"dna double helix model"
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