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- All Subjects: Synthetic Biology
- All Subjects: bivalent
- Creators: Green, Alexander
- Creators: Gillum, David
This dissertation aims to 1) develop new strategy to identify high affinity nucleic acid aptamers against biological ligand; and 2) explore highly orthogonal RNA riboregulators in vivo for constructing multi-input gene circuits with NOT logic. With the aid of a DNA nanoscaffold, pairs of hetero-bivalent aptamers for human alpha thrombin were identified with ultra-high binding affinity in femtomolar range with displaying potent biological modulations for the enzyme activity. The newly identified bivalent aptamers enriched the aptamer tool box for future therapeutic applications in hemostasis, and also the strategy can be potentially developed for other target molecules. Secondly, by employing a three-way junction structure in the riboregulator structure through de-novo design, we identified a family of high-performance RNA-sensing translational repressors that down-regulates gene translation in response to cognate RNAs with remarkable dynamic range and orthogonality. Harnessing the 3WJ repressors as modular parts, we integrate them into biological circuits that execute universal NAND and NOR logic with up to four independent RNA inputs in Escherichia coli.
Industries and research utilizing genetically-engineered organisms are often subject to strict containment requirements such as physical isolation or specialized equipment to prevent an unintended escape. A relatively new field of research looks for ways to engineer intrinsic containment techniques- genetic safeguards that prevent an organism from surviving outside of specific conditions. As interest in this field has grown over the last few decades, researchers in molecular and synthetic biology have discovered many novel ways to accomplish this containment, but the current literature faces some ambiguity and overlap in the ways they describe various biocontainment methods. Additionally, the way publications report the robustness of the techniques they test is inconsistent, making it uncertain how regulators could assess the safety and efficacy of these methods if they are eventually to be used in practical, consumer applications. This project organizes and clarifies the descriptions of these techniques within an interactive flowchart, linking to definitions and references to publications on each within an Excel table. For each reference, variables such as the containment approach, testing methods, and results reported are compiled, to illustrate the varying degrees to which these techniques are tested.
Industries and research utilizing genetically-engineered organisms are often subject to strict containment requirements such as physical isolation or specialized equipment to prevent an unintended escape. A relatively new field of research looks for ways to engineer intrinsic containment techniques- genetic safeguards that prevent an organism from surviving outside of specific conditions. As interest in this field has grown over the last few decades, researchers in molecular and synthetic biology have discovered many novel ways to accomplish this containment, but the current literature faces some ambiguity and overlap in the ways they describe various biocontainment methods. Additionally, the way publications report the robustness of the techniques they test is inconsistent, making it uncertain how regulators could assess the safety and efficacy of these methods if they are eventually to be used in practical, consumer applications. This project organizes and clarifies the descriptions of these techniques within an interactive flowchart, linking to definitions and references to publications on each within an Excel table. For each reference, variables such as the containment approach, testing methods, and results reported are compiled, to illustrate the varying degrees to which these techniques are tested.
Industries and research utilizing genetically-engineered organisms are often subject to strict containment requirements such as physical isolation or specialized equipment to prevent an unintended escape. A relatively new field of research looks for ways to engineer intrinsic containment techniques- genetic safeguards that prevent an organism from surviving outside of specific conditions. As interest in this field has grown over the last few decades, researchers in molecular and synthetic biology have discovered many novel ways to accomplish this containment, but the current literature faces some ambiguity and overlap in the ways they describe various biocontainment methods. Additionally, the way publications report the robustness of the techniques they test is inconsistent, making it uncertain how regulators could assess the safety and efficacy of these methods if they are eventually to be used in practical, consumer applications. This project organizes and clarifies the descriptions of these techniques within an interactive flowchart, linking to definitions and references to publications on each within an Excel table. For each reference, variables such as the containment approach, testing methods, and results reported are compiled, to illustrate the varying degrees to which these techniques are tested.