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Due to nucleic acid’s programmability, it is possible to realize DNA structures with computing functions, and thus a new generation of molecular computers is evolving to solve biological and medical problems. There is evidence that genetic heredity diseases and cancer can be the result of genetic heterogeneity, thus there is a need for diagnostics and therapeutic tools with multiplex and smart components to compute all the molecular drivers. DNA molecular computers mimics electronic computers by programming synthetic nucleic acids to perform similarly to central processing units. Considering how the evolution of integrated circuits made possible the revolution of silicon-based computers, integrated DNA molecular circuits can be developed to allow modular designing and scale to complex DNA nano-processors. This dissertation covers the development of four-way junction (4J) DNA logic gates that can be wired to result in functionally complete gates, and their immobilization on a modular DNA board that serves as a scaffold for logic gate integration, fast signal processing, and cascading. Connecting 4J DNA logic gates YES and NOT resulted in OR, NAND, and IMPLY logic circuits; the three circuits can operate under the input of miRNAs, either oncogenic or/and tumor-suppressors, and give two possible diagnoses: healthy or cancerous. The DNA board can expand as the DNA circuit grows in the number of integrated 4J units. Signal propagation across a wired of 4J YES logic gates showed signal completion in < 3 min, accounting for a signal propagation rate of 4.5 nm/min and that up to 6 units can be cascaded before the signal dissipates. Lastly, an approach to chemically ligate all oligonucleotide components of the DNA molecular device is presented, in which we also found a route for the bioconjugation of 5’ to 5’ and 3’ to 3’ oligonucleotides.
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A Laboratory Class: Constructing DNA Molecular Circuits for Cancer Diagnosis
t has been shown that active learning strategies are effective in teaching complex STEM concepts. In this study, we developed and implemented a laboratory experiment for teaching the concepts of Boolean logic gates, molecular beacon probes, molecular computing, DNA logic gates, microRNA, and molecular diagnosis of hepatocellular carcinoma, which are related to DNA molecular computing, an interdisciplinary cutting-edge research technology in biochemistry, synthetic biology, computer science, and medicine. The laboratory experience takes about 110–140 min and consists of a multiple-choice pretest (15 min), introductory lecture (20 min), wet laboratory experiment (60–90 min), and a post-test (15 min). Students are tasked to experimentally construct three molecular logic circuits made of DNA oligonucleotides and use them for the fluorescence-based detection of microRNA markers related to diagnostics of hepatocellular carcinoma. The class was taught to undergraduate students from freshman to senior academic levels majoring in chemistry, biochemistry, biotechnology, and biomedical sciences. Students were engaged during the session and motivated to learn more about the research technology. A comparison of students’ scores on the pretest and post-test demonstrated improvement in knowledge of the concepts taught. Visual observation of the fluorescence readout led to a straightforward interpretation of the results. The laboratory experiment is portable; it uses inexpensive nontoxic reagents and thus can be employed outside a laboratory room for outreach and science popularization purposes.
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- Award ID(s):
- 2226021
- PAR ID:
- 10545002
- Publisher / Repository:
- American Chemistry Society
- Date Published:
- Journal Name:
- Journal of Chemical Education
- ISSN:
- 0021-9584
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1021/acs.jchemed.4c00675
