Matching Items (3)
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- All Subjects: Molecules
- Creators: Zhang, Peiming
Description
DNA has recently emerged as an extremely promising material to organize molecules on nanoscale. The reliability of base recognition, self-assembling behavior, and attractive structural properties of DNA are of unparalleled value in systems of this size. DNA scaffolds have already been used to organize a variety of molecules including nanoparticles and proteins. New protein-DNA bio-conjugation chemistries make it possible to precisely position proteins and other biomolecules on underlying DNA scaffolds, generating multi-biomolecule pathways with the ability to modulate inter-molecular interactions and the local environment. This dissertation focuses on studying the application of using DNA nanostructure to direct the self-assembly of other biomolecular networks to translate biochemical pathways to non-cellular environments. Presented here are a series of studies toward this application. First, a novel strategy utilized DNA origami as a scaffold to arrange spherical virus capsids into one-dimensional arrays with precise nanoscale positioning. This hierarchical self-assembly allows us to position the virus particles with unprecedented control and allows the future construction of integrated multi-component systems from biological scaffolds using the power of rationally engineered DNA nanostructures. Next, discrete glucose oxidase (GOx)/ horseradish peroxidase (HRP) enzyme pairs were organized on DNA origami tiles with controlled interenzyme spacing and position. This study revealed two different distance-dependent kinetic processes associated with the assembled enzyme pairs. Finally, a tweezer-like DNA nanodevice was designed and constructed to actuate the activity of an enzyme/cofactor pair. Using this approach, several cycles of externally controlled enzyme inhibition and activation were successfully demonstrated. This principle of responsive enzyme nanodevices may be used to regulate other types of enzymes and to introduce feedback or feed-forward control loops.
ContributorsLiu, Minghui (Author) / Yan, Hao (Thesis advisor) / Liu, Yan (Thesis advisor) / Chen, Julian (Committee member) / Zhang, Peiming (Committee member) / Arizona State University (Publisher)
Created2013
Description
Single molecule identification is one essential application area of nanotechnology. The application areas including DNA sequencing, peptide sequencing, early disease detection and other industrial applications such as quantitative and quantitative analysis of impurities, etc. The recognition tunneling technique we have developed shows that after functionalization of the probe and substrate of a conventional Scanning Tunneling Microscope with recognition molecules ("tethered molecule-pair" configuration), analyte molecules trapped in the gap that is formed by probe and substrate will bond with the reagent molecules. The stochastic bond formation/breakage fluctuations give insight into the nature of the intermolecular bonding at a single molecule-pair level. The distinct time domain and frequency domain features of tunneling signals were extracted from raw signals of analytes such as amino acids and their enantiomers. The Support Vector Machine (a machine-learning method) was used to do classification and predication based on the signal features generated by analytes, giving over 90% accuracy of separation of up to seven analytes. This opens up a new interface between chemistry and electronics with immediate implications for rapid Peptide/DNA sequencing and molecule identification at single molecule level.
ContributorsZhao, Yanan, 1986- (Author) / Lindsay, Stuart (Thesis advisor) / Nemanich, Robert (Committee member) / Qing, Quan (Committee member) / Ros, Robert (Committee member) / Zhang, Peiming (Committee member) / Arizona State University (Publisher)
Created2014
Description
Platelets are specialized blood cells that play crucial role in normal physiologic and pathologic processes such as hemostasis, inflammation, wound healing, and host defense. Activation of platelets is essential for platelet function and it includes a complex interplay of adhesion and intracellular signaling molecules. Platelets are known to be activated during vessel injury by a complex interaction of soluble agonists and once activated, they adhere to sub-endothelial matrix to aggregate and secrete granules leading to the formation of platelet aggregate that is necessary for thrombus formation. Platelet integrin plays a central role in platelet adhesive reactions by serving as a receptor for fibrinogen involved in bidirectional transmembrane signaling. In order to elucidate the interaction of integrin with cytoplasmic signaling molecules during inside-out and outside-in signaling, we have studied the kinetics of the recruitment of talin, kindling, filmin-A, skelemin, Scr and syk to the B3 cytoplasmic tails. Platelets were isolated from human blood and activated with ADP/Epinephrine for different times. The complexes of *** with signaling proteins were obtained by immunoprecipitation of platelet lysates with anit-*** monoclonal antibody and then analyzed by Western blotting using antibodies directed against selected signaling proteins. Our results show different kinetics in recruitment of signaling molecules to the B3 integrin cytoplasmic tail during inside-out and outside in signaling.
ContributorsYantas, Alexa Susan (Author) / Ugarova, Tatiana (Thesis director) / Podolnikova, Nataly (Committee member) / Turaga, Ramya (Committee member) / Barrett, The Honors College (Contributor)
Created2012-05