RNA secondary structure inference and functionalized virus-like particles for tumor cell detection and enumeration
Abstract/Contents
- Abstract
- In the new biotechnology age, a rich understanding of the properties of biological macromolecules allows chemical engineers to precisely manipulate these materials for a desired application. This body of work focuses on two areas of molecular understanding research, the development of tools to study the structure and functions of RNAs and the engineering of virus-like particles for the purpose of detecting circulating tumor cells. Single nucleotide resolution tools like selective 2'-hydroxl acylation by primer extensions (SHAPE) provide a facile method to probe the solution states of RNAs. We benchmarked SHAPE-directed RNA structure modeling on six molecules and determined that the error rates of SHAPE were comparable to previous benchmarks of other chemical probing methods. To address the limitations identified from our benchmark, we introduced the mutate and map method. Using high throughput RNA structure probing, we generated an information rich matrix that can be used to improve RNA structure determination. Coupling systematic mutagenesis with high-throughput chemical mapping enables accurate base-pair inference of domains from several structured RNAs. It was determined that this new method reduced the error rates. Combining this method with the Rosetta/FAFAR algorithm, we were able to produce a nucleotide-resolution three-dimensional model of the double-glycine riboswitch. Virus-like particles made from the protein shell of viruses constitute a versatile nanoparticle platform with tunable properties while remaining non-infectious. In this work, we first examine general rules and methodologies to functionalize virus-like particles. Using this obtained intuition, we have synthesized cancer cell-specific luminescent nanoparticles for tumor cell detection and enumeration. We explored a series of peptide tags and solution conditions to improve the conjugation efficiency of various ligands to the Hepatitis B core virus like particle. These improved methods and design principles then enabled the advancement of technology for circulating tumor cell detection. We have developed a filter-plate assay to immobilize and decorate these rare cells with cancer cell-specific luminescent nanoparticles. A charge-coupled device system provided enough resolution to see individual spots reflective of single cells. We find that the total light intensity correlate with the number of marked cells spiked into a mixture of unmarked cells. These new protocols allow for a rapid, non-laboratory based procedure that can be readily performed and interpreted by physicians. We envision that such protocols will provide real-time analysis to oncologists by noninvasive cancer monitoring and enable more effective cancer treatment.
Description
| Type of resource | text |
|---|---|
| Form | electronic; electronic resource; remote |
| Extent | 1 online resource. |
| Publication date | 2015 |
| Issuance | monographic |
| Language | English |
Creators/Contributors
| Associated with | VanLang, Christopher Chi-Bao |
|---|---|
| Associated with | Stanford University, Department of Chemical Engineering. |
| Primary advisor | Swartz, James R |
| Thesis advisor | Swartz, James R |
| Thesis advisor | Dunn, Alexander Robert |
| Thesis advisor | Peehl, Donna, 1952- |
| Advisor | Dunn, Alexander Robert |
| Advisor | Peehl, Donna, 1952- |
Subjects
| Genre | Theses |
|---|
Bibliographic information
| Statement of responsibility | Christopher Chi-Bao VanLang. |
|---|---|
| Note | Submitted to the Department of Chemical Engineering. |
| Thesis | Thesis (Ph.D.)--Stanford University, 2015. |
| Location | electronic resource |
Access conditions
- Copyright
- © 2015 by Christopher C VanLang
- License
- This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).
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