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ab
Massimo Caine , Ninon Hori , Sandrine Zuchuat , Aurlia Weber , Verena Ducret , Patrick
a
Massimo Caine
University of Geneva, Geneva,
Switzerland
Ninon Horie
University of Geneva and
^pitaux Universitaires de
Ho
Gen
eve, Geneva, Switzerland
lia
Sandrine Zuchuat, Aure
Weber, Verena Ducret, Patrick
Linder, and Karl Perron
University of Geneva, Geneva,
Switzerland
ABSTRACT More than 60 years have passed since the work of Rosalind
Franklin, James Watson, and Francis Crick led to the discovery of the 3D-DNA
double-helix structure. Nowadays, due to the simple and elegant architecture of
its double helix, the structure of DNA is widely known. The biological role of
the DNA molecule (e.g., genetic information), however, along with the cellular
mechanisms involving the DNA double helix (e.g., DNA replication) are topics
that have not yet reached a broader public. In this educational article, we aim
to provide a way for schoolchildren to live a three-dimensional experience that
focuses on the DNA double helix structure. Moreover, taking advantage of an
engaging and visual protocol, students will experience an overview of its
biological implications. To do so, starting from a gene sequence, students will
have the opportunity to build their own 3D-DNA double helix structure using
PlayMais akes.
KEYWORDS arts (visual and performing), DNA double helix, DNA replication, genetic
traits, modeling
DNA is the biological medium that carries the genetic information in all living organisms. It can be seen as a very long right-handed spiral ladder made up
of two biopolymers (complementary DNA strands) that together form a double
helix structure. The chemical structure of the two complementary strands displays opposite direction such that they are antiparallel to each other. As a result,
at one end of the DNA molecule, one strand will expose a chemical structure
(i.e., a phosphate group), whereas the other strand will notvice versa for the
other end of the DNA molecule. Each DNA strand consists of repeating fundamental units called nucleotides. Nucleotides are composed of a phosphate
group, a deoxyribose (monosaccharide sugar), and a nucleobase (simply called
base). Sugars and phosphates form the backbone of each strand, whereas four
different basesadenine (A), guanine (G), cytosine (C), and thymine (T)hold
the two DNA strands together. To do so, each base specically forms hydrogen
bonds with a base from the other strand. In detail, an adenine will always pair
with a thymine, whereas a guanine will always pair with a cytosine. This complementarity is essential for the double helix arrangement of the DNA molecule in
space and is the basis of faithful DNA replication prior to cell division (Watson
and Crick 1953).
The order of nucleotides comprising a DNA sequence is not random. Specic
sequences of nucleotides, called genes, encode fundamental information for cell
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EDUCATION STANDARDS
This activity has been developed accordingly to the
recent Next Generation Science Standards (NGSS), module MS-LS3 Heredity: Inheritance and Variation of
FIGURE 1 DNA replication. (AF) A schematic representation of the DNA replication process. Phosphate-sugar backbones are represented as gray strands. Nucleotides are depicted using the following color code: adenine-green, thymine-orange, guanine-yellow, cytosine-blue. (BC) The first of the two parental strands comprising the original DNA double helix is used as a template to synthetize the
complementary strand. (DE) The second parental strand is then used to synthetize a second complementary strand. (F) At the end of the
process, two identical DNA double helix molecules are produced.
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M. Caine et al.
FIGURE 2 Transcription and translation. (AD) The RNA-polymerase locates the gene within the DNA double helix and transcribes the
sequence into a messenger RNA molecule (orange strand). (EI) The ribosome translates the information contained within the RNA molecule into the corresponding protein (hexagonal sequence strand).
sequence that has been taken as an instructive example is that of the green uorescent protein (GFP)
gene. This gene bears the instructions necessary for
the synthesis of a protein that allows the jellysh
Aequorea victoria to glow in the dark waters of the
sea (Shinomura, Johnson, and Saiga 1962). Furthermore, the GFP protein is commonly used in several
laboratory protocols due to the fact that its uorescence can be observed in cells where it is expressed
(Chale et al. 1994). Thus, for you it will be possible to combine an explanation of DNA structure
(i.e., 3D-DNA molecule) with the sequence and the
biological instructions embedded in it (i.e., GFP
gene and protein uorescence). Moreover, taking
advantage of the coding frame of the GFP gene
sequence provided (Figure 3, Figure S1 in the online
supplementary material), this experience can also be
used to introduce the concepts of transcription and
translation (Concannon and Buzzetta 2010).
FIGURE 3 Using the freeware SnapGene viewer, the initial portion of the GFP sequence is reported here. This software can be freely
downloaded and used by teachers to analyze the GFP sequence. To do this, all the instructions needed are reported in the supplementary
material.
3D-DNA Molecule
33
the DNA,
experience rsthand the mechanisms of DNA
replication,
describe the relationship between DNA and genetic
traits, and
apply the learned concepts to further experiences.
EXTENSIONS
Once the building activity has been completed,
students will have the chance to apply the learned
structural concepts to two crucial biological aspects of
the DNA molecule, i.e., semiconservative DNA replication and DNA mutations. Depending on the time
available, such extensions may be proposed either as
side activities or as a part of the same teaching module.
This will allow you to push further the engagement of
students on a deeper critical thinking about the relationship between structure and biological function of
the DNA molecule.
1. Semiconservative replication of the DNA molecule: For this exercise you will need to prepare in
advance a 3DPlayMais DNA molecule of 10- to
20-nucleotides length. The GFP gene sequence can
still be used as a reference. Then, the idea is to provide half of the class with one of the two strands
and the other half with the other strand (these
strands shall also be prepared by you and will be
the exact copy of the two strands comprising the
already prepared DNA molecule). It will be important to stress with students that the two strands
provided show different sequences of nucleotides.
The task of the students will be to build the complementary strand to the one they received, according to the law of base pairing. Once their job is
done, they will be able to appreciate that, even
though the class received two different strands with
two different sequences, at the end of the exercise
all the students will have in their hands the very
same 3D-DNA double helix molecule.
2. DNA mutation: (This exercise requires a prior
explanation of the genetic code. Students will need
to master the concept of sense and anti-sense strands
and how triplets of nucleotides (codons) determine
the beginning and the end of protein synthesis).
Using the GFP gene sequence as a reference, you
will build a 3DPlayMais DNA molecule of approximately 20 nucleotides. Doing so, you will introduce a single nucleotide exchange. Precisely, it will
be necessary to substitute the third adenine of the
reference sequence (the rst strand that is built
according to the method described) with a thymine
(i.e., an orange ake instead of a green ake). This
modication will introduce an early STOP-codon
instead of the original amino acid (lysine), rendering
the synthesis of the GFP protein impossible
(Figure 4). The students exercise will be to spot the
mistake within the sequence and explain the consequences related to this nucleotide exchange (i.e., the
jellysh will not be able to glow anymore). From
here you will have the chance to discuss and explain
the concept of DNA mutation and its implications.
MATERIALS
The Gene Sequence
Nowadays, DNA sequencing (Maxam and Gilbert
1977; Sanger, Nicklen, and Coulson 1977) is a widely
used technique to determine the exact sequence of
nucleotides from a specic DNA sample. Furthermore,
FIGURE 4 This sequence represents the result of the introduction of a single nucleotide mutation. An early STOP-codon (red asterisk)
results in an interruption of the amino acid sequence and therefore in aborted protein synthesis.
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M. Caine et al.
PlayMais Flakes
We have been looking for various media enabling us
to build a long DNA molecule with children or students. Soon after the discovery of the DNA structure,
Exline (1969) proposed a do-it-yourself protocol to
build a DNA molecule using common ofce material
3D-DNA Molecule
METHODS
We hereby present two methods for assembling the
DNA molecule. The time necessary for each protocol/
step is reported at the beginning of each section. The
rst method (suited for 11- to 13-year-old students) will
allow the students to experience rsthand the polymerization process of DNA, acting as the machinery that
performs this function within the cells. In this case,
you will provide students with the GFP reference
sequence that will be used to build their own 3D-DNA
molecule (Figure 3). This can be done by a single group
of children or, alternatively, by multiple small groups.
In the latter case, different parts of the gene should be
assigned to the different groups such that the PlayMaismolecule fragments can eventually be joined together
in a single DNA molecule. To do so, either the initial
portion of the GFP gene (Figure 3) or its whole
sequence (Figure S1 in the online supplementary material) can be used, according to the number of students
participating to the activity and to the time available.
The second method proposed is a simplied version of
the rst one, and it is mostly suitable for a class of
younger students (i.e., age 910). It allows the visualization of the DNA structure rather than the biological
process of its synthesis.
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FIGURE 6 (A) A box of PlayMais flakes. This may be ordered from the official website www.playmais.com or bought in standard super-
markets as the brand is widely distributed in many countries. The box contains (B) the flakes representing the nucleobases (orange, blue,
green, and yellow), (C) the deoxyriboses (white), and (D) the phosphate groups (gray).
(Figure 8B).
Stick the wet end of the gray ake onto one end of a
Green
Blue
Yellow
Orange
White
Gray
Notes: The green, blue, yellow, and orange flakes represent the
four different bases comprising the four nucleotides. White flakes
represent the monosaccharide sugar (deoxyribose), and the gray
flakes represent the phosphate group.
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M. Caine et al.
FIGURE 7 PlayMais nucleotides. (A) Chemical structure of a nucleotide. (B) PlayMais DNA units consisting of a phosphate (gray flake),
a deoxyribose (white flake), and a base (colored flake). (C) PlayMais nucleotides.
FIGURE 8 Assembly of a PlayMais nucleotide. (A) White, gray, and colored flakes will be used. (BD) The gray flake is wet at one of its
ends and stuck onto one end of a white flake. (EF) To complete the nucleotide, a colored flake is wet and stuck onto the white flake. (G)
All the nucleotides needed are prepared before starting strand assembly.
3D-DNA Molecule
37
FIGURE 9 Assembly of the first PlayMais strand. (A) Two PlayMais nucleotides are selected according to the reference sequence.
(BC) The gray flake of one of the two PlayMais nucleotides is wet and stuck onto the white flake of the second one, respecting the nucleobase rotation of 45 around the backbone chain. (DE) First strand overview.
FIGURE 10 Building of the second strand. (AB) The first PlayMais nucleotide added is complementary to the PlayMais nucleotide of
the old strand. (CD) The second PlayMais nucleotide is added to the first one respecting the 45 right-handed rotation. (EG) Once the
double helix fragments are completed, they can be joined into a single DNA molecule.
FIGURE 11 Construction of the phosphate-sugar backbones. (A) A damp sponge and the white/gray flakes for the side chains are
required for the first step of the construction. (B) One end of a gray flake is gently pressed onto a damp sponge. (CD) The wet end of the
gray flake is stuck onto the end of a white flake. (E) This step is repeated until the two side chains have been obtained (composed of
approximately 20 flakes each).
3D-DNA Molecule
39
FIGURE 12 Base-pairing and assembly of the whole DNA structure. (A) Colored flakes to assemble the base-pairs (B) Base-pairing of
an A with a T on one hand and of a C with a G on the other hand. (CD) Addition of the base pairs as a spiral to the deoxyriboses of a side
chain. (EF) Assembly of the second side chain to the rest of the structure.
The purpose of this second part is to prepare the different base-paired akes that will be added to the phosphate-sugar backbones.
FIGURE 13 Interaction with students. (A) Students are actively engaged in the construction of the DNA molecule under the teachers
supervision. (B) Example of a 30-m long DNA molecule built by 9- to 13-year-old students.
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M. Caine et al.
CONCLUSIONS
The activity that we propose represents an easy way
to illustrate a lesson describing the support of life. It is
safe for students and engages their attention through a
simple and visual protocol (Figure 13AB). By using
this simple approach, it will be possible for you to
address fundamental questions such as (a) What are the
basic components of DNA? (b) What are the structures
that make the double helix possible? and (c) How does
the DNA synthesis take place? Moreover, the two
building methods allow a broad range of applications
through different age levels. Thus, you will be able to
decide which protocol to choose according to the age
of your students, maximizing their engagement and
optimizing their learning process. As a matter of fact,
3D-DNA Molecule
ACKNOWLEDGMENTS
The authors would like to thank all the members of
K. P. lab for precious discussions and suggestions. M.
C. wishes also to thank Ms. A. Caine for her valuable
comments and for her kind patience. Massimo Caine
and Ninon Horie contributed equally to this work.
FUNDING
This work has been supported by the Section of
Biology, Faculty of Science of the University of
Geneva, by the H. D. Wright Foundation, and by a private foundation based in Geneva, Switzerland.
SUPPLEMENTARY MATERIAL
Supplementary material for this article can
be accessed on the
publishers website at
http://dx.doi.org/10.1080/00368121.2015.1029427
REFERENCES
Concannon, J., and M. Buzzetta. 2010. Students conceptualizing transcription and translation from a cellular perspective. Science Activities 47(3): 8388.
Chalfie, M., Y. Tu, G. Euskirchen, W. W. Ward, and D. C. Prasher. 1994.
Green fluorescent protein as a marker for gene expression. Science
263: 80205.
Exline, J. D. 1969. A do-it-yourself model of the DNA molecule. Science
Activities 2(2): 2830.
Karounias D., E. Papanikolau, and A. Psarreas. 2006. Modelling the DNA
double helix using recycled materials. Science in School 2: 2428.
Maxam, A. M., and W. Gilbert. 1977. A new method for sequencing
DNA. Proceedings of the National Academy of Sciences of the
United States of America 74(2): 56064.
National Research Council. 1996. National science education standards.
Washington, DC: National Academy Press.
National Research Council. 2013. The next generation science standards.
Washington, DC: National Academy Press.
Sanger, F., S. S. Nicklen, and A. R. Coulson. 1977. DNA sequencing with
chain-terminating inhibitors. Proceedings of the National Academy
of Sciences of the United States of America 74(12): 546367.
Shinomura, O., F. H. Johnson, and Y. Saiga. 1962. Extraction, purification
and properties of aequorin, a bioluminescent protein from the
luminous hydromedusan Aequorea. Journal of Cellular and Comparative Physiology 59: 22339.
Watson, J. D., and F. H. C. Crick. 1953. Molecular structure of nucleic
acid. Nature 171: 73738.
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APPENDIX A:
INSTRUCTION SHEET (FOR TEACHERS)
Introduction
Building Method 1
This building method is suited for a class of 11- to 13year-old students. Their task will be to build a 3D-PlayMais DNA molecule using as a template the gene
sequence that codes for the GFP protein. Before starting
the building process, you should introduce students to
the concept of genes and specically to the biological
properties of the GFP protein (i.e., bioluminescence in
the jellysh Aequorea victoria). The 100-nucleotide
sequence that is proposed (Figure 3) is suited to a class of
2030 students. Ideally, you may divide them into 10
groups of 23 students so that each group can prepare a
fragment of 10 nucleotides. Together with the building
instructions, you shall provide students with the gures
reported in the article (Figures 810). This will help them
42
through the building process. The 10-nucleotide fragments will then be assembled together to form a longer
3DPlayMais DNA molecule of 100 nucleotides in size.
This approach will promote cooperative learning between
students, not only within individual groups but also
among the entire classroom. Such a method can be
extended to a sequence with a nal length adapted to
your needs. To do this, you may take advantage of the
full-length GFP sequence provided in the online supplementary material (Figure S1 in the online supplementary
material). Once the building activity has been completed,
in line with the timing of your teaching module, you may
propose them the extensions of this activity (i.e., semiconservative DNA replication and DNA mutations). This
will allow you to further engage them with the biological
functions related to the DNA structure in their hands.
Materials
Worksheet 1
PlayMais akes
Damp sponges
Extensions material (see methods)
Building Method 2
This second method allows you to set up a teaching module for younger students, i.e., 9 to 10 years
old. The purpose of this simplied building method
is to introduce the students to the three-dimensional
structure of DNA rather than its biological functions
(that may nonetheless be introduced later in the students training with Building Method 1). As was suggested for the previous method, you may divide
students in groups and assign to each of them the task
of building of a 10-nucleotide 3D-PlayMais DNA
molecule. Also in this case you shall provide students
with the gures reported in the article (Figure 1113)
so that they can use them as a reference. Once this
assignment is completed, the different fragments can
be joined into a single molecule to promote cooperative learning throughout the classroom.
Materials
Worksheet 2
PlayMais akes
Damp sponges
M. Caine et al.
APPENDIX B: WORKSHEET 1
Group name__________________ Date___________
Objectives
Using PlayMais akes as biological tools you will be able to build a 3D-PlayMais DNA molecule as if you were
the molecular machinery performing this function inside the cells.
Material
Building instructions
Sequence template:
ATG AGT AAA GGA GAA GAA CTT TTC ACT GGA GTT GTC CCA ATT CTT GTT GAA TTA GAT
GGT GAT GTT AAT GGG CAC AAA TTT TCT GTC AGT GGA GAG GGT GAA GGT
PlayMais akes
A damp sponge
Activity assessment
Q1:Which is the essential unit comprising DNA molecules?
Q2:What are nucleotides composed of?
Q3:How many nucleotides do you know?
Q4:What is the base-pairing law?
Q5:How many nucleotide-pairs does it take for a DNA molecule to complete a 360 turn around its axis?
Q6:The double-strand architecture of the DNA molecule allows a very precise and important mechanism.
Which one?
Q7:Base-pairing law is essential for the semiconservative replication of DNA. Could you explain how?
Q8:The sequence that you used as a template bears some specic information embedded in it. If you were to
forget a single base pair while building your DNA molecule, do you think this information would have been
present anyway? Explain why.
3D-DNA Molecule
43
APPENDIX C: WORKSHEET 2
Group name__________________ Date___________
Objectives
Starting from simple PlayMais akes you will build a 3D-DNA molecule. By doing this you will be able
to appreciate the architecture of the most important molecule for living beings: DNA.
Material
Building instructions
PlayMais akes
A damp sponge
Activity Assessment
Q1:What do the different ake colors represent?
Q2:Is it possible to pair a green ake with a blue ake? And a green ake with a yellow ake?
Q3:How many nucleotide base pairs can you count before that the double strand makes a 360 turn around its
axis?
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