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 45 for “"Duplex DNA"”.
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Structural characterization of G-Quadruplexes within duplex DNA
… G-Quadruplex (GQ) is a repetitive, guanine rich DNA sequence that occurs throughout the genome. This specific DNA motif is capable of forming an alternative DNA secondary structure similar to a rectangular prism. The most common GQ motif consists of four sets of three guanine bases separated by …
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Crystal structure of the anticancer drug cisplatin bound to duplex DNA
Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1996.
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Interactions of small molecules with duplex DNA and lesion containing G-quadruplex DNA
… approaches to study their interactions with duplex DNA. The nickel complexes were found to selectively oxidize guanines in bulged DNA structures in the presence of oxidant and notably NiCR-2H oxidizes guanines more efficiently than NiCR. According to 1 H NMR studies, NiCR-2H binds strongly to …
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REVERSIBLE QUINONE METHIDE ALKYLATION OF DNA
Alkylation of DNA has been found to cause cancer and also to serve as its treatment. Quinone methides (QMs) are highly electrophilic molecules implicated in numerous metabolism processes. Studies of QM's reversible reaction with nucleophiles of DNA are important to understand the mechanism of its …
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Direct observation of XPD helicase base-pair stepping and regulation by RPA2
Although it is known that single-stranded DNA binding proteins (SSB) can stimulate helicase activity, the mechanism by which this occurs may be more complex than sequestering ssDNA products of duplex separation. Here, we present a singlemolecule helicase assay with base-pair sensitivity, which …
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A structural study of M-DNA
In alkaline conditions, a complex called M-DNA is formed between a divalent metal ion, cobalt, nickel or zinc, and duplex DNA. The rate of formation and stability of M-DNA is dependent on many factors, including but not limited to temperature, pH, DNA sequence, and metal or DNA concentrations. It …
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Single molecule studies of helicase mechanisms
… the canonical helicase function of unwinding duplex DNA, the RecQ family of helicases is known to preferentially bind to non-canonical DNA structures such as G-quadruplexes and Holliday junctions. Ensemble biochemical research has shown that BLM probably has roles in the maintenance of genome …
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Controlling Plasmon Coupling in Biomolecule-Linked Nanoparticle Assemblies
… of 13 nm gold "satellite" particles tethered by duplex DNA to a 50 nm gold "core" particle. Comparison of core-satellite assemblies formed with duplex DNA tethers of varying length demonstrates that, while core-satellite separation is controlled by the number of base pairs in the DNA tether, …
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The Biochemical Characterization of Drosophila melanogaster RecQ4 Helicase
… is stimulated by the presence of single-stranded DNA 3' of the duplex DNA region to be unwound. The enzyme is also capable of annealing complementary DNA strands, though this is inhibited by AMPPNP, a non-hydrolyzable analog of ATP. RecQ4 also forms a stable complex with single-stranded DNA in the …
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Structural Studies of Hmg-D-Dna Interactions
… all of which share the HMG domain, a small DNA-binding structural motif. HMG1/2 proteins interact directly with nucleosomes, modulate chromatin structure, and modulate the activation of gene expression by a number of transcriptional activators. The structure of HMG-D bound to linear duplex …
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Single molecule investigations into DNA replication, recombination and repair
Double-stranded DNA breaks (DSBs) is a principal cytotoxic damage that can be repaired by several well-known repair pathways. One of the most prominent routes is the homologous recombination (HR). The mechanism of repair has been studied primarily by biochemical analysis over the years. Recent …
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Synthesis of bespoke matrices to investigate a novel anti-tumour molecular target using affinity chromatography. The design, synthesis and evaluation of biotinylated biarylheterocycles used as novel affinity probes in the identification of anti-tumour molecular targets.
… this biological activity was independent of duplex DNA binding affinity. The compounds were tested in the NCI 60-cell line panel and COMPARE analysis suggests they have a novel mechanism of action, targeting the product of a ¿gene-like sequence¿ of unidentified function. The identity of …
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DNA Constraints for Rational Control of Macromolecular Conformation
The DNA double helix is stable and rigid, making it an ideal nanoscale construction element. Duplex DNA has been used as a static framework to organize DNA, proteins, or nanoparticles, and dynamic DNA nanomachines have been built. However, assemblies in which DNA controls the intramolecular states …
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Characterization of inter-genomic and telomeric G-quadruplex structures through atomic force microscopy
The G-quadruplex DNA structure, a secondary folding motif of DNA, is found throughout the genome. The dynamics of these structures has been seen to affect processes such as telomerase elongation and regulation of gene transcription. Typical investigation techniques require these structures to be …
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Novel nucleotide analogues for forming stable DNA triple helices
DNA triple helices are an important tool in a variety of medicinal and biotechnological applications, such as gene therapy and chemotherapeutics. DNA triple helices are formed by binding of a triplex-forming oligonucleotide (TFO) to a DNA duplex, via specific recognition of the individual base …
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Studies on approaches for sequencing cytosine modifications and the identification of their protein readers
… by biophysical confirmation of its pairing in duplex DNA. The unnatural base pair is tolerated by DNA polymerases, allowing optimisation of an expanded Sanger sequencing strategy to directly detect 5-formylcytosine and 5-hydroxymethylcytosine in DNA oligonucleotides. Chapter 3 builds on a novel …
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Antigenic Variation and Telomere Structure in Trypanosoma brucei
… effect. Telomeres typically contain simple DNA repeats (TTAGGG in animals and trypanosomatids) that are the binding sites for telomeric proteins, and end in 3' protrusions known as overhangs. In mammals, telomeres fold back in structures known as t-loops, in which the overhang is …
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Spectroscopic Analyses Of Factors Affecting Formation And Stability Of I-Motif Dna
The four-stranded i-motif (iM) conformation of DNA has importance to a variety of biochemical systems that include nanomaterials and oncogene regulation. Fundamental studies to understand iM formation and its structure in solution still remain to be done. In this dissertation, we will discuss the …
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Investigation of the Role of Groove Hydration and Charged Nucleosides in DNA Charge Transfer
Structural analyses of DNA oligonucleotides indicate the presence of bound water molecules in the major and minor grooves of DNA. These water molecules participate in DNA charge transfer by their reaction with guanosine radical cation to form 7,8-dihydro-8-oxo-guanine (8-oxoG), which when treated …
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