An official website of the United States government
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.
more »
« less
Introduction to Fluorescence in General Chemistry Using the Intercalation of Propidium Iodide with DNA
The phenomenon of fluorescence is very important from multiple standpoints in the chemical and biological sciences. This paper introduces an experiment in a first-semester chemistry laboratory course that uses a current biomedical research method, the detection of double-stranded DNA using the intercalator propidium iodide. Fluorescence is detected both using blacklight illumination and also with white light and a spectrometer, using the two excitation bands for propidium. This experiment also involves students obtaining DNA from strawberries and then determining the amount of DNA they have isolated using fluorescence methods. The experiment provides students with an initial experience in fluorescence-based analytical chemistry and the concepts of fluorescence as a quantum phenomenon.
more »
« less
- Award ID(s):
- 2111446
- PAR ID:
- 10540581
- Editor(s):
- Holme, Thomas A
- Publisher / Repository:
- American Chemical Society
- Date Published:
- Journal Name:
- Journal of Chemical Education
- ISSN:
- 0021-9584
- Subject(s) / Keyword(s):
- Laboratory, fluorescence, imaging, DNA, quantum mechanics, analytical chemistry.
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Holme, Thomas A (Ed.)This paper reports a laboratory experiment that determines the kinetics of the reaction of coumarin-102, a fluorescent dye, with sodium hydroxide. The reaction is studied by monitoring the loss of coumarin-102 fluorescence during ring-opening saponification by hydroxide using smartphone cameras and near-UV (“blacklight”) illumination. The order of the reaction in coumarin-102 is determined by examining the time course of fluorescence decay over time and fitting the data to integrated rate law models. The order of the reaction in sodium hydroxide is determined by varying the concentration of NaOH and comparing the impact on the rate of the reaction. This represents an easy-to-implement kinetics experiment that uses an engaging phenomenon (fluorescence), a convenient data-acquisition technology (smartphone cameras) and an important image-processing software program (ImageJ). This gives students the ability to work with the determination of the rate law for both coumarin-102 and for sodium hydroxide, using complementary methods. This experiment is both informative and enjoyable for students, enabling them to directly observe kinetics—quite literally with open eyes—making scientific concepts more tangible and engaging. The experiment has also been adapted in a manner consistent with the principles of evidence-centered design using content of kinetics and the scientific practice of mathematical reasoning.more » « less
-
Talanquer, Vicente; Holme, Thomas A (Ed.)Fluorescence experiments hold great potential to develop and deepen student understanding of fundamental chemical concepts because the phenomenon is engaging and also illustrates many different chemical concepts and applications, including in quantum mechanics, spectroscopy, kinetics, equilibrium, and stoichiometry, through easily observable effects. Thus, many fluorescence experiments have been published for higher education. However, less attention has been given to analyzing students’ actual learning and experiences in systematic ways. In this paper, we share findings from interviews with students who completed three different fluorescence laboratory experiments in general chemistry courses at an urban public commuter university, analyzed through the lens of meaningful learning. Interview data for the affective learning dimension of meaningful learning was done with Galloway et al.’s 18-word affective matrix with addition of a new category that emerged strongly in the interviews: “enjoyed”. Interview transcripts were also analyzed for elements corresponding to the psychomotor and cognitive domains of meaningful learning. Results documented how important the affective and psychomotor domains were to students’ experiences in this setting. In addition to the three domains of meaningful learning, we also documented the particular role of the process of “visualization” to the students and examined how students connected their observations to molecular-level processes and corresponding models using Johnstone’s triangle as a framework. Our findings indicate that students primarily engaged with and appreciated the psychomotor domain and the visualization at the macroscopic level of the fluorescence experiments, which contributed to their understanding of the submicroscopic level but not at the symbolic level. By engaging students in the affective domain, the visually compelling experiments support deeper connections between macroscopic observations and submicroscopic models. We hope that this research informs future directions in designing curriculum and supports the effective integration of fluorescence experiments into general chemistry instruction.more » « less
-
Abstract Transcription is the critical first step in expressing a gene, during which an RNA polymerase (RNAP) synthesizes an RNA copy of one strand of the DNA that encodes a gene. Here we describe a laboratory experiment that uses a single assay to probe two important steps in transcription: (1) RNAP binding to DNA, and (2) the transcriptional activity of the polymerase. Students probe both these steps in a single experiment using a fluorescence‐based electrophoretic mobility shift assay (EMSA) and commercially availableEscherichia coliRNAP. As an inquiry‐driven component, students add the transcriptional inhibitor rifampicin to reactions and draw conclusions about its mechanism of inhibition by determining whether it blocks polymerase binding to DNA or transcriptional activity. Depending on the curriculum and learning goals of individual courses, this experimental module could be easily expanded to include additional experimentation that mimics a research environment more closely. After completing the experiment students understand basic principles of transcription, mechanisms of inhibition, and the use of EMSAs to probe protein/DNA interactions.more » « less
-
Previous work has highlighted the difficulties students have when explaining wave behavior. We present an investigation of chemistry students’ understanding of the double-slit experiment, where students were asked to explain a series of PhET simulations illustrating a single continuous light source, single-slit diffraction, and double-slit interference. We observed a variation in student reasoning and students were categorized into groups based on their ability to explain and generate a mechanism for the double-slit experiment. Some students struggled to explain the features of waves which impacted their reasoning about interference and caused them to rely on intuition to generate explanations. Other students were able to productively incorporate their previous knowledge about wave behavior, with their observations from the simulations, to build a robust mechanism for wave interference. However, students generally exhibited a limited understanding of interference, and specifically attending to the key features of waves during instruction can promote more sophisticated reasoning about this phenomenon.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1021/acs.jchemed.4c00493
