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Showing 1 to 13 of 13 for “"DNA--Conformation"”.
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Characterization of nanoparticle-DNA conjugate and control of DNA conformation on particle surface
… hybridization and de-hybridization phenomena of DNA which are one of its fundamental functions. In particular, conjugates of gold nanoparticles and DNA (Au NP-DNA) have been extensively explored for their potential in biological applications such as DNA delivery for gene therapy and disease …
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Computational tools for modeling and measuring chromosome structure
DNA conformation within cells has many important biological implications, but there are challenges both in modeling DNA due to the need for specialized techniques, and experimentally since tracing out in vivo conformations is currently impossible. This thesis contributes two computational projects …
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C8-Arylguanine Modified Hairpin Oligonucleotides: Synthesis, Conformational Analysis, and Tools for the Investigation of Z-DNA Formation
Z-DNA is the only DNA conformation that has a left-handed helical twist. Z-DNA has been implicated in carcinogenesis from its role in gene expression. Z-DNA formation has been linked to mutagenesis since it may play a role in genetic instability and can induce gene deletions. However, the specific …
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A Novel Mechanism for Site-Directed Mutagenesis of Large Catabolic Plasmids Using Natural Transformation
… is the process by which cells take up DNA from the surrounding medium under physiological conditions, altering the genotype in a heritable fashion. This occurs without chemical or physical treatment of the cells. Certain Acinetobacter strains exhibit a strong tendency to incorporate …
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Computational study of graphene nanopore sensor for DNA sensing
… to the physical dimension, of the translocating DNA molecule, that can be resolved. Typical solid-state membranes are too thick and usually fail to recognize single nucleotides on a DNA strand. Graphene is a sub-nanometer membrane, comprising of carbon atoms arranged in a honeycomb lattice, with …
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DNA supercoiling with a twist
The level of torsion in double-stranded DNA regulates base-pair stability and DNA conformation. It is important in initiation and regulation of specific DNA metabolic processes as well as chromatin assembly. High mobility group proteins (HMGB) are architectural proteins whose HMG DNA binding …
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The effect of negative supercoiling on the formation and positioning of nucleosome cores in vitro
The effect of the negative supercoiling of DNA on the formation and positioning of nucleosome cores was investigated in a 1915bp plasmid (pHP2) containing a section of the early H1-H4 histone gene spacer of Psammechinus miliaris, previously shown to position the histone octamer (Retief et al., …
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Re-evaluation of analytical chemistry techniques in studying DNA structures
… to examine the structural changes that DNA adopts when subjected to a number of external/internal factors. A self-complementary sequence, d(CG)9, and a non-self-complementary sequence (mixed sequence) were used to study the conformational effects displayed by each type of oligonucleotide …
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Fundamentals of Excess Electron Transport in Biologically Relevant Systems
… lesions that form via ultraviolet irradiation of DNA. While the distribution of thymine dimers is non-random, it is also not yet predictable. Thymine dimer accumulation is likely to be controlled by both its formation and reversion. Formation of thymine dimers occurs via direct excitation of …
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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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Intact and Damaged DNA and their Interaction with DNA-Binding Proteins: a Single Molecule Approach
… we study the architecture of intact and damaged DNA and their interaction with DNA-binding proteins using a combination of atomic force microscopy (AFM) and fluorescence correlation spectroscopy (FCS). In the beginning of this scientific work we therefore focus our efforts on the development of a …
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Localization of metal ions in DNA
M-DNA is a novel complex formed between DNA and transition metal ions under alkaline conditions. The unique properties of M-DNA were manipulated in order to rationally place metal ions at specific regions within a double-stranded DNA helix. Investigations using thermal denaturation profiles and the …