional repertoire is indebted to complex structures that RNA can adopt and its flexibility as an interacting molecule. It has become possible to experimentally measure these two crucial aspects of RNA regulatory role with such technological advancements as next-generation sequencing (NGS). NGS methods can rapidly obtain the nucleotide sequence of many

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33

Ding, Yang. "Parametric RNA Partition Function Algorithms." Thesis, Boston College, 2010. http://hdl.handle.net/2345/1813.

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Thesis advisor: Peter Clote<br>In addition to the well-characterized messenger RNA, transfer RNA and ribosomal RNA, many new classes of noncoding RNA(ncRNA) have been discovered in the past few years. ncRNA has been shown to play important roles in multiple regulation and development processes. The increasing needs for RNA structural analysis software provide great opportunities on computational biologists. In this thesis I present three highly non-trivial RNA parametric structural analysis algorithms: 1) RNAhairpin and RNAmultiloop, which calculate parition functions with respect to hairpin n

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34

Defenbaugh, Dawn. "Analysis of hepatitis delta virus RNA structure effects on RNA-protein interactions and viral replication /." Connect to Electronic Thesis (CONTENTdm), 2008. http://worldcat.org/oclc/459757001/viewonline.

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35

Delli, Ponti Riccardo 1987. "Approaches to characterize structural properties of RNA." Doctoral thesis, Universitat Pompeu Fabra, 2019. http://hdl.handle.net/10803/665962.

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The secondary structure of an RNA molecule is fundamental for its function. However, structural conservation and the structure of RNA in vivo are still poorly understood. Data from recent high-throughput experiments can provide new insights, but they have not yet been systematically exploited. The aim of my doctoral studies was to exploit these experimental data to develop computational approaches for discovering and analyzing structural properties of RNA. I developed two algorithms: CROSS predicts the secondary structure propensity profile of an RNA, and CROSSalign discovers structural simila

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36

Schlegel, Thomas. "Inferring secondary structure from RNA alignment und their trees." [S.l.] : [s.n.], 2007. http://deposit.ddb.de/cgi-bin/dokserv?idn=984848657.

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37

Peele, Price Jason. "Control of RNA Structure by CspA Proteins in Rhizobia." Thesis, Washington State University, 2017. http://pqdtopen.proquest.com/#viewpdf?dispub=10605605.

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<p> Rhizobia are soil bacteria that can associate with some legumes and participate in symbiotic nitrogen fixation. Bacterial CspA family members are small, single stranded nucleic acid binding proteins conserved throughout all domains of life. Here, the role of CspA family proteins in the symbiotic development of <i>Sinorhizobium meliloti</i> with <i>Medicago sativa</i> (alfalfa) is investigated. Expression and genetic deletion strain analysis revealed that CspA family proteins are differentially expressed in symbiosis and contribute to symbiotic effectiveness. RNAseq analysis of native co-im

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38

Kinkelin, Kerstin. "Structure and function of RNA Polymerase II-Bye1 complexes." Diss., Ludwig-Maximilians-Universität München, 2013. http://nbn-resolving.de/urn:nbn:de:bvb:19-161817.

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39

Proutski, Vitali. "RNA secondary structure of the 3'-UTR of flaviviruses." Thesis, University of Oxford, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.299156.

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40

Curti, Elena. "Structure function studies of selected RNA and DNA polymerases." Thesis, University of Leeds, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.414158.

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41

KARTJE, ZACHARY. "GUIDE RNA MODIFICATION AND STRUCTURE-FUNCTION OF CRISPR-CAS9." OpenSIUC, 2018. https://opensiuc.lib.siu.edu/dissertations/1610.

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CRISPR (clustered regularly interspaced short palindromic repeats)-guided nucleases such as Cas9 remain atop the most exciting biological systems in gene editing and therapeutic potential. The modern adaptation of the Streptococcus pyogenes (Spy) Cas9 machinery for directed DNA editing relies on two major components; a Cas9 protein, and an RNA guide. This study aims at modification of the guide RNA to probe structural requirements and modification tolerance while studying the biochemical properties of the ribonucleoprotein complex. We find that the SpyCas9-RNP is not only capable of heavy subs

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42

Allain, Frederic Hai-Trieu. "Structure determination of protein-RNA complexes by NMR spectroscopy." Thesis, University of Cambridge, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.627304.

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43

Yeoman, Justin Alexander. "Studies into the structure and interactions of telomerase RNA." Thesis, University of Cambridge, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.611310.

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44

Danhart, Eric M. "Protein and RNA structure and function by NMR spectroscopy." The Ohio State University, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=osu15005487808765.

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45

Omnes, Loïc. "Deep learning methods for long RNA secondary structure prediction." Electronic Thesis or Diss., université Paris-Saclay, 2025. http://www.theses.fr/2025UPASG032.

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Le rôle essentiel des ARNs a été démontré dans divers processus biologiques et maladies. Toutefois, on ignore encore la fonction de nombreux ARNs. Une meilleure connaissance de leur rôle pourrait permettre de découvrir de nouveaux biomarqueurs ou cibles thérapeutiques et ainsi d'améliorer l'efficacité des traitements médicaux.Cependant, la validation expérimentale de leur fonction est très coûteuse, ce qui pose un frein à l'étude de leurs rôles. Il est possible de pallier ce problème grâce à des outils informatiques.En particulier, l'apprentissage profond est aujourd'hui fréquemment utilisé po

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46

Zeng, Cong. "Classification of RNA Pseudoknots and Comparison of Structure Prediction Methods." Thesis, Paris 11, 2015. http://www.theses.fr/2015PA112127/document.

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De nombreuses recherches ont constaté l'importance des molécules d'ARN, car ils jouent un rôle vital dans beaucoup de procédures moléculaires. Et il est accepté généralement que les structures des molécules d'ARN sont la clé de la découverte de leurs fonctions.Au cours de l'enquête de structures d'ARN, les chercheurs dépendent des méthodes bioinformatiques de plus en plus. Beaucoup de méthodes in silico de prédiction des structures secondaires d'ARN ont émergé dans cette grosse vague, y compris certains qui sont capables de prédire pseudonoeuds, un type particulier de structures secondaires d'

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47

Hannoush, Rami Nabil. "RNA folding : synthesis, structure and biological properties of hairpins based on 2',5'-linked RNA loops." Thesis, McGill University, 2002. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=82890.

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Ribonucleic acids (RNA) are polymers of ribonucleotides linked together by 3',5'-phosphodiester linkages and play a prominent role in protein biosynthesis. Much less common are ribonucleic acids based on 2',5'-phosphodiester linkages (2',5'-RNA). In this study, the synthesis, physical and biological properties of several 2' ,5'-linked oligoribonucleotides are described.<br>One aspect of this thesis deals with the synthesis and structural studies of 2',5'-dodecaribonucleotides. Their base sequence was designed to promote intramolecular folding by base pairing leading to the formation of

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48

Andronescu, Mirela Stefania. "Computational approaches for RNA energy parameter estimation." Thesis, University of British Columbia, 2008. http://hdl.handle.net/2429/2794.

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RNA molecules play important roles, including catalysis of chemical reactions and control of gene expression, and their functions largely depend on their folded structures. Since determining these structures by biochemical means is expensive, there is increased demand for computational predictions of RNA structures. One computational approach is to find the secondary structure (a set of base pairs) that minimizes a free energy function for a given RNA conformation. The forces driving RNA folding can be approximated by means of a free energy model, which associates a free energy parameter to a

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49

Liu, Xinyi, and 刘欣怡. "A general RNA secondary structure algorithm with vertical tree grammar." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2013. http://hdl.handle.net/10722/196439.

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Our understanding of the functions played by RNA molecules is expanded with the understanding of RNA structures. Except for primary structure, RNA molecules present pairings within a sequence, which is called RNA secondary structure. Since its discovery, RNA secondary structure has drawn considerable attention because it is widely appeared. Many programs for RNA secondary structure prediction have been developed, including [4, 20, 38, 39, 46]. Based on our knowledge, however, there is a family of RNA secondary structure which can not be covered by any of these algorithms. And even without con

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50

Bourdelat-Parks, Brooke Nicole. "Thermodynamic studies of tandem mismatches and other structural elements in Hairpin and duplex nucleic acids." Diss., Georgia Institute of Technology, 2003. http://hdl.handle.net/1853/5387.

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