DNA Structure and Sequencing Tutorial

Project leaders: Cas Kramer and Annette Cashmore.

Experience shows that some of the fundamental principles involved in the molecular biology of DNA are actually quite difficult for students to grasp when taught via either conventional lectures or practical classes. Successful acquisition of such knowledge is, however, crucial for the comprehension of more complex DNA processes. Two interlinked hands-on tutorials have been designed to increase students’ understanding of both DNA structure and the importance of this structural knowledge in strategically significant technologies such as DNA sequencing. 

Description of DNA structure tutorial 

students building DNA modelIn the first tutorial, a semi-space-filling atomic model of a DNA molecule (purchased from Spiring Enterprises Ltd.) is used to conceptualise a number of issues related to the basic atomic structure of the double-helix. In addition, each student pair was given an atomic model of one of the four DNA building blocks (a nucleotide, consisting of one of the four DNA bases, one sugar group and one phosphate group).

Physical handling of these semi-space-filling models helped the students to distinguish the bases, to visualise the interaction between bases and to understand the rules governing DNA base pairing. The directional nature of DNA strands and the double helical structure of DNA (including the major and minor grooves) are easily seen when using these models. The tutorial on DNA structure culminates with the opportunity to read the DNA sequence of the model and subsequently build a replica mini-DNA model, using simplified and stylised DNA models (also purchased from Spiring Enterprises Ltd.). Having to build the replica model reiterates the basic principles of DNA base pairing and DNA structure.

Description of DNA sequencing tutorial 

female student building a DNA modelThe second tutorial comprises a sequencing scenario to simulate the dideoxy method of DNA sequencing using ‘pop-it’ beads (purchased from Philip Harris Education) as DNA building blocks, to determine the sequence of a short stretch of DNA.

In our activity, students act as DNA polymerase (Taq) to synthesise short DNA products by making copies of a provided nine-base-pair template sequence. To copy this sequence a DNA primer is selected (represented by a 5-bead pop-it chain) and then further bases are added onto this primer, following the base-pairing rules learned in the DNA structure tutorial session. Beads of different colours are provided in four bags. The majority of beads in each bag are pink these represent normal bases (i.e. deoxy nucleoside triphosphates, dNTPs). One out of every seven beads in each bag is of a different colour and represents the terminating bases, which are dideoxy nucleoside triphosphates (ddNTPs) that lack the hydroxyl group necessary for the connection of additional bases. If a normal base is selected this is added to the chain and synthesis continues. However, if a terminating base is selected further bases cannot be linked to the chain. When twenty such chains have been produced these are sorted by size (simulating electrophoresis).

Subsequently, the sequence of bases is read by looking at the coloured beads terminating each chain, from shortest to longest. This section of the tutorial provides a useful scenario to visualise the complex process of DNA sequencing.

If you wish to access any of the key documents relating to this tutorial, please visit the Virtual Genetics Education Centre.

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