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dna double helix model

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					                                                         Modelling
                                                       the DNA
                                                     double helix
                                                     using recycled
                                                       materials
                                                                      Dionisios Karounias,
                                                                       Evanthia Papanikolaou and
                                                                        Athanasios Psarreas, from
                                                                        Greece, describe their
                                                                        innovative model of the
                                                                        DNA double helix – using
                                                                        empty bottles and cans!


                                                                                      Molecular structure of DNA
                                                                    T     his proj-
                                                                          ect to
                                                               construct a 3D
                                                                                        The basic unit of DNA is the
                                                                                      nucleotide, consisting of a phosphate
                                                                                      group, a sugar molecule (deoxyribose)
                                                            model of a DNA            and one of four nucleobases (also
                                                          molecule, using every-      known as bases): adenine (A), thymine
                                                       day materials, stimulated      (T), guanine (G) or cytosine (C). The
                                                   the students’ interest, encour-    DNA molecule consists of successive
                                               aged teamwork, dexterity and the       nucleotides arranged in a double helix
                                         investigation of the properties of mate-     – a spiral ladder – the sides of which
                                         rials, and allowed the students to           are formed from sugar and phosphate
                                         express their own opinions and solve         groups, with each step consisting of a
                                         problems. More specifically, students        pair of bases. The base pairs are formed
                                         learned the basic structural elements of     from complementary nucleotides: ade-
                                         DNA and their 3D molecular organisa-         nine pairs with thymine, while guanine
                                         tion.                                        pairs with cytosine.



24   Science in School Issue 2 : Summer 2006                                                            www.scienceinschool.org
                                                                                                         Teaching activities




                                Phosphate      O
                                group        O P =O
                                               O
                                                  5’
                                               CH2                Base
                                                         O
                                               C4’ H             H C
                                                                   1’
                                                    3’       2
                                               H C               C H
                                                   OH            H    Deoxyribose                   5’

                              A nucleotide
                                                                                                                                            1’




                                                                                                                       3’

The model                                     Additional materials                             Deoxyribose
  Each of the three constituents of the       ·        6 m thin rope                             Deoxyribose is modelled with a
nucleotide were represented with 3D           ·        20 plastic drinking straws              Sprite can with three red bottle caps
objects (see Table 1) which were con-         ·        20 nuts and thin double-threaded        attached, representing the carbon
nected to form a double helix with ten                 bolts                                   atoms at the 1’, 3’ and 5’ positions
steps (base pairs). See below.                ·        4 sheets of coloured confectionery      (above right). An orange bottle cap at
                                                       cellophane (blue, green, red and        position 3’ represents the hydroxide
Table 1: DNA molecular components                      yellow).                                that will be connected to the next
and the corresponding model materials                                                          nucleotide.
                                              Tools                                            1. Puncture the can in positions 1’, 3’
                                              ·        Scalpel or sharp knife for cutting         and 5’, as shown above .
    DNA molecule          Model                        the plastic bottles                     2. Puncture four bottle caps (three
                                              ·        Thick nail for the making holes in
                                                       plastic and aluminium
                                                                                                  red and one orange) in the centre.
                                                                                               3. Using a nut and bolt, attach a red
    Phosphate group       Coca Cola® can
                                              ·        Small pliers                               cap firmly in position 1’ so that a
                                              ·        Stapler                                    bottle can be screwed on.
    Deoxyribose           Sprite® can         ·        Two pieces of thin telephone cable,     4. Firmly attach two caps, one red and
    molecule                                           about 40 cm long, for passing the          one orange, to one end of a straw
                                                       rope through the straws.                   (first the red, then the orange).
                                                                                               5. Pass the straw through the can,
    Base                  Plastic bottle
                                              Method                                              using holes 3’ and 5’.
                                                First, each of the three nucleotide            6. Fix the can to the straw, threading
                                              constituents (deoxyribose, phosphate                another red cap to the side of the
Materials                                     and base) are modelled, reflecting the              can in position 5’. The final result
Recycled materials                            geometry of the molecule as far as                  can be seen above right.
   Our choice of materials reflected          possible. Next, the components are
their abundance in the school recy-           assembled to form nucleotides and                Phosphate group
cling bins.                                   the DNA helix is constructed.                      Using the same nail, puncture the
·   20 aluminium Coca Cola® cans                Puncture the aluminium cans and                centre of the Coca Cola can base,
·   20 aluminium Sprite® cans                 the bottle caps with the same nail.              which represents the phosphate
·   20 plastic Coca Cola bottles
    (500 ml)
                                              Heating the nail will enable the caps            group. Thread the straw attached to
                                              to be more easily pierced. Choose a              the Sprite can (deoxyribose) through
·   60 red caps from Coca Cola bottles        suitable thickness of nail to enable             the Coca Cola can (phosphate group),
·   10 plastic Fanta® bottles (500 ml)        the plastic drinking straws to pass              with the top of the Coca Cola can clos-
·   20 orange caps from Fanta bottles         through the holes and fit firmly, creat-         est to the Sprite can. The phosphate
·   a thin piece of paper or plastic,
    approximately 1 m long.
                                              ing a stable link between the structur-          group is now attached to the deoxyri-
                                              al elements.                                     bose in position 5’ (see page 26, left).


www.scienceinschool.org                                                                      Science in School Issue 2 : Summer 2006   25
                    Phosphate group

                                                                    a




                                                         b
5’                   Deoxyribose

                                   1’


                                                  c

               3’


  The straw connects the two cans,               Using these building blocks and the     tle (guanine) to enter and lock firmly.
and also makes it easy to pass the thin        coloured cellophane, the structural          For symmetry and the scale of the
rope through both cans, connecting             elements that represent the bases can     model, the two pairs of linked com-
the nucleotides into a molecule chain          be created (see page 27).                 plementary bases should be 42 cm
(see below). For this reason, it is                                                      long. Each coloured bottle is screwed
important not to bend the straw.               Thymine (T)                               into the bottle cap (carbon) at position
To maintain the correct scale between           Place green cellophane in a Coca         1’ of a deoxyribose molecule, forming
the molecule and the model, the                Cola bottle without a base.               four different nucleotides (see page 28).
distance from the base of the Coca                                                          This representation of the hydrogen
Cola can to the orange cap should              Adenine (A)                               bonds enables the easy connection
be 23 cm.                                        To the base of a Fanta bottle, attach   and detachment of complementary
                                               the neck of another Coca Cola bottle.     bases. This, in turn, facilitates not
Complementary base pairs                       Place blue cellophane inside both         only the separation of the DNA
   Next, plastic bottles representing          parts.                                    strands but also the change in posi-
the bases are modelled so that they              Thymine (T), represented by the         tion of bases for teaching purposes.
can only be connected to their com-            colour green, is connected by two
plementary base (adenine to thymine,           hydrogen bonds to adenine (A), rep-       Constructing the DNA molecule
and guanine to cytosine).                      resented by the colour blue. To model        Having constructed 20 nucleotides,
   To construct two complementary              this, push the blue neck firmly into      we can build a double helix with 10
base pairs, cut two Fanta bottles and          the green bottle without the base.        steps – two strands of 10 nucleotides
three Coca Cola bottles in cross-sec-                                                    each. Because the distance from the
tion, using the scalpel and scissors.          Guanine (G)                               end of the Coca Cola can (phosphate
Take care!                                       Place red cellophane in a Fanta         group) to the orange cap (hydroxide
1. Remove the base of two Coca Cola            bottle.                                   linked with the next phosphate
    bottles (incision c above centre)                                                    group) is 23 cm, the strand of 10
2. From the third Coca Cola bottle,            Cytosine (C)                              nucleotides will be 2.3 m long.
    remove                                       Place yellow cellophane in a Coca          Attach the telephone cable to
    a) the neck, cutting 10 cm below           Cola bottle without a base. Firmly        approximately 3 m of the thin rope
       the mouth (incision a) and              attach the base of another Coca Cola      and use the stiff cable to pass the rope
    b) the lower part of the bottle,           bottle, upside down.                      through the straws of the nucleotides
       cutting 4 cm above the base               Guanine (G), represented by the         to form two strands of molecules,
       (incision b).                           colour red, is connected by three         which are hung vertically 2 m high
   Using scissors, make five to six            hydrogen bonds to cytosine (C), rep-      and 65 cm apart. The two strands of
incisions, 2 cm long, in the neck and          resented by the colour yellow. To         the DNA molecule are read in the
the base of the third Coca Cola bottle.        model this, open the base of the yel-     direction 5’ to 3’ and are anti-parallel.
These can then open to allow other             low bottle (cytosine) along the inci-     In the model, the direction in which
bottles in (see above right).                  sions to allow the base of the red bot-   we read the word Coca Cola coincides


26   Science in School Issue 2 : Summer 2006                                                               www.scienceinschool.org
                                                                                                Teaching activities




 with the direction 5’ to 3’. Thus, in       so that a thin bar can be passed            wrapping around Earth’s equator 16
 one of the strands, the words Coca          through the roll and used to twist          times.
 Cola can be read from top to bottom         the linked strands clockwise, 360
 and in the other strand, from bottom        degrees (see page 28, bottom right).        Using the model in class
 to top. Our model DNA strands are                                                         The model was constructed and used
 thus also anti-parallel.                    Scale                                       in three phases over one to two weeks.
   We must also make sure that the              The model represents a DNA
 bases on one strand are complementa-        molecule at a scale of 320 000 000:1,       Phase 1: Constructing the model
 ry to those on the opposite strand.         that is, 320 million times bigger than        Students aged 14 followed the con-
 Adenine should be opposite thymine          it really is. If we tried to represent an   struction directions with interest and
 and cytosine opposite guanine.              entire human DNA molecule with our          were involved in resolving practical
   If these criteria have been met, tie      model, we would need a double               problems.
  a paper roll at the end of each strand     helix 640 000 km long, capable of
                                                                                         Phase 2: Representing a DNA
                                                                                         molecule
Table 2: Sizes and proportions of a DNA molecule and the model
                                                                                            In the appropriate unit of their biol-
                                                                                         ogy course, students aged 15 were
                                   DNA molecule                    Model                 given a worksheet where they recog-
                                                                                         nised and matched the prepared
    Diameter                                2 nm                    0.65 m
                                                                                         structural materials of the model with
    Helix step                             3.4 nm                     1.1 m              those of the DNA molecule as illus-
                                                                                         trated in their textbook. They com-
    Helix length                       7.14 nm                       2.30 m              posed and twisted the double chain of
    Helix length: diameter                   3.57                      3.53              the model. They asked a lot of ques-
                                                                                         tions and had an intense and interest-
    Helix step: diameter                      1.7                       1.7              ing discussion.


www.scienceinschool.org                                                              Science in School Issue 2 : Summer 2006   27
Phase 3: Copying a DNA                           2. Separating the two strands.
molecule                                         3. Beginning to create daughter
  In their free time and as a                       strands complementary to the
theatre game, the same 15-year-old                  parental strand (DNA polymerase).
students pretended to be suitable                4. Splitting the rest of the hydrogen
enzymes and, with the help of                       bonds.
the model, performed the following               5. Creating daughter strands comple-
steps:                                              mentary to the parental strand
1. Splitting hydrogen bonds between                 (DNA polymerase).
   the complementary bases, from the             6. Checking for possible errors and
   top of the molecule until the sixth              correcting them if necessary.
   base (bottle) pair on the model
   (enzyme: DNA helicase).




            Students learn much more quickly and easily when                 nail to puncture the bottle tops and a sharp implement
            they are actively involved in the lesson. Teaching the           to cut the plastic bottles. Alternatively, the model could
            structure of DNA is made much easier if a 3D repre-              be made in a design-technology class and then used in
            sentation of the molecule is used. Jigsaw puzzle-type            biology lessons. Group work could be designed so that
            activities give a 2D picture, but it is difficult to visualise   teams race each other to prepare a DNA model. The
            the shape of the molecule. This ingenious project                model could be used as a teaching tool to demonstrate
            describes how a scale model of DNA can be made                   DNA replication, either in mitosis or in the polymerase
            using cans and bottles. It would be easy to collect the          chain reaction. The fact that the model is to scale will
            materials required to make this model, as students               help the students appreciate the spatial relationship of
  REVIEW




            could recycle cans and bottles.                                  the components of the DNA molecule. I feel that stu-
            It may be a good idea for a technician or teacher to do          dents will enjoy learning about DNA using this idea,
            some of the preparation work; this would decrease the            which means that the lesson will be both understood
            amount of time needed in the lesson as well as                   and remembered.
            addressing safety considerations with the use of a hot                                             Shelley Goodman, UK



28     Science in School Issue 2 : Summer 2006                                                                    www.scienceinschool.org