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A 3D-DNA Molecule Made of PlayMais

a

ab

Massimo Caine , Ninon Hori , Sandrine Zuchuat , Aurlia Weber , Verena Ducret , Patrick
a

Linder & Karl Perron

a

University of Geneva, Geneva, Switzerland

Hpitaux Universitaires de Genve, Geneva, Switzerland

Published online: 11 Jul 2015.

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To cite this article: Massimo Caine, Ninon Hori, Sandrine Zuchuat, Aurlia Weber, Verena Ducret, Patrick Linder & Karl
Perron (2015) A 3D-DNA Molecule Made of PlayMais, Science Activities: Classroom Projects and Curriculum Ideas, 52:2, 31-44,
DOI: 10.1080/00368121.2015.1029427
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Science Activities:, 52:3144, 2015

Copyright Taylor & Francis Group, LLC
ISSN: 0036-8121 print / 1940-1302 online
DOI: 10.1080/00368121.2015.1029427

A 3D-DNA Molecule Made of PlayMais

Downloaded by [Universit de Genve] at 02:27 12 July 2015

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

Address correspondence to Karl

Perron, BiOutils, Department of Plant
Biology, Microbiology Unit, University
of Geneva, 30 Quai Ernest-Ansermet,
1211 Geneva 4, Switzerland. E-mail:
karl.perron@unige.ch
Color versions of one or more of the
figures in the article can be found
online at www.tandfonline.com/vsca.

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
31

of its cellular environment: proteins. To do so, the rst

step consists in a process called transcription (Figure 2A
D). The RNA-polymerase transcribes the gene sequence
into a messenger molecule called ribonucleic acid, RNA
(Figure 2CD). Like DNA, RNA is made up of nucleotides and is synthetized using as a template the sequence of
the gene from which it is transcribed (Figure 2D). The
instructions contained within the RNA molecule are then
used for protein synthesis. This second step performed by
macromolecular machines (i.e., ribosomes) is called translation (Figure 2EI).

EDUCATION STANDARDS
This activity has been developed accordingly to the
recent Next Generation Science Standards (NGSS), module MS-LS3 Heredity: Inheritance and Variation of

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function. Moreover, within a single cell, thousands of

genes act coordinately towards a common purpose: to
support the organisms life. Therefore, it is crucial that
these instructions are transmitted from one generation to
the next when cells divide. DNA-polymerase is the cellular machinery that fullls this function (Figure 1A). It replicates the DNA molecule using each strand of the
parental molecule as a template to build a new complementary strand (Figure 1BE). In this way, the newly synthetized strand will respect the nucleotide sequence of the
one it is replacing, and two new DNA molecules will be
formed at each replication round (Figure 1F). Due to this
old/new strand double helix synthesis, the process is
called semiconservative replication. The replication process ensures that instructions are preserved and transmitted to subsequent generations. These DNA-encoded
instructions allow the cell to build the main components

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.

32

M. Caine et al.

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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).

Traits (National Research Council [NRC] 2013), since

it develops and uses a didactic model to support the
teaching of inheritance and trait variation (NRC 2013).
Furthermore, it also respects the formerly used National
Science Education Standards (NSES), grades 58, Content Standard C, with particular focus on the section
Reproduction and Heredity (NRC 1996). Importantly,
it pushes the learning process from the point of view of
individual organisms toward the cellular dimension of
living organisms (NRC 1996).

TEACHING APPROACH AND

LEARNING OBJECTIVES
In order to introduce students to the abovementioned concepts, their task will be to build a 3DDNA molecule taking advantage of a sequence of
nucleotides forming an actual gene sequence. The

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

In this context, students will be able to act as if they

were the machinery that builds the DNA molecule,
gaining an overview of the cellular processes involving
DNA molecules. Importantly, students will build a
PlayMais DNA molecule following the gene sequence
template provided and, by doing so, they will be
engaged in critical and dynamic learning of the biological functions that are embedded within the DNA structure (NRC 2013). Thus, at the end of this experience,
students should be able to

visualize and explore the double strand structure of

the DNA,

experience rsthand the mechanisms of DNA

replication,

describe the relationship between DNA and genetic

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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.
34

M. Caine et al.

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automated DNA sequencers are capable of performing

sequencing reactions as well as reading them. In modern sequencers, the four bases making up the DNA
sequence are detected using different uorescent labels
and are represented as peaks of various colors that can
then be interpreted to determine the nucleotide
sequence (Figure 5).
The original GFP gene sequence has been
completely sequenced, and it is made up of approximately 700 nucleotides. In the context of this activity,
in order to keep a reasonable timing for the teaching
module, we suggest using a portion of the GFP gene
sequence consisting of its rst 100 nucleotides
(Figure 3). To prepare this sequence, we kept the rst
thirty-ve nucleotide triplets (codons), and we
removed the remaining part of the gene. Nonetheless,
the whole GFP gene sequence can be found in the supplementary material (Figure S1 in the online supplementary material) and can be used at will to build the
whole gene molecule.
As a reference sequence for the assembly of the 3DDNA molecule (see Building Methods), the 50 30
strand of the double helix will be used:
50 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 30

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

FIGURE 5 Example of a Sanger sequencing read. The colored

peaks represent the fluorescent labels that identify the corresponding base. The base sequence is represented at the top of
the graph. The G curve should be drawn in yellow (see Materials
PlayMais Flakes), but as this color is not easily readable, it is represented here in black.

3D-DNA Molecule

(e.g., paper clips). Karounias, Papanikolau, and Psarreas

(2006), for a similar activity, used empty cans and plastic bottles. In this case, even though the nal result is a
remarkable display of the DNA molecule, we believe
that a simpler protocol will equally engage students
and will prevent risks associated with the handling of
cut aluminum cans and/or plastic bottles. Accordingly,
we found that the most suitable material consists of
PlayMais akes.
A box of PlayMais (Figure 6) contains hundreds of
small, colorful akes made from cornstarch. They are
thus recyclable and safe for the environment. Despite
its playful appearance, this medium is attractive in
many ways. It is safe for children, very easy to use (a
damp sponge is enough), light, malleable, and easy to
obtain. Since it does not take long to build a DNA
molecule with this model, you will have time to
explain more precisely the underlying concept before
the students begin the construction. Each ake color
represents a given component of the DNA molecule
(Figure 6BD) as summed up in Table 1.

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.
35

FIGURE 6 (A) A box of PlayMais flakes. This may be ordered from the official website www.playmais.com or bought in standard super-

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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).

In both cases, before starting the lesson, you may ask

students what they know about the architecture of
DNA molecules, nucleotide base pairing, which is the
functional role of double strand (i.e., semiconservative
replication) and how somatic traits are passed from one
generation to another (e.g., you may refer to eye colors,
height, or other body traits). This will allow you to
engage students with biological/functional questions
that will be assessed once the activity is completed (see
also Appendixes AC).

Advanced Building Method

Considering the Biological Process
(1 Hr Protocol)
Construction of the PlayMais Nucleotides
(30 Min)
The purpose of this step is to prepare the main units
of the DNA molecule, namely the nucleotides
(Figure 7AC).

Take a white ake (deoxyribose), a gray ake (phos-

phate group), and a colored ake (nucleobase)

(Figure 8A).

Using a damp sponge, wet one end of a gray ake

(Figure 8B).

Stick the wet end of the gray ake onto one end of a

white ake by gently pushing them together. Keep

them in position with your hands for approximately
30 s (Figure 8CD).

Once the gray and white akes are stuck together,
take the colored ake (i.e., orange, yellow, blue, or
green) and wet one of the ends with the damp
sponge. Stick the wet end of the colored ake onto
the side of the white ake (Figure 8EF).

Repeat these steps until all the DNA units that you
will need, according to the reference sequence (see
The Gene Sequence), have been prepared. Note:
The reference sequence provides information about
only one of the two strands. In order to build both
strands, it will be necessary to assemble the nucleotides of the reference sequence plus their complementary nucleotides (i.e., for each guanine nucleotide
that you assemble, also assemble a cytosine nucleotide and vice versa. For each adenine nucleotide that
you assemble, also assemble a thymine nucleotide
and vice versa) (Figure 8G).

Building the First DNA Strand (15 Min)

First, one of the two DNA strands will be prepared. In this case, the rst DNA strand to be built

TABLE 1 Flake Color Code

PlayMais flakes color
Adenine base
Cytosine base
Guanine base
Thymine base
Deoxyribose
Phosphate group

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.

36

TABLE 2 Flake Combinations

PlayMais flake combination
Adenine
Cytosine
Guanine
Thymine

Green C White C Gray

Blue C White C Gray
Yellow C White C Gray
Orange C White C Gray

Note: Here are represented the different flake combinations

needed to build the PlayMais nucleotides.

M. Caine et al.

FIGURE 7 PlayMais nucleotides. (A) Chemical structure of a nucleotide. (B) PlayMais DNA units consisting of a phosphate (gray flake),

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a deoxyribose (white flake), and a base (colored flake). (C) PlayMais nucleotides.

will be the one reported on the reference sequence.

It is better not to make excessively long strands
because you will need to twist the double helix
while adding the second strand. Shorter strands
(e.g., 10 nucleotides) make this process easier. Eventually, the DNA double helix fragments shall be
joined in a single larger molecule.

Take the rst and the second nucleotides according

to the reference sequence (Figure 9A).

Wet the end of the gray ake of the second nucleo-

tide and stick it onto the white ake of the rst

nucleotide (Figure 9B).
Note: In order to facilitate the rotation of the
DNA double helix, when you add a nucleotide,
this should be slightly rotated compared to the
previous one (clockwise rotation) (Figure 9C). The
standard conformation of the DNA double helix
takes 10 nucleotide-pairs for one complete turn
around its axis. In order to achieve this, stick the

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

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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.

nucleotides of the rst strand with its base rotated

45 compared to the base of the previous nucleotide (Figure 9C). In principle, 36 should be
enough (360 /10 nucleotides), but the elastic torsion of the double helix, when completed, will
tend to reduce this angle. Therefore, we recommend a rotation of 45 between each nucleotide.

Continue as described in the rst steps for the remaining nucleotides of the sequence (Figure 9DE).

Building the Complementary Strand like

a DNA Polymerase (15 Min)
During this step, students will act as if they were a
DNA polymerase synthetizing the complementary
strand. Using the remaining units, students will add
them one by one to the previously built rst strand. To
do so, students will have to respect the law of base-pairing (Figure 10A).

The building of the new strand starts from the last

nucleotide of the old strand (i.e., the last one that

has been added). In this way, the synthesis direction of the DNA polymerase will be respected.
Moreover, as described in the introduction, the two
strands comprising the double helix possess an antiparallel orientation. To respect such a design, the
strands backbone will start with a gray ake and end
38

with a white ake (as done with the old strand)

(Figure 9D).
Choose a nucleotide that is complementary to the
one of the old strand where it will be stuck. Wet the
free surface of its colored akes and stick it onto the
colored ake of the corresponding nucleotide
(Figure 10B).
Take the second nucleotide that you want to add and
wet both its colored ake and its gray ake. First,
stick the gray ake onto the white ake of the previous nucleotide, maintaining a right-handed angle of
45 between the two nucleobases (Figure 10C). Second, stick the two colored akes of the complementary nucleotides (old and new strand) together
(Figure 10D). Perform this second step gently, since
the elasticity of the torsion will start pulling the two
strands apart.
Continue adding nucleotides until the double helix
is completed (Figure 10E). While adding the
nucleotides, remember to respect the right-handed
rotation (i.e., circa 45 ) of the newly added
nucleotides.
Finally, if the gene has been built in distinct fragments, eventually these fragments shall be joined
together according to the reference sequence
(Figure 10FG). To do so, wet the gray akes of each
fragment and stick them onto the corresponding
white akes from the other fragment (Figure 10F).
M. Caine et al.

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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

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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.

Simple Method (40 Min Protocol)

Construction of the Phosphate-Sugar
Backbones (10 Min)

and gently pushing them together as explained

above. Note: each backbone chain should display a
gray ake at its beginning and a white ake at its
end (Figure 11BE).

The purpose of this rst part is to assemble the

two side chains of the double helix made up of
white akes (sugar molecules) and gray akes (phosphate groups) (Figure 11A). As suggested previously,
shorter chains (i.e., 10 nucleotides) will facilitate the
torsion of the double helix.

The purpose of this second part is to prepare the different base-paired akes that will be added to the phosphate-sugar backbones.

Prepare the two backbone chains (sequence of white

First, prepare the different base-pairs that you will

and gray akes) of approximately 20 akes each (i.e.,

10 gray akes and 10 white akes). To do this, stick
alternating gray and white akes, wetting their ends

need (i.e., stick green akes, adenine, with orange

akes, thymine, and then stick blue akes, cytosine,
with yellow akes, guanine) (Figure 12A).

Base-Pairing (20 Min)

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.
40

M. Caine et al.


Stick the base-pairs to the white akes of one of the

two backbones such that they form a spiral around

the chain (Figure 12B). Since this simplied protocol focuses on understanding the structural design of
the DNA molecule rather than its biological implications, here it is not necessary to follow the sequence
of the reference gene.

As explained in the previous method, in order to
respect the standard 3D-DNA architecture, there
should be an angle of circa 45 between each base
pair.

Assembly of the Whole DNA Structure

(10 Min)

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The last step is to assemble the second side chain to

the structure that has just been built.

Take the second backbone and twist it around the

other one so that it follows the double helix model

(Figure 12C). Start from the white ake of the
second chain and stick it onto the last base-pair of
the complementary strand (Figure 12EF). To stick
the phosphate-sugar chain to the base-pairs, wet the
free end of the base-pairs one after the other while
sticking them to the backbone.
Note: when you stick the base-pair onto the backbone, it should form an angle of approximately 45
compared to the previous base-pair (clockwise rotation) (Figure 12EF). To do this, slightly rotate the
backbone with your ngers while sticking it onto the
base-pair.

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

while manipulating the 3D-PlayMais DNA molecule

in a fun and engaging context, students are likely to
better remember and assimilate the concepts that will
be useful for the understanding of the biological mechanisms involving DNA (e.g., replication, transcription,
and translation).

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 Hori
e 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
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acid. Nature 171: 73738.

41

APPENDIX A:
INSTRUCTION SHEET (FOR TEACHERS)
Introduction

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In the context of this teaching module, you will

have the opportunity to set up a lesson aimed to trigger
and develop a deeper involvement of students concerning the DNA molecule architecture and its biological
function. In order to introduce this activity, before giving a preliminary explanation of the DNA molecule,
you may address your students with the following
questions:

What is the architecture of a DNA molecule?

What do we mean by nucleotide base-pairing?

What is the role of the double strand in DNA
replication?

Some somatic traits (e.g., eye color) are passed
from one generation to the next. How is this
information stored within the cells?

What are DNA mutations and what are their
implications?
Once you have their attention on these fundamental
aspects, you can provide a general explanation of the
chemical and physical aspects of the DNA molecule.
Note that the two building methods range from 45 min
to 1 hr. Therefore, this initial part should be adapted to
t the time available to your teaching module.
Then, according to the level/age of your students,
you may choose the building method that you believe
most appropriate.

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:

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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

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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?

44

M. Caine et al.