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Visualizing the Invisible: A Guide to Designing, Printing, and Incorporating Dynamic 3D Molecular Models to Teach Structure–Function Relationships

    Authors: Michelle E. Howell1,2, Karin van Dijk1, Christine S. Booth1, Tomáš Helikar1, Brian A. Couch2,*, Rebecca L. Roston1,*
    VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Department of Biochemistry, University of Nebraska, Lincoln, NE 68588-0664; 2: School of Biological Sciences, University of Nebraska, Lincoln, NE 68588-0118
    AUTHOR AND ARTICLE INFORMATION AUTHOR AND ARTICLE INFORMATION
    • Received 24 July 2018 Accepted 13 September 2018 Published 31 October 2018
    • ©2018 Author(s). Published by the American Society for Microbiology.
    • [open-access] This is an Open Access article distributed under the terms of the Creative Commons Attribution-Noncommercial-NoDerivatives 4.0 International license (https://creativecommons.org/licenses/by-nc-nd/4.0/ and https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode), which grants the public the nonexclusive right to copy, distribute, or display the published work.

    • Supplemental materials available at http://asmscience.org/jmbe
    • *Corresponding authors. Dr. Brian A. Couch. Mailing address: School of Biological Sciences, University of Nebraska, 204 Manter Hall, Lincoln, NE 68588-0118. Phone: 402-472-8130. E-mail: [email protected]. Dr. Rebecca L. Roston. Mailing address: Department of Biochemistry, University of Nebraska, N123 Beadle Center, Lincoln, NE 68588-0664. Phone: 402-472-2936. E-mail: [email protected].
    Source: J. Microbiol. Biol. Educ. October 2018 vol. 19 no. 3 doi:10.1128/jmbe.v19i3.1663
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    Abstract:

    3D printing represents an emerging technology with significant potential to advance life-science education by allowing students to directly explore the relationship between macromolecular structure and function. In this article and supplemental video guide, we describe our development of a model-based instructional module on DNA supercoiling and outline practical tips for implementing models in undergraduate classrooms. We also present a procedure to design and print 3D dynamic models for classroom use. Furthermore, we describe repositories of 3D biomolecule files to make using models accessible and cost-effective.

References & Citations

1. American Association for the Advancement of Science 2011 Vision and change in undergraduate biology education: a call to action: a summary of recommendations made at a national conference organized by the American Association for the Advancement of Science July 15–17, 2009 Washington, DC
2. ASBMB 2008 Biochemistry/molecular biology and liberal education: a report to the Teagle Foundation 95 The American Society for Biochemistry and Molecular Biology Washington, DC
3. Tansey JT, Baird T Jr, Cox MM, Fox KM, Knight J, Sears D, Bell E 2013 Foundational concepts and underlying theories for majors in “biochemistry and molecular biology” Biochem Mol Biol Educ 41 289 296 24019234
4. Roberts JR, Hagedorn E, Dillenburg P, Patrick M, Herman T 2005 Physical models enhance molecular three-dimensional literacy in an introductory biochemistry course Biochem Mol Biol Educ 33 105 110 10.1002/bmb.2005.494033022426 21638554 http://dx.doi.org/10.1002/bmb.2005.494033022426
5. Jittivadhna K, Ruenwongsa P, Panijpan B 2010 Beyond textbook illustrations: hand-held models of ordered DNA and protein structures as 3D supplements to enhance student learning of helical biopolymers Biochem Mol Biol Educ 38 359 364 10.1002/bmb.20427 http://dx.doi.org/10.1002/bmb.20427
6. Canning DR, Cox JR 2001 Teaching the structural nature of biological molecules: molecular visualization in the classroom and in the hands of students Chem Educ Res Pract Eur 2 109 122 10.1039/B1RP90013G http://dx.doi.org/10.1039/B1RP90013G
7. Gilbert JK 2004 Models and modelling: routes to more authentic science education Int J Sci Math Educ 2 115 130 10.1007/s10763-004-3186-4 http://dx.doi.org/10.1007/s10763-004-3186-4
8. Gross BC, Erkal JL, Lockwood SY, Chen C, Spence DM 2014 Evaluation of 3D printing and its potential impact on biotechnology and the chemical sciences Analyt Chem 86 3240 3253 10.1021/ac403397r http://dx.doi.org/10.1021/ac403397r
9. Chia HN, Wu BM 2015 Recent advances in 3D printing of biomaterials J Biol Eng 9 4 10.1186/s13036-015-0001-4 25866560 4392469 http://dx.doi.org/10.1186/s13036-015-0001-4
10. Azimi P, Zhao D, Pouzet C, Crain NE, Stephens B 2016 Emissions of ultrafine particles and volatile organic compounds from commercially available desktop three-dimensional printers with multiple filaments Environ Sci Technol 50 1260 1268 10.1021/acs.est.5b04983 26741485 http://dx.doi.org/10.1021/acs.est.5b04983
11. Mayer RE 2001 Multimedia learning 2nd ed Cambridge University Press Cambridge, MA 10.1017/CBO9781139164603 http://dx.doi.org/10.1017/CBO9781139164603

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2018-10-31
2019-08-22

Abstract:

3D printing represents an emerging technology with significant potential to advance life-science education by allowing students to directly explore the relationship between macromolecular structure and function. In this article and supplemental video guide, we describe our development of a model-based instructional module on DNA supercoiling and outline practical tips for implementing models in undergraduate classrooms. We also present a procedure to design and print 3D dynamic models for classroom use. Furthermore, we describe repositories of 3D biomolecule files to make using models accessible and cost-effective.

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Figures

Image of FIGURE 1

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FIGURE 1

A selection of 3D models with interactive features. A) The λ transcription factor has interchangeable amino acids that allow investigation of point mutations on DNA binding. B) A DNA helix with LEGO-style replaceable base pairs allows investigation of DNA mutations. Models in A and B can be used together to allow investigation of compensatory mutations. Multicolored, detailed models of a DNA helix (C) or protein α-helix and water molecule (D) allow investigation of chemical details, for example, the size of the major and minor grooves or the diameter of the inside of a helix. Flexible models of Phe-tRNA (E), single-stranded RNA and DNA (F), and a long DNA duplex with magnetic ends (G) allow students to engage with the molecular dynamics, investigating folding of complex structures and demonstrating chemical attack, base stacking, or DNA supercoiling.

Source: J. Microbiol. Biol. Educ. October 2018 vol. 19 no. 3 doi:10.1128/jmbe.v19i3.1663
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Image of FIGURE 2

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FIGURE 2

Investigating DNA supercoiling. In step 1, students wrapped the DNA model (white) around a nucleosome model (blue) and characterized the resulting supercoil. In steps 2–4, students mimicked Topoisomerase II by cleaving the DNA and passing the intact strand of DNA through the cleaved site before re-adhering the ends. In step 5, students characterized the resulting supercoil and evaluated Topoisomerase II activity.

Source: J. Microbiol. Biol. Educ. October 2018 vol. 19 no. 3 doi:10.1128/jmbe.v19i3.1663
Download as Powerpoint
Image of FIGURE 3

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FIGURE 3

Course integration of 3D instructional models. Integration tips are outlined for in-class activities (blue sequence), in-class demonstrations (teal sequence), and out-of-class homework (green sequence). 1 Based on cognitive theory of multimedia learning ( 11 ), instructors are recommended to include 2D and 3D models in addition to lecture. 2 For small classes, a one-on-one interaction with the instructor is preferred; for large classes or homework assignments, an adaptive response-guided activity can be substituted. 3 Formative assessments can provide instant feedback if they include in-class questions. UG = undergraduate; HS = high school.

Source: J. Microbiol. Biol. Educ. October 2018 vol. 19 no. 3 doi:10.1128/jmbe.v19i3.1663
Download as Powerpoint

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