Matching Items (17)
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- All Subjects: Synthetic Biology
- All Subjects: engineering
Description
The principle of Darwinian evolution has been applied in the laboratory to nucleic acid molecules since 1990, and led to the emergence of in vitro evolution technique. The methodology of in vitro evolution surveys a large number of different molecules simultaneously for a pre-defined chemical property, and enrich for molecules with the particular property. DNA and RNA sequences with versatile functions have been identified by in vitro selection experiments, but many basic questions remain to be answered about how these molecules achieve their functions. This dissertation first focuses on addressing a fundamental question regarding the molecular recognition properties of in vitro selected DNA sequences, namely whether negatively charged DNA sequences can be evolved to bind alkaline proteins with high specificity. We showed that DNA binders could be made, through carefully designed stringent in vitro selection, to discriminate different alkaline proteins. The focus of this dissertation is then shifted to in vitro evolution of an artificial genetic polymer called threose nucleic acid (TNA). TNA has been considered a potential RNA progenitor during early evolution of life on Earth. However, further experimental evidence to support TNA as a primordial genetic material is lacking. In this dissertation we demonstrated the capacity of TNA to form stable tertiary structure with specific ligand binding property, which suggests a possible role of TNA as a pre-RNA genetic polymer. Additionally, we discussed the challenges in in vitro evolution for TNA enzymes and developed the necessary methodology for future TNA enzyme evolution.
ContributorsYu, Hanyang (Author) / Chaput, John C (Thesis advisor) / Chen, Julian (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)
Created2013
Description
Synthetic biology is constantly evolving as new ideas are incorporated into this increasingly flexible field. It incorporates the engineering of life with standard genetic parts and methods; new organisms with new genomes; expansion of life to include new components, capabilities, and chemistries; and even completely synthetic organisms that mimic life while being composed of non-living matter. We have introduced a new paradigm of synthetic biology that melds the methods of in vitro evolution with the goals and philosophy of synthetic biology. The Family B proteins represent the first de novo evolved natively folded proteins to be developed with increasingly powerful tools of molecular evolution. These proteins are folded and functional, composed of the 20 canonical amino acids, and in many ways resemble natural proteins. However, their evolutionary history is quite different from natural proteins, as it did not involve a cellular environment. In this study, we examine the properties of DX, one of the Family B proteins that have been evolutionarily optimized for folding stability. Described in chapter 2 is an investigation into the primitive catalytic properties of DX, which seems to have evolved a serendipitous ATPase activity in addition to its selected ATP binding activity. In chapters 3 and 4 we express the DX gene in E. coli cells and observe massive changes in cell morphology, biochemistry, and life cycle. Exposure to DX activates several defense systems in E. coli, including filamentation, cytoplasmic segregation, and reversion to a viable but non-culturable state. We examined these phenotypes in detail and present a model that accounts for how DX causes such a rearrangement of the cell.
ContributorsStomel, Joshua (Author) / Chaput, John C (Thesis advisor) / Korch, Shaleen (Committee member) / Roberson, Robert (Committee member) / Ghirlanda, Gionvanna (Committee member) / Arizona State University (Publisher)
Created2011
Description
Advances in chemical synthesis have enabled new lines of research with unnatural genetic polymers whose modified bases or sugar-phosphate backbones have potential therapeutic and biotechnological applications. Maximizing the potential of these synthetic genetic systems requires inventing new molecular biology tools that can both generate and faithfully replicate unnatural polymers of significant length. Threose nucleic acid (TNA) has received significant attention as a complete replication system has been developed by engineering natural polymerases to broaden their substrate specificity. The system, however, suffers from a high mutational load reducing its utility. This thesis will cover the development of two new polymerases capable of transcribing and reverse transcribing TNA polymers with high efficiency and fidelity. The polymerases are identified using a new strategy wherein gain-of-function mutations are sampled in homologous protein architectures leading to subtle optimization of protein function. The new replication system has a fidelity that supports the propagation of genetic information enabling in vitro selection of functional TNA molecules. TNA aptamers to human alpha-thrombin are identified and demonstrated to have superior stability compared to DNA and RNA in biologically relevant conditions. This is the first demonstration that functional TNA molecules have potential in biotechnology and molecular medicine.
ContributorsDunn, Matthew Ryan (Author) / Chaput, John C (Thesis advisor) / LaBaer, Joshua (Committee member) / Lake, Douglas (Committee member) / Mangone, Marco (Committee member) / Arizona State University (Publisher)
Created2015
Description
Membranes are a key part of pervaporation processes, which is generally a more
efficient process for selective removal of alcohol from water than distillation. It is
necessary that the membranes have high alcohol permeabilities and selectivities.
Polydimethylsiloxane (PDMS) based mixed matrix membranes (MMMs) have
demonstrated very promising results. Zeolitic imidazolate framework-71 (ZIF-71)
demonstrated promising alcohol separation abilities. In this dissertation, we present
fundamental studies on the synthesis of ZIF-71/PDMS MMMs.
Free-standing ZIF-71/ PDMS membranes with 0, 5, 25 and 40 wt % ZIF-71
loadings were prepared and the pervaporation separation for ethanol and 1-butanol from
water was measured. ZIF-71/PDMS MMMs were formed through addition cure and
condensation cure methods. Addition cure method was not compatible with ZIF-71
resulting in membranes with poor mechanical properties, while the condensation cure
method resulted in membranes with good mechanical properties. The 40 wt % ZIF-71
loading PDMS nanocomposite membranes achieved a maximum ethanol/water selectivity
of 0.81 ± 0.04 selectivity and maximum 1-butnaol/water selectivity of 5.64 ± 0.15.
The effects of synthesis time, temperature, and reactant ratio on ZIF-71 particle
size and the effect of particle size on membrane performance were studied. Temperature
had the greatest effect on ZIF-71 particle size as the synthesis temperature varied from -
20 to 35 ºC. The ZIF-71 synthesized had particle diameters ranging from 150 nm to 1
μm. ZIF-71 particle size is critical in ZIF-71/PDMS composite membrane performance
for alcohol removal from water through pervaporation. The membranes made with
micron sized ZIF-71 particles showed higher alcohol/water selectivity than those with
smaller particles. Both alcohol and water permeability increased when larger sized ZIF-
71 particles were incorporated.
ZIF-71 particles were modified with four ligands through solvent assisted linker
exchange (SALE) method: benzimidazole (BIM), 5-methylbenzimidazole (MBIM), 5,6-
dimethylbenzimidazole (DMBIM) and 4-Phenylimidazole (PI). The morphology of ZIF-
71 were maintained after the modification. ZIF-71/PDMS composite membranes with 25
wt% loading modified ZIF-71 particles were made for alcohol/water separation. Better
particle dispersion in PDMS polymer matrix was observed with the ligand modified ZIFs.
For both ethanol/water and 1-butanol/water separations, the alcohol permeability and
alcohol/water selectivity were lowered after the ZIF-71 ligand exchange reaction.
efficient process for selective removal of alcohol from water than distillation. It is
necessary that the membranes have high alcohol permeabilities and selectivities.
Polydimethylsiloxane (PDMS) based mixed matrix membranes (MMMs) have
demonstrated very promising results. Zeolitic imidazolate framework-71 (ZIF-71)
demonstrated promising alcohol separation abilities. In this dissertation, we present
fundamental studies on the synthesis of ZIF-71/PDMS MMMs.
Free-standing ZIF-71/ PDMS membranes with 0, 5, 25 and 40 wt % ZIF-71
loadings were prepared and the pervaporation separation for ethanol and 1-butanol from
water was measured. ZIF-71/PDMS MMMs were formed through addition cure and
condensation cure methods. Addition cure method was not compatible with ZIF-71
resulting in membranes with poor mechanical properties, while the condensation cure
method resulted in membranes with good mechanical properties. The 40 wt % ZIF-71
loading PDMS nanocomposite membranes achieved a maximum ethanol/water selectivity
of 0.81 ± 0.04 selectivity and maximum 1-butnaol/water selectivity of 5.64 ± 0.15.
The effects of synthesis time, temperature, and reactant ratio on ZIF-71 particle
size and the effect of particle size on membrane performance were studied. Temperature
had the greatest effect on ZIF-71 particle size as the synthesis temperature varied from -
20 to 35 ºC. The ZIF-71 synthesized had particle diameters ranging from 150 nm to 1
μm. ZIF-71 particle size is critical in ZIF-71/PDMS composite membrane performance
for alcohol removal from water through pervaporation. The membranes made with
micron sized ZIF-71 particles showed higher alcohol/water selectivity than those with
smaller particles. Both alcohol and water permeability increased when larger sized ZIF-
71 particles were incorporated.
ZIF-71 particles were modified with four ligands through solvent assisted linker
exchange (SALE) method: benzimidazole (BIM), 5-methylbenzimidazole (MBIM), 5,6-
dimethylbenzimidazole (DMBIM) and 4-Phenylimidazole (PI). The morphology of ZIF-
71 were maintained after the modification. ZIF-71/PDMS composite membranes with 25
wt% loading modified ZIF-71 particles were made for alcohol/water separation. Better
particle dispersion in PDMS polymer matrix was observed with the ligand modified ZIFs.
For both ethanol/water and 1-butanol/water separations, the alcohol permeability and
alcohol/water selectivity were lowered after the ZIF-71 ligand exchange reaction.
ContributorsYin, Huidan (Author) / Lind, Mary Laura (Thesis advisor) / Mu, Bin (Committee member) / Nielsen, David (Committee member) / Seo, Don (Committee member) / Lin, Jerry (Committee member) / Arizona State University (Publisher)
Created2017
Description
The portability of genetic tools from one organism to another is a cornerstone of synthetic biology. The shared biological language of DNA-to-RNA-to-protein allows for expression of polypeptide chains in phylogenetically distant organisms with little modification. The tools and contexts are diverse, ranging from catalytic RNAs in cell-free systems to bacterial proteins expressed in human cell lines, yet they exhibit an organizing principle: that genes and proteins may be treated as modular units that can be moved from their native organism to a novel one. However, protein behavior is always unpredictable; drop-in functionality is not guaranteed.
My work characterizes how two different classes of tools behave in new contexts and explores methods to improve their functionality: 1. CRISPR/Cas9 in human cells and 2. quorum sensing networks in Escherichia coli.
1. The genome-editing tool CRISPR/Cas9 has facilitated easily targeted, effective, high throughput genome editing. However, Cas9 is a bacterially derived protein and its behavior in the complex microenvironment of the eukaryotic nucleus is not well understood. Using transgenic human cell lines, I found that gene-silencing heterochromatin impacts Cas9’s ability to bind and cut DNA in a site-specific manner and I investigated ways to improve CRISPR/Cas9 function in heterochromatin.
2. Bacteria use quorum sensing to monitor population density and regulate group behaviors such as virulence, motility, and biofilm formation. Homoserine lactone (HSL) quorum sensing networks are of particular interest to synthetic biologists because they can function as “wires” to connect multiple genetic circuits. However, only four of these networks have been widely implemented in engineered systems. I selected ten quorum sensing networks based on their HSL production profiles and confirmed their functionality in E. coli, significantly expanding the quorum sensing toolset available to synthetic biologists.
My work characterizes how two different classes of tools behave in new contexts and explores methods to improve their functionality: 1. CRISPR/Cas9 in human cells and 2. quorum sensing networks in Escherichia coli.
1. The genome-editing tool CRISPR/Cas9 has facilitated easily targeted, effective, high throughput genome editing. However, Cas9 is a bacterially derived protein and its behavior in the complex microenvironment of the eukaryotic nucleus is not well understood. Using transgenic human cell lines, I found that gene-silencing heterochromatin impacts Cas9’s ability to bind and cut DNA in a site-specific manner and I investigated ways to improve CRISPR/Cas9 function in heterochromatin.
2. Bacteria use quorum sensing to monitor population density and regulate group behaviors such as virulence, motility, and biofilm formation. Homoserine lactone (HSL) quorum sensing networks are of particular interest to synthetic biologists because they can function as “wires” to connect multiple genetic circuits. However, only four of these networks have been widely implemented in engineered systems. I selected ten quorum sensing networks based on their HSL production profiles and confirmed their functionality in E. coli, significantly expanding the quorum sensing toolset available to synthetic biologists.
ContributorsDaer, René (Author) / Haynes, Karmella (Thesis advisor) / Brafman, David (Committee member) / Nielsen, David (Committee member) / Kiani, Samira (Committee member) / Arizona State University (Publisher)
Created2017
Description
Two-dimensional transition metal dichalcogenides (TMDCs) such as
molybdenum disulfide (MoS2), tungsten disulfide (WS2), molybdenum diselenide (MoSe2) and tungsten diselenide (WSe2) are attractive for use in biotechnology, optical and electronics devices due to their promising and tunable electrical, optical and chemical properties. To fulfill the variety of requirements for different applications, chemical treatment methods are developed to tune their properties. In this dissertation, plasma treatment, chemical doping and functionalization methods have been applied to tune the properties of TMDCs. First, plasma treatment of TMDCs results in doping and generation of defects, as well as the synthesis of transition metal oxides (TMOs) with rolled layers that have increased surface-to-volume ratio and are promising for electrochemical applications. Second, chemical functionalization is another powerful approach for tuning the properties of TMDCs for use in many applications. To covalently functionalize the basal planes of TMDCs, previous reports begin with harsh treatments like lithium intercalation that disrupt the structure and lead to a phase transformation from semiconducting to metallic. Instead, this work demonstrates the direct covalent functionalization of semiconducting MoS2 using aryl diazonium salts without lithium treatments. It preserves the structure and semiconducting nature of MoS2, results in covalent C-S bonds on basal planes and enables different functional groups to be tethered to the MoS2 surface via the diazonium salts. The attachment of fluorescent proteins has been used as a demonstration and it suggests future applications in biology and biosensing. The effects of the covalent functionalization on the electronic transport properties of MoS2 were then studied using field effect transistor (FET) devices.
molybdenum disulfide (MoS2), tungsten disulfide (WS2), molybdenum diselenide (MoSe2) and tungsten diselenide (WSe2) are attractive for use in biotechnology, optical and electronics devices due to their promising and tunable electrical, optical and chemical properties. To fulfill the variety of requirements for different applications, chemical treatment methods are developed to tune their properties. In this dissertation, plasma treatment, chemical doping and functionalization methods have been applied to tune the properties of TMDCs. First, plasma treatment of TMDCs results in doping and generation of defects, as well as the synthesis of transition metal oxides (TMOs) with rolled layers that have increased surface-to-volume ratio and are promising for electrochemical applications. Second, chemical functionalization is another powerful approach for tuning the properties of TMDCs for use in many applications. To covalently functionalize the basal planes of TMDCs, previous reports begin with harsh treatments like lithium intercalation that disrupt the structure and lead to a phase transformation from semiconducting to metallic. Instead, this work demonstrates the direct covalent functionalization of semiconducting MoS2 using aryl diazonium salts without lithium treatments. It preserves the structure and semiconducting nature of MoS2, results in covalent C-S bonds on basal planes and enables different functional groups to be tethered to the MoS2 surface via the diazonium salts. The attachment of fluorescent proteins has been used as a demonstration and it suggests future applications in biology and biosensing. The effects of the covalent functionalization on the electronic transport properties of MoS2 were then studied using field effect transistor (FET) devices.
ContributorsChu, Ximo (Author) / Wang, Qing Hua (Thesis advisor) / Sieradzki, Karl (Committee member) / Green, Alexander (Committee member) / Chan, Candace (Committee member) / Arizona State University (Publisher)
Created2018
Description
Synthetic biology is an emerging field which melds genetics, molecular biology, network theory, and mathematical systems to understand, build, and predict gene network behavior. As an engineering discipline, developing a mathematical understanding of the genetic circuits being studied is of fundamental importance. In this dissertation, mathematical concepts for understanding, predicting, and controlling gene transcriptional networks are presented and applied to two synthetic gene network contexts. First, this engineering approach is used to improve the function of the guide ribonucleic acid (gRNA)-targeted, dCas9-regulated transcriptional cascades through analysis and targeted modification of the RNA transcript. In so doing, a fluorescent guide RNA (fgRNA) is developed to more clearly observe gRNA dynamics and aid design. It is shown that through careful optimization, RNA Polymerase II (Pol II) driven gRNA transcripts can be strong enough to exhibit measurable cascading behavior, previously only shown in RNA Polymerase III (Pol III) circuits. Second, inherent gene expression noise is used to achieve precise fractional differentiation of a population. Mathematical methods are employed to predict and understand the observed behavior, and metrics for analyzing and quantifying similar differentiation kinetics are presented. Through careful mathematical analysis and simulation, coupled with experimental data, two methods for achieving ratio control are presented, with the optimal schema for any application being dependent on the noisiness of the system under study. Together, these studies push the boundaries of gene network control, with potential applications in stem cell differentiation, therapeutics, and bio-production.
ContributorsMenn, David J (Author) / Wang, Xiao (Thesis advisor) / Kiani, Samira (Committee member) / Haynes, Karmella (Committee member) / Nielsen, David (Committee member) / Marshall, Pamela (Committee member) / Arizona State University (Publisher)
Created2018
Description
Currently in synthetic biology only the Las, Lux, and Rhl quorum sensing pathways have been adapted for broad engineering use. Quorum sensing allows a means of cell to cell communication in which a designated sender cell produces quorum sensing molecules that modify gene expression of a designated receiver cell. While useful, these three quorum sensing pathways exhibit a nontrivial level of crosstalk, hindering robust engineering and leading to unexpected effects in a given design. To address the lack of orthogonality among these three quorum sensing pathways, previous scientists have attempted to perform directed evolution on components of the quorum sensing pathway. While a powerful tool, directed evolution is limited by the subspace that is defined by the protein. For this reason, we take an evolutionary biology approach to identify new orthogonal quorum sensing networks and test these networks for cross-talk with currently-used networks. By charting characteristics of acyl homoserine lactone (AHL) molecules used across quorum sensing pathways in nature, we have identified favorable candidate pathways likely to display orthogonality. These include Aub, Bja, Bra, Cer, Esa, Las, Lux, Rhl, Rpa, and Sin, which we have begun constructing and testing. Our synthetic circuits express GFP in response to a quorum sensing molecule, allowing quantitative measurement of orthogonality between pairs. By determining orthogonal quorum sensing pairs, we hope to identify and adapt novel quorum sensing pathways for robust use in higher-order genetic circuits.
ContributorsMuller, Ryan (Author) / Haynes, Karmella (Thesis director) / Wang, Xiao (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Department of Chemistry and Biochemistry (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Description
One of the primary bottlenecks to chemical production in biological organisms is the toxicity of the chemical. Overexpression of efflux pumps has been shown to increase tolerance to aromatic compounds such as styrene and styrene oxide. Tight control of pump expression is necessary to maximize titers and prevent excessive strain on the cells. This study aimed to identify aromatic-sensitive native promoters and heterologous biosensors for construction of closed-loop control of efflux pump expression in E. coli. Using a promoter library constructed by Zaslaver et al., activation was measured through GFP output. Promoters were evaluated for their sensitivity to the addition of one of four aromatic compounds, their "leaking" of signal, and their induction threshold. Out of 43 targeted promoters, 4 promoters (cmr, mdtG, yahN, yajR) for styrene oxide, 2 promoters (mdtG, yahN) for styrene, 0 promoters for 2-phenylethanol, and 1 promoter for phenol (pheP) were identified as ideal control elements in aromatic bioproduction. In addition, a series of three biosensors (NahR, XylS, DmpR) known to be inducible by other aromatics were screened against styrene oxide, 2-phenylethanol, and phenol. The targeted application of these biosensors is aromatic-induced activation of linked efflux pumps. All three biosensors responded strongly in the presence of styrene oxide and 2-phenylethanol, with minor activation in the presence of phenol. Bioproduction of aromatics continues to gain traction in the biotechnology industry, and the continued discovery of aromatic-inducible elements will be essential to effective pathway control.
ContributorsXu, Jimmy (Author) / Nielsen, David (Thesis director) / Wang, Xuan (Committee member) / School of Life Sciences (Contributor) / Chemical Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
Synthetic biology is an emerging engineering disciple, which designs and controls biological systems for creation of materials, biosensors, biocomputing, and much more. To better control and engineer these systems, modular genetic components which allow for highly specific and high dynamic range genetic regulation are necessary. Currently the field struggles to demonstrate reliable regulators which are programmable and specific, yet also allow for a high dynamic range of control. Inspired by the characteristics of the RNA toehold switch in E. coli, this project attempts utilize artificial introns and complementary trans-acting RNAs for gene regulation in a eukaryote host, S. cerevisiae. Following modification to an artificial intron, splicing control with RNA hairpins was demonstrated. Temperature shifts led to increased protein production likely due to increased splicing due to hairpin loosening. Progress is underway to demonstrate trans-acting RNA interaction to control splicing. With continued development, we hope to provide a programmable, specific, and effective means for translational gene regulation in S. cerevisae.
ContributorsDorr, Brandon Arthur (Author) / Wang, Xiao (Thesis director) / Green, Alexander (Committee member) / Harrington Bioengineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05