The Genetic Code Kit: An Open-Source Cell-Free Platform for Biochemical and Biotechnology Education

Abstract

Teaching the processes of transcription and translation is challenging due to the intangibility of these concepts and a lack of instructional, laboratory-based, active learning modules. Harnessing the genetic code in vitro with cell-free protein synthesis (CFPS) provides an open platform that allows for the direct manipulation of reaction conditions and biological machinery to enable inquiry-based learning. Here, we report our efforts to transform the research-based CFPS biotechnology into a hands-on module called the "Genetic Code Kit" for implementation into teaching laboratories. The Genetic Code Kit includes all reagents necessary for CFPS, as well as a laboratory manual, student worksheet, and augmented reality activity. This module allows students to actively explore transcription and translation while gaining exposure to an emerging research technology. In our testing of this module, undergraduate students who used the Genetic Code Kit in a teaching laboratory showed significant score increases on transcription and translation questions in a post-lab questionnaire compared with students who did not participate in the activity. Students also demonstrated an increase in self-reported confidence in laboratory methods and comfort with CFPS, indicating that this module helps prepare students for careers in laboratory research. Importantly, the Genetic Code Kit can accommodate a variety of learning objectives beyond transcription and translation and enables hypothesis-driven science. This opens the possibility of developing Course-Based Undergraduate Research Experiences (CUREs) based on the Genetic Code Kit, as well as supporting next-generation science standards in 8-12th grade science courses. Keywords: biochemical education, learn by doing, cell-free protein synthesis (CFPS), in vitro transcription and translation, synthetic biology (synbio), central dogma of molecular biology (CDMB), chemical education and teaching, augmented reality (AR) Abbreviations: CFPS, cell-free protein synthesis; CUREs, course-based undergraduate research experiences; sfGFP, superfolder green fluorescent protein.

The Fold-Illuminator: A low-cost, portable, and disposable incubator-illuminator device

“…The transilluminators detected the glow from fluorescent dye and indicated a complete reaction, allowing for hands-on learning of previously lecture-only material. The use of cell-free systems to teach the genetic code in a learn-by-doing manner is also emerging [ 5 , 9 , 28 ]. In this process, students are able to learn the fundamental concepts of transcription and translation in an engaging, hands-on manner.…”

“…In this process, students are able to learn the fundamental concepts of transcription and translation in an engaging, hands-on manner. Additionally, students who performed this lab showed significant score increases in learning gains compared to the control group [ 5 ].…”

“…Fluorescent reporters have transformed the way that many biochemical processes are applied in the real-world. In recent years, fluorescent reporters have enabled many novel applications in diagnostics [ [1] , [2] , [3] ], point-of-care testing [ 4 ] and education [ 5 ]. The development of reporters, which range in composition and mechanism from small molecule fluorophores and fluorogens to nanomaterials and fluorescent proteins [ 6 ], has allowed for the observation of biochemical processes in real time [ 7 ].…”

“…Costing on average less than $3.00 for the pair, our design constraints utilize a LED/light filter combination as an affordable, portable option that would allow the user to obtain more confidence in their reaction results in less time. Additionally, biochemical reactions such as cell-free protein synthesis benefit from incubation at temperatures in the range of 30–37 ° C [4] , [5] . While not all applications may require a built-in incubator, our design constraints required compatibility with this optional add-on.…”

Analysis of the Innovation Trend in Cell-Free Synthetic Biology

“…The flexibility and efficiency of CFPS also enable commercial ventures beyond the traditional mass production and delivery pipeline in the form of distributed, or decentralized, production of bioactive molecules, including conjugate vaccines and antibody analogs [17,41]. Furthermore, distributed cellfree synthetic biology has demonstrated value for point-of-use testing for pathogens and water contaminants [21,42] as well as inexpensive biology education platforms [43,44]. CFPS applications also continue to grow for discovering and optimizing enzymes to make commodity chemicals [45], natural products [46], and biomaterials [47], although price and scalability remain significant hurdles to industrial production volumes [7].…”