A new three-dimensional educational model kit for building DNA and RNA molecules: Development and evaluation*

Authors

  • Leila Maria Beltramini,

    Corresponding author
    1. Centro de Biotecnologia Molecular Estrutural (CBME/CEPID/FAPESP), Instituto de Física de São Carlos, Universidade de São Paulo, São Paulo, Brasil CEP 13560.970
    • Centro de Biotecnologia Molecular Estrutural (CBME/CEPID/FAPESP), Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador Sãocarlense, 400, CEP 13560.970
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  • Ana Paula Ulian Araújo,

    1. Centro de Biotecnologia Molecular Estrutural (CBME/CEPID/FAPESP), Instituto de Física de São Carlos, Universidade de São Paulo, São Paulo, Brasil CEP 13560.970
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  • Tales Henrique Gonçalves de Oliveira,

    1. Centro de Biotecnologia Molecular Estrutural (CBME/CEPID/FAPESP), Instituto de Física de São Carlos, Universidade de São Paulo, São Paulo, Brasil CEP 13560.970
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  • Luciano Douglas dos Santos Abel,

    1. Centro de Biotecnologia Molecular Estrutural (CBME/CEPID/FAPESP), Instituto de Física de São Carlos, Universidade de São Paulo, São Paulo, Brasil CEP 13560.970
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  • Aparecido Rodrigues da Silva,

    1. Centro de Biotecnologia Molecular Estrutural (CBME/CEPID/FAPESP), Instituto de Física de São Carlos, Universidade de São Paulo, São Paulo, Brasil CEP 13560.970
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  • Neusa Fernandes dos Santos

    1. Centro de Biotecnologia Molecular Estrutural (CBME/CEPID/FAPESP), Instituto de Física de São Carlos, Universidade de São Paulo, São Paulo, Brasil CEP 13560.970
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  • *

    This work was supported by the Brazilian funding agencies Fundaçao de Amparo à Pesquisa do Estado de Sao Paulo (FAPESP) and CNPq.

Abstract

International specialized literature focused on research in biology education is sadly scarce, especially regarding biochemical and molecular aspects. In this light, researchers from this Centre for Structural Molecular Biotechnology developed and evaluated a three-dimensional educational model named “Building Life Molecules DNA and RNA.” The development of the model and its evaluation as a potential tool in the teaching-learning process were based on a pilot study involving 226 learners and teachers. Questionnaires were elaborated, containing simple and objective questions, similar to those used in research on science teaching, to orient the evaluation process. Our results show that the model has high educational potential, aiding participants in their conceptual understanding of these molecular structures and their functions, DNA semiconservative replication, and RNA transcription. In addition, it was observed that this model leads students to critical associations of these concepts with actual scientific themes of molecular biology and biotechnology, such as cloning, transgenic organisms, and the genome.

Structural molecular biology emerged from a historical process guided by findings in biochemistry and genetics. This development began with a change in paradigm, pointing out that organisms are highly complex systems resulting from a long evolutionary process, which was responsible for the current macromolecular organization.

The elucidation of DNA and the protein structure resolutions are among the major problems that have been investigated and/or elucidated through structural molecular biology, which has fostered technological advances as a whole. Research in this field has influenced the knowledge in other areas of science and caused an impact on society's vision of science.

However, there is a disparity between what society can understand about biological phenomena and the acquaintance with the concepts involved in the processes, which are comprehended by the few who produce such knowledge. Published data indicate that this profile is not an exclusive feature of Brazilian society. In fact, the public worldwide has a poor understanding of molecular biology, or indeed of several other fields of science [14].

Therefore, there is an urgent need to adapt educational programs to the dissemination of structural molecular biology concepts, which means, for instance, to make clear that genes are the parts of DNA that encode proteins and that the proteins perform specific biological functions when correctly organized into well defined three-dimensional structures.

To enhance the comprehension and interest of educators and students with respect to molecular biological phenomena, researchers from the Centre for Structural Molecular Biotechnology (CBME,11 Centro de Biotecnologia Molecular Estrutural), in partnership with the Centre for Scientific and Cultural Dissemination, both of the University of São Paulo at São Carlos, developed a model kit consisting of small plastic elements that emphasize chemical bonds and keep the real dimensions of the molecular distances in the nucleic acid structures. The kit was designated Building the Life Molecules DNA and RNA.

THE DEVELOPMENT OF THE PROPOSED MODEL

Several molecular models of DNA structure have been developed for teaching purposes and patented. However, the components of various models were designed in a simplified way, resulting in limitations in their teaching potential. According to these patents, there is one model in which nucleotides are represented as a single piece so that the functional groups on the different nucleotides are not distinguishable [5]; in another model, the DNA double strand is spatially represented, but the nucleotides are indistinguishable from each other [6]. In two additional models, the nucleotides are distinguished, but the covalent and the hydrogen bonds between the nitrogenous bases are not emphasized [7, 8]. A fifth model only represents the DNA spatial structure, the nucleotides present a single configuration without any difference between their chemical groups and covalent bonds, and the hydrogen bonds are not emphasized [9]. The most elaborate model is made of more flexible material, and the nitrogenous bases are different from one another in shape and size, but the sugar molecule and phosphate group are both represented by a single horizontal structure [10]. The components of all these models do not have enough flexibility to enable the building of the double helix. In addition, none of the patents includes a description of the model's use, neither provides theoretical background for understanding processes such as DNA semiconservative replication or RNA transcription.

In this light, it was resolved that the model Building Life Molecules DNA and RNA should be developed with the following particularities: (1) representation of the chemical groups composing DNA and RNA molecules should be different from one another; (2) dimensions of each piece should be scaled to be proportioned to the real sizes of molecular structures; and (3) the plastic used to manufacture the model kit should be inexpensive and ensure suitable flexibility when handled.

Initially, the dimensions of the pieces that constitute the model were defined and designed with AutoCAD (version 2000) and Mechanical Desktop (version 6) softwares. Afterwards, to manufacture the templates, the designed components were transferred and sculpted in steel plates by the electro-erosion technique, which were then adapted to a Romi 100R injector machine. The model pieces were manufactured in different colors and also distinct types of plastic, such as low density polyethylene, polyethylene plus copolymer, and random polypropylene.

THE MODEL BUILDING LIFE MOLECULES DNA AND RNA

Fig. 1 shows the different components of the model developed: (a) phosphate-sugar complex (PSC), (b) nitrogenous bases, and (c) hydrogen bonds. All the pieces can be associated in a conceptually appropriate way so that it allows the user to assemble three-dimensional models of DNA and RNA molecules.

The nitrogenous bases can be identified by their initial letter in relief: A for adenine, G for guanine, T for thymine, C for cytosine, and U for uracil. These bases can also be distinguished by their size and number of connector holes to accommodate hydrogen bonds. Regarding the size of the molecular structures, the purine bases (A) and (G) are bigger than the pyrimidine bases (C), (T), and (U), since the former have two aromatic rings and the later, only one ring. The connector holes are double in (A), (T), and (U) and triple in (G) and (C), considering the distinct number of hydrogen bonds that (A), (T), and (U) commonly make, comparing with (U) and (G).

BUILDING THE NUCLEOTIDES OF THE DNA MOLECULE

The DNA nucleotide can be built connecting a PSC with one of the different nitrogenous bases (Fig. 1d). Usually, the carbons of the pentose are numbered in sequence (Fig. 1e), in a way that the phosphate group can be connected to the carbon 5′ of the pentose, whereas the nitrogenous base can be connected to carbon 1′ through a lateral stick. Furthermore, the piece has a hole at position 3′ and another stick on the phosphate group with the aim of fitting it to the next piece at the 5′ position.

BUILDING A SINGLE STRAND AND DOUBLE HELIX OF DNA

Through consecutive phosphodiester connections, the phosphate groups connect the carbon 3′ of one pentose to the carbon 5′ of the next, ending up in a single polynucleotide strand (Fig. 2a). The connections formed when these sticks fit the holes of neighboring pieces represent covalent phosphodiester bonds.

The pairing between bases is not random, so the connector holes match the number of hydrogen bonds required to form the connection between complementary nucleotides. Both A and T bases have two connector holes, and the piece that symbolizes the two hydrogen bonds accomplishes the connection between them, whereas C and G bases have three holes, and the interaction between them is modeled by the piece that symbolizes three hydrogen bonds. This complementarity of the nucleotide pieces enforces the molar ratio between bases first described by Erwin Chargaff in 1950, A = T and G = C, and soon confirmed in DNA from all forms of life.

With the help of these “Chargaff rules,” it is possible to build the complementary antiparallel strand by binding the hydrogen bonds between nucleotide pairs (Fig. 2b). Finally, the model should be twisted anticlockwise and pressed flat. When the pressure is released, the flexible plastic adopts the helical shape (Fig. 2c).

Pieces may be used in different combinations of colors, depending on the focus to be achieved. Thus, different colors may be used to distinguish each of the nucleotides, or only the bases, or the base pairs, the antiparallel strands (as in Fig. 2c), each turn of the DNA helix, or even the phosphate-sugar backbone, differentiating the DNA and RNA molecules in relation to the type of sugar (deoxyribose or ribose).

UNDERSTANDING THE SEMICONSERVATIVE DNA REPLICATION PROCESS

After the DNA double helix has been built, the replication process can be started by the breaking of hydrogen bonds. The user can play the role of enzymes that catalyze this process. The complementary ratio between the bases implies that the sequence of one strand specifies the sequence of the other. From this, it follows that the new complementary nucleotides can be added along each strand (Fig. 3). To make this process readily comprehensible, we suggest the use of different colors for the pieces representing the new nucleotides, to lead the user to the correct conceptual correlations.

BUILDING THE MESSENGER RNA

As in the process simulation of DNA replication, the transcription process and the building of the RNA molecule start with the temporary breaking of the hydrogen bonds between the bases that hold the complementary DNA strands together. After this, the user has to play the role of an enzyme complex whose key enzyme is RNA polymerase, fitting free ribonucleotides on the region corresponding to one gene on one of the DNA chains (Fig. 4, a and b) and building the messenger RNA molecule (mRNA) (Fig. 4c). The pieces used to construct the ribonucleotides are basically the same as those used previously. However, the user can represent the PSCs of the RNA molecule by another color to distinguish the ribose from the deoxyribose. The pairing relation between bases should be maintained, although the T base should be replaced by the U base in the mRNA molecule when transcribing the A base.

After the transcription process, the synthesized mRNA chain detaches from the DNA and migrates out to the cytoplasm, where it associates with a ribosome on which it can be decoded, synthesizing a protein. To simulate this step, the user should detach the mRNA molecule and rebuild the original DNA duplex by reconnecting the hydrogen bonds. The model may also be useful for the understanding of mRNA primary transcripts of a gene sequence of the DNA, which include regions that do not encode protein and have to be subsequently removed (introns) between the sequences (exons).

Additionally, another teaching tool developed by us, the Amino Acids Disk, can be used to simulate the translation. Fig. 4d shows this tool, which is made up of two superimposed rotating disks. The top disk has three openings; when it is turned, it reveals information about the amino acids hidden on the bottom disk (the names, usual abbreviations, structural formulae, and biochemical characteristics). A table of the genetic code can be found on the back, and consequently, the user can decode the mRNA, identifying the amino acids to be incorporated during the protein synthesis and the anticodon sequence in the transporter RNA.

Finally, depending on the topic to be explored and the contents to be taught to a target public, the kit components may even be used to simulate DNA sequencing, aiding the understanding of the genome sequencing process. The pieces from the kit have great versatility and flexibility; thus, with imagination and creativity, some of our researchers and graduate students have already built tRNA molecules, RNA renditions, and RNA hairpin models. The kit brings a detailed manual of instructions with the major simulations described above, in Portuguese and English versions.

During the last 2 years, the model has been presented to the scientific community through exhibitions and workshops, at national and international congresses in the areas of biology, genetics, biochemistry, and molecular biology, and the public response was excellent. However, to support the model as a teaching-learning tool, its educational potential should be evaluated methodically.

EVALUATION OF THE MODEL AND METHODOLOGY EMPLOYED

The literature emphasizes that the teaching of science is based on the construction of knowledge through the formation of discussion groups [1115] and on the use of tools such as games, movies and videos, Internet sites, and software packages [1620]. Theoretical explanations associated with the use of educational resources facilitate the understanding of biological concepts, and the participants are constantly challenged to solve the proposed questions. Therefore, an evaluation strategy was developed using a methodology based on construction of knowledge in discussion groups, associated with handling of the model to exploit its educational potential.

Tutors from the dissemination team of CBME asked questions graded in complexity and content, instigating the curiosity of the participants to handle the model, leading to recognition of their own conceptions about the topic. Previous ideas should allow the creation of correlations and analogies with the new content and lead them to a conceptual change and the correct concepts.

Tutors were previously trained to conduct and develop this creative process and to motivate the participants to simulate all the processes presented in the first part of this article, and to acquire or revise the following knowledge. (a) Chromosomes are structures found inside the nucleus of all eukaryotic cells, whereas in prokaryotic cells, the genetic material is dispersed in the cytoplasm; (b) a chromosome is composed of a DNA molecule associated with proteins; (c) the DNA molecular structure is built from four types of nucleotides, generating countless code sequences; (d) the genetic code is biochemically transmitted through this molecule; (e) the DNA molecule is reproduced by semiconservative replication; (f) genes are functional segments of the DNA molecule, structurally composed of the base sequences that encode specific proteins; (g) specific information in the gene is transferred from the DNA to the mRNA in a process called transcription, and the transcribed information is then read for protein production in a process called translation; and (h) there are basic structural differences between DNA and RNA molecules.

The evaluation process involved 226 people (32 high school teachers from different areas, 142 high school students from public and private schools, and 52 undergraduates from the Exact Science course at the Physics Institute of São Carlos, University of São Paulo). The participants were organized in sets of 5–6 people per tutor, during 3 h of activity at their institutions or in the Biology Teaching Laboratory at the Physics Institute of São Carlos.

Questionnaires similar to those used in research on science teaching containing simple and objective questions were elaborated [1823] to orient the evaluation process. Some aspects of the functional and educational applicability of the model were evaluated immediately after the end of the activities offered to the 226 participants. In addition, the previous knowledge and the newly acquired knowledge of the 95 high school students in our sample were checked, respectively, before (pre-test) and 2 weeks after (post-test) the activity.

RESULTS AND DISCUSSION

Initially, the dissemination team from CBME invited only the high school teachers to participate in the evaluation, since their opinions should be pertinent to us as an aid in subsequent changes made to improve the methodology and for continuation of the study. The data obtained supported the model as an educational tool and the methodology employed in the activity. Therefore, using the same procedures, the analysis was extended, and other discussion group were organized for undergraduates and high school students.

All the activities were opened with questions related to the comprehension of the structure of different cell types. The verbal answers contributed to the understanding of the different organelles and their specific functions, including the organization and importance of the nucleus that contains the DNA. At this stage, the tutors proposed manipulation of the model components. The participants observed the formats of the pieces and the similarities between them and the chemical groups composing the DNA structure. Motivated by the methodological environment and the educational potential of the model, the groups sequentially built the deoxyribonucleotides, the DNA polymer, and the complementary antiparallel chain, including its format in the double helix, and simulated the semiconservative replication process. Afterward, tutors proposed other questions focusing on the concepts of gene and genetic code, the importance of the DNA in protein synthesis, and the role of the DNA in the context of the diversity of biological phenomena, including signaling in the processes of division, differentiation and cell death, replacement of cells, and growth and multicellular development.

The groups understood the basic differences between the DNA and RNA molecules, building the ribonucleotides, choosing a sequence representing a gene from the DNA molecule, and simulating the transcription process by building the messenger RNA. Next, using the table of the genetic code from the Amino Acids Disk, the groups simulated protein synthesis, starting with the assembled mRNA models, identifying the amino acids to be incorporated and the anticodon sequences of the respective transporter RNAs. Concluding the activity, the participants correlated the acquired concepts with important historic aspects of biochemistry, genetics, and molecular biology, and the scientific advances in biotechnology, such as cloning and the development of transgenic organisms.

Immediately after the accomplishment of the activities, the evaluation questionnaires were given to find out the opinions of the participants about the functional and educational applicability of the model. The data were tabulated, and the results can be observed in the Table I.

Analyzing the answers of the 226 participants, irrespective of the educational level of the participants, a positive pattern of acceptance was obtained for all 11 aspects evaluated, showing that the model is a useful tool in the teaching-learning process. Only the last aspect, related to the use of the model outside the school environment, showed a smaller acceptance compared to other items.

Additionally, most of the students and teachers remarked during the activities that the model facilitated the building of knowledge in an entertaining way. We believe that besides the clear potential of the model, the methodology followed by the tutors was able to motivate the participants to manipulate the components and also aided the acquisition of content in reduced teaching hours. Teachers corroborated this view, declaring that this methodology could easily be used in class together with the model.

Another trial was carried out with 95 students from the 2nd and 3rd years of public and private high schools that make up our sample. This second step of evaluation was designed to test the material as an educational resource, comparing the basic knowledge level of the students about the structure and importance of the DNA molecule and genes before (pre-test) and 2 weeks after (post-test) the discussion groups and model handling activities.

Evaluations were corrected by checking against an answer sheet previously elaborated by the dissemination team of the CBME. Answers were planed in four categories: C for correct answers; PC for partially correct answers; W for wrong answers; and NA for questions not answered. The data obtained can be observed in Table II.

Although the basic content about nucleic acids is usually taught in the 2nd year and reviewed during the 3rd year of high school in Brazil, the students showed a great deal of difficulty of answering the questions posed before the activity. In general, almost all the students revealed serious conceptual flaws about these topics. The concepts of genes and DNA appeared to overlap, i.e. the student used the same definition for both concepts.

From the 95 students in our sample, only 17 answered correctly that the molecule of DNA is inside the nucleus of eukaryotic cells, whereas the genetic material is dispersed in the cytoplasm in prokaryotic cells. Twenty-seven students mentioned that DNA is located in the blood, without specifying in which cellular type. This previous conception may be the consequence of an informal knowledge, acquired by news in the media concerning the use of samples of blood for DNA paternity tests and to detect several diseases.

The same low profile of correct answers was observed regarding the location of the genes. Only 16 students described the genes correctly as segments of the DNA molecule. We also verified that some of those same students had not answered the other questions regarding the molecular concept of the gene appropriately and had not established links with protein synthesis. Additionally, the highest rates of unanswered questions were associated with the structural composition, localization, and importance of the genes.

Although the participants of our sample essentially belong to the same socioeconomic and cultural region, we believe that the same lamentable profile of conceptual difficulties may be repeated in other regions across the country due to the characteristics and problems facing the teaching of science in Brazil, which persist despite numerous attempts at improvement. Biology programs in high schools are broad, generally taught in a segmented form and basically prioritize descriptive aspects, encouraging memorization rather than analysis, reflection, and questioning [24]. Our data also corroborate several other studies that demonstrate the low level of understanding of the students of various countries about genetics topics, including inheritance, structural and functional concepts of DNA molecules, and advances in biotechnology [2123].

However, according to the data presented in Table II, after the activities of these trials, most students corrected their flaws, presenting a better performance in the conceptual constructions for all the questions. The numbers of wrong answers and void answers decreased, whereas the rate of correct and partially correct answers increased considerably.

This educational experience showed that the visualization of three-dimensional structures of organic molecules, which in itself are attractive and artistic, creates a significant impact on the comprehension of the structure-function paradigm in biology. Our observations showed that discussion groups stimulated the integration of the participants, encouraging creativity and the construction of knowledge of the basic concepts surrounding the educational model, and that this process also leads to critical associations of these concepts with actual scientific themes of molecular biology and biotechnology, such as cloning, transgenic organisms, and the genome. The data presented in this work support the model as a teaching-learning tool, which can be used in modules or as a whole, according to the needs of the educator, the level of target audience, and the time available.

Figure FIGURE 1..

Plastic components of the model Building Life Molecules DNA and RNA.a, phosphate group connected to the pentose (PSC); b, nitrogenous bases adenine, guanine, thymine, cytosine, and uracil; c, double and triple hydrogen bonds; d and e, comparative correlation between nucleotide assembled from components of the model (PSC linked to cytosine base) and its chemical formula (dCMP).

Figure FIGURE 2..

a, single strand of the DNA molecule. b, antiparallel double strands of the DNA molecule joined by the complementary nucleotides, through double and triple hydrogen bonds. c, three-dimensional structure of the DNA double helix.

Figure FIGURE 3..

Semiconservative replication of the DNA molecule using the plastic pieces of the model.

Figure FIGURE 4..

a and b, simulation of the mRNA polymerization process (transcription) using the pieces of the model. c, mRNA molecule. d, illustration of the Amino Acids Disk model, which is composed of superimposed rotating disks that display abbreviations, chemical structures, and biochemical characteristics of the 20 amino acids commonly found in protein structures.

Table Table I. Opinion profile of teachers and students at high schools and undergraduates from São Carlos city, about some functional aspects and the educational value of the model Building Life Molecules DNA and RNA produced by the Centre for Structural Molecular Biotechnology, São Carlos, SP, Brazil
Evaluated aspectsYesNoOccasionally
Data are expressed as a percentage of all questionnaires.
Is it suitable for a reduced number of teaching hours?78418
Is it suitable for activities with a large number of students?73720
Is it easy to handle?8929
Can it make learning more attractive?94 6
Can it encourage reflexive reasoning?93 7
Can it arouse curiosity?92 8
Can it facilitate learning of the fundamental concepts of this topic?96 4
Can it help broaden the knowledge?91 9
Can it make the classes more dynamic?95 5
Could it be used easily in the classroom?79714
Could it be used outside the school environment (e.g. with friends as a leisure activity)?661519
Table Table II. Profile of the basic knowledge level of 95 students from high schools in São Carlos city about the structure and importance of the DNA molecule and genes, before and two weeks after model handling, carried out in the context of discussion groups
Questions
Data are expressed as percentages.
 CPCWNACPCWNA
What are the genes made of? 5247142361012
Where are the genes found?1710175641301811
Why are the genes important? 2716574336138
What is DNA?91733414734127
Where is DNA found?18232831751843
Why is DNA important?2312344661959

Acknowledgements

We are grateful to our tutors and to Dr. Nelma Regina Segnini Bossolan of the Institute of Physics of the University of São Paulo at São Carlos for their collaboration in the organization and development of the activities.

Footnotes

  1. 1

    The abbreviations used are: CBME, Centre for Structural Molecular Biotechnology; PSC, phosphate-sugar complex.

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