Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
Results
Showing 1 to 20 of 30 for “"RNA folding"”.
-
RNA folding via algebraic dynamic programming
… and solve one of the open problems. Ab initio RNA secondary structure folding of a single sequence was chosen as a perfect fit to the requirements. First, because of the compactness of the field, showing a clear path from the first description of the Nearest Neighbor model by Tinoco and others …
-
Investigating and Reprogramming RNA Folding with Molecular Probes
Ribonucleic acid (RNA) performs versatile, essential functions in all known organisms and viruses. These functions require the RNA to fold into specific secondary and tertiary structures, and in many cases to switch among multiple structural states. Predicting and experimentally determining RNA …
-
Fast Protein and RNA Folding on a Rough Energy Landscape
… approach with other experimental methods, the folding process of protein assembly, protein molecules, and RNA molecules was focused in this work. For the first time, time-resolved self-assembly of a light-harvesting protein complex was studied using the laser T-jump method. Experiment results …
-
Protein and RNA folding: from bulk towards high throughput single molecule experiments
The folding energy landscapes of RNA and proteins have been studied using experiments and molecular dynamics (MD) simulations. Firstly, the folding of an RNA hairpin has been looked at with the fluorescent probe 2-aminopurine. The effect of stem and loop dynamics have been separately analyzed. …
-
Fluorescence Investigations of RNA Folding: Group I Intron P4-P6 Domain and Xpt G -Riboswitch Aptamer Domain
Keywords. RNA folding, covalently attached pyrene fluorescence, P4-P6 domain of the Tetrahymena group I intron RNA, xpt G-riboswitch aptamer domain, FRET.
-
Parallelization of dynamic programming recurrences in computational biology
… polyhedral methods to parallelize the Nussinov RNA folding algorithm to build a family of accelerators that can trade resources for parallelism and are between 15-130x faster than a modern dual core CPU implementation. A Zuker RNA folding accelerator we built on a single workstation with four …
-
A test of the Snowball model
… assumptions. Here I use a computational model of RNA folding to test both predictions and assumptions of the snowball model. In this model, two populations are allowed to evolve in allopatry on a holey fitness landscape. I find that the number of DMIs involving pairs of loci (i.e., simple DMIs) …
-
Sequence Dependence of the Folding of Kink-Turns in RNA
The kink-turn in RNA is a secondary structural motif which produces a tight kink in the axis of the RNA helix. It exists in a dynamic equilibrium between the folded and the unfolded state in free solution. The population of the folded kink-turn species can be increased by the addition of metal ions …
-
Review of algorithms for RNA secondary structure prediction with pseudoknots
… that are formed from the base pairing of an RNA secondary loop structure with a complementary base which lies somewhere outside of the loop. The result is a structure, which plays a vital role in cell structure rigidity, regulation of protein synthesis, and in the structural organization of …
-
Engineering RNA logic with synthetic splicing ribozymes
… biological systems and to program self-modifying RNA systems. In addition, splicing ribozymes are easy to engineer, malleable, modular, and scalable. I used the model ribozyme from Tetrahymena to explore the principles behind engineering biological splicing systems in vivo. I show that the core …
-
DEVELOPMENT OF E-SRS (ENVIRONMENT-SENSING RESPONSE SYSTEM) AS A NOVEL METHOD TO DISTINGUISH GENETIC ENVIRONMENTS AND RESOLVE CLOSELY RELATED NUCLEIC ACID SEQUENCES
… and response system with two components: 1) An RNA based sensor that changes conformation and activates upon binding specific NTS; 2) A Response System that is triggered by the activated sensor to initiate some physical response, such as emitting a fluorescent signal to indicate presence of the …
-
RNA structure analysis : algorithms and applications
… thesis, efficient algorithms for aligning RNA secondary structures and mining unknown RNA motifs are presented. As the major contribution, a structure alignment algorithm, which combines both primary and secondary structure information, can find the optimal alignment between two given …
-
Aminormotiffinder - a graph grammar based tool to effectively search a minor motifs in 3D RNA molecules
RNA Motifs are three dimensional folds that play important role in RNA folding and its interaction with other molecules. They basically have modular structure and are composed of conserved building blocks dependent upon the sequence. Their automated in silico identification remains a challenging …
-
Symmetry-breaking motility and RNA secondary structures
… functionalized particles, the designability of RNA secondary structures, and the statistical mechanics of homopolymer RNAs. For the work on spontaneous motility, we were motivated by in vitro experiments investigating the symmetry-breaking motility of functionalized spherical beads to develop a …
-
RNA secondary structure prediction using hybrid methods
… work presents a novel two-stage framework for RNA secondary structure prediction, introducing deep learning models that address local substructure prediction and global structure assembly. Drawing insights from RNA folding kinetics, the stage-1 (S1) model proposes local substructures as …
-
Thermodynamics of neutral sets and sequence length changes in the genotype-phenotype map of RNA secondary structure
The genotype-phenotype (GP) map of RNA secondary structure connects RNA sequences and the corresponding folded molecular structures. This relationship is required for modelling the evolution of functional RNA structures. In this thesis, we fill two gaps in the understanding of the RNA GP map: we …
-
Energy Landscaping - On the Relationship between Functionality and Sequence Mutations for Multifunctional Biomolecules
The process of protein and RNA folding has been understood in general terms through the principle of minimal frustration, and is usually thought of as being guided by a folding funnel on the energy landscape, which is based around the native structure. However, more recently, various biomolecules …
-
The evolutionary impacts of secondary structures within genomes of eukaryote-infecting single-stranded DNA viruses
… immune responses. Although computational DNA/RNA folding methods based-on free energy minimisation approaches are capable of predicting structures that form within virus genomes, these methods are not entirely accurate. Notably, many of structures that are accurately predicted will likely have …
-
Laser-assisted single-molecule refolding
<p>Non-coding RNAs must fold into precise secondary and tertiary structures in order to perform the biological functions. Due to the flexibility of RNA, the RNA folding energy landscape can be rugged and full of local minimum (kinetic trap). To provide a means to study kinetically trapped RNAs, we …
-
Structure and molecular recognition in riboswitches
Riboswitches are cis-acting gene regulatory RNAs, which function without involvement of proteins. They have been implicated as drug targets and are attractive systems for the study of RNA-ligand binding and RNA folding. The purine riboswitch was used as a model system for RNA-ligand docking. …
Page 1 of 2