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Showing 1 to 20 of 169 for “"Secondary Structures"”.
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Symmetry-breaking motility and RNA secondary structures
… 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 …
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Classifying RNA secondary structures using support vector machines
… regions, RNA commonly exhibits an intricate secondary structure, consisting of relatively short, double helical segments alternated with single stranded regions. The amount of sequence data available is rising rapidly day by day. One of the problems encountered on a specific molecule is …
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De Novo Design of secondary structures: Synthesis and conformational studies
… proved that these oligomers fold into ordered structures with increasing sequence length. Theoretical calculations employing ab initio MO theory suggest a helix with 11-membered hydrogenbonded rings as the preferred secondary structure type. The novel structures enrich the field of peptidic …
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Identification of evolutionarily conserved nucleic acid secondary structures within viral genomes
… certain DNA and RNA virus genomes form complex secondary structures through Watson-Crick base-pairing interactions between bases on the same DNA or RNA strand. Both computational and experimental methods are available for determining the secondary structure conformations of nucleotide sequences …
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Stability of Nucleic Acid Secondary Structures and Their Contribution to Gene Expression
… bases of the bop gene mRNA can form a secondary structural element (a "stem-loop"). Using biophysical methods, the goal was to determine if the stem-loop structure exists in solution conditions that mimic the in vivo biological environment (42°C and 4M KCl) (2-4). The salt-dependent …
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Development of nanobodies as tools to investigate G-quadruplex DNA secondary structures
… in DNA can fold into four-stranded alternative secondary structures called G-quadruplexes (G4). G4s are suggested to be involved in key genome functions such as transcription, genome stability and epigenetic regulation, together with numerous connections to cancer biology. The detection G4s in …
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A Predictive Model Which Uses Descriptors of RNA Secondary Structures Derived from Graph Theory.
<p>The secondary structures of ribonucleic acid (RNA) have been successfully modeled with graph-theoretic structures. Often, simple graphs are used to represent secondary RNA structures; however, in this research, a multigraph representation of RNA is used, in which vertices represent stems and …
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Development of pattern recognition technique for classification of RNA secondary structures by small molecules
<p>Three-dimensional RNA structures are notoriously difficult to determine, and the link between secondary structure and RNA conformation is only beginning to be understood. In this dissertation, I will discuss the development of a pattern recognition technique which utilizes differential binding …
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The tree alignment model : algorithms, implementations and applications for the analysis of RNA secondary structures
Phylogenetic analysis of nucleotide sequences and amino acid sequences has proven to be extremely powerful in the analysis of genomes. The comparative analysis of coding regions, i.e. regions where the order of nucleotides code for proteins, has been studied extensively. But what if the signal is …
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The evolutionary impacts of secondary structures within genomes of eukaryote-infecting single-stranded DNA viruses
Secondary structures forming through base-pairing in virus genomes have been proven to regulate several processes during viral replication cycles, including genome replication, transcription, post-transcriptional activities, protein synthesis, genome packaging, generation of viral sub-genomes and …
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DEVELOPMENT OF A MICROSCALE ELECTROCHEMICAL PLATFORM FOR THE ANALYSIS OF THERMAL PROFILES OF IMMOBILIZED DNA SECONDARY STRUCTURES
Understanding the thermal stability of DNA secondary structures is important to the pharmaceutical industry, as drug molecules that strongly bind will increase the stability of the structure, leading to higher measured melting temperatures. Development of an electronic platform that can measure the …
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Synthesis of cyclometalated gold (III) complexesfunctionalized by alkynyl derivatives. Study of the interaction with DNA secondary structures.
… interaction of the studied complexes with DNA secondary structures. In this work, bidentate and tridentate ligands, in particular derived from both phenylpyridine and diphenylpyridine, respectively, have been employed as framework structure in order to stabilize the studied gold complexes. …
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A Graph-Based Algorithm to Determine Protein Structure from Cryo-EM Data
… Previous work has shown that features known as secondary structures can be located in these density maps. A second source of information about proteins is sequence analysis, which predicts locations of secondary structures along the protein sequence but does not provide any information about the …
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Structural and Functional Analysis of Secondary Structure Block to mRNA Utilization
<p>Experimentally introduced secondary structure, formed by a cis-targeted hammerhead ribozyme in exon 2 two nucleotides dowstream of the 3' splice site of a yeast ACT-E. <em>coli lacZ fusion</em> gene, virtually abolishes splicing in vivo and inhibits B-galactosidase production. This is the first …
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Analytic Combinatorics Applied to RNA Structures
… likened to a lock and key system. γ-structures are a subset of RNA pseudoknot structures filtered by topological genus that lend themselves nicely to combinatorial analysis. Namely, the coefficients of their generating function can be approximated for large n. This paper is an …
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Genetic interactions of repriming and translesion synthesis
… impediments such as DNA damage or non-B-DNA secondary structures. To probe the genetic interactions of PRIMPOL, genome-wide CRISPR/Cas9 knockout screens were undertaken in the human TK6 cell line. The most interesting group of hits were RAD18, UBE2A and REV1 - three genes with key roles in …
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Fast learning optimized prediction methodology for protein secondary structure prediction, relative solvent accessibility prediction and phosphorylation prediction
… the number of sequences and the number of structures. There has been an exponential growth in the number of available protein sequences and a slower growth in the number of structures. There is therefore an urgent need to develop computed structures and identify the functions of these …
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