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.
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Showing 1 to 20 of 24 for “"DNA recognition"”.
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DNA Recognition by Helix-Loop-Helix Proteins
… bipartite b/HLH domain responsible for specific DNA binding and dimerization. The HLH region dictates dimerization affinity and specificity while the basic region (b) is primarily responsible for sequence-specific DNA binding. In some family members, such as the Myc oncoproteins, the HLH motif is …
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Selection studies of zinc finger-DNA recognition
Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 1997.
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Side chain mobility and hydration in homeodomain-DNA recognition
Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 1998.
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Synthesis of photochemically active complexes for DNA recognition and binding
… (IQ) based cations and their potential use as DNA binding agents. The P ligand was aimed to compare with the IQ ligand as they have similar structures. Two series of compounds were synthesized; one series comprising organic cations, including PC2, PC3, PC4, IQC2 and IQC3. The other one contains …
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Metallo-supramolecular cylinders and their peptide conjugates. Synthesis, dynamics and DNA recognition
… cylinders, that are known for their major groove DNA binding properties, and ii) the synthesis and DNA binding studies of the cylinders conjugated to short peptides and amino acids. In Chapter 1 an overview of the DNA molecular recognition by synthetic agents and biomolecules is presented, with a …
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Light-induced modulation of DNA recognition by the Rad4/XPC damage sensor protein.
… trigger the biological assembly/disassembly of DNA damage repair proteins on DNA. Specifically, this work focuses on photo-regulation of DNA damage recognition by the xeroderma pigmentosum C complex (XPC-Rad23B; Rad4-23 in yeast). Rad4/XPC specifically recognizes various bulky …
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Protein-DNA Recognition Models for the Homeodomain and C2H2 Zinc Finger Transcription Factor Families
… target genes by binding to short, degenerate DNA sequence motifs. The goal of this research is to build improved models of TF binding site recognition. This can facilitate the determination of regulatory networks and also allow for the prediction of binding site motifs based only on the TF …
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The role of damaged DNA recognition proteins in the genotoxicities of ultraviolet light and the anticancer drug cisplatin
Thesis (Ph. D.)--Massachusetts Institute of Technology, Division of Toxicology, 1994.
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Sequence-specific recognition of DNA by RSRI endonuclease of Rhodobacter sphaeroides, an isoschizomer of EcoRI
… the interaction of RsrI endonuclease with its DNA recognition sequence and to determine whether RsrI recognizes DNA using a mechanism similar to that of EcoRI, I have purified milligram amounts of the enzyme to near homogeneity from its natural source, Rhodobacter sphaeroides strain 630. The …
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Development of High Pressure Surface Plasmon Resonance for the Study of Biosystems
… binding of the BamH1 restriction enzyme to its DNA recognition site.
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Supramolecular anticancer agents and their effects on cells and biomolecules
… upon existing drugs. In chapter three, the DNA three-way junction binding of a number of supramolecular cylinders is described. Three-way junction binding is a new mode of DNA recognition and relevant to the DNA replication fork, present in dividing cells. Chapter four outlines a number of …
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Metallo-Supramolecular complexes and their interactions with biomolecules and cells
… of these assemblies are outlined with a focus on DNA recognition. In chapter 2 the synthesis and characterisation of an array of palladium(II) and platinum(II) tetra-stranded, dinuclear complexes is described. The synthesis of two palladium(II) triangles and a palladium(II) pyramid are also …
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Probabilistic models to resolve cell identity and tissue architecture
… chromatin with sequencing (ATAC-seq), DNA accessibility provides a readout of intermediate gene regulation steps at single-cell resolution, with technologies measuring both RNA and ATAC providing the necessary evidence to build mechanistic models of regulation. Existing methods address …
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Learning hierarchical motif embeddings for protein engineering
… a highly accurate predictive model on the DNA recognition code of the Type II restriction enzymes. Based on the promising prediction results, we used the trained models to generate de novo restriction enzymes and paved the way towards the computational design of a restriction enzyme that …
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Regulatory variation and human disease
… variation within any given transcription factor recognition sequence. To lay the groundwork for the assessment of regulatory variation in human disease, I comprehensively analyzed heritable genome-wide binding patterns of a major sequence-specific regulator (CTCF) in relation to genetic …
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Development and Application of a Fluorescence Anisotropy Microplate Assay for Analyzing the Interaction of Steroid Hormone Receptors With DNA and Coactivators
… transcription is the binding of the ER to its DNA recognition sequence, the estrogen response element (ERE). To analyze this interaction, we used ultra low-volume microplates to develop the simple and rapid fluorescence anisotropy microplate assay (FAMA). The FAMA was applied to the binding of …
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Interplay Between Estrogen Response Element Sequences and Ligands Controls Binding of Estrogen Receptor to Regulated Genes
… activation is the interaction of ER with its DNA recognition sequence, the estrogen response element (ERE). Although the ER preferentially interacts with the consensus ERE (PuGGTCAnnnTGACCPy), natural genes use diverse sequences to regulate estrogen action. To investigate the influence of ERE …
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Battling Bacteria: Characterizing the NOD-Like Receptor (NLR) Immune Response to <i>Brucella abortus</i> and <i>Borrelia burgdorferi</i> in Host-pathogen Interactions
… infectious diseases. Characterized by Pattern Recognition Receptors (PRRs), which sense conserved molecular motifs known as Pathogen-Associated Molecular Patterns (PAMPs), the innate immune system sets a system of checks and balances to regulate inflammation in host defense. In this …
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A Novel Method to Detect Bacterial Restriction-Modification (R-M) Systems
… sequenced microbial genomes has revealed many DNA sequences that code for previously unknown restriction endonucleases and their corresponding methyltransferases. These findings show that numerous restriction enzymes abundant in bacteria have yet to be discovered. Traditionally, restriction …
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DNA target site recognition by the Ll.LtrB group II intron RNP
… retroelements that site-specifically insert into DNA target sequences. The group II intron mobility pathway is mediated by a ribonucleoprotein particle (RNP) composed of excised intron RNA and an intron-encoded protein (IEP). The intron lariat inserts at a specific DNA target sequence and is then …
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