We present our very first video game! Targeted toward middle- and high-school students, DNAFactory demonstrates the steps a Gene Synthesis factory or laboratory would go through to produce DNA molecules; specifically, when creating a DNA sample, the target sequence is subdivided into shorter DNA fragments called oligos, which can be synthesized using a chemical process. Then a Polymerase Chain Reaction (PCR) or other assembly method is used to merge these shorter fragments into the longer DNA molelcule, relying on overlaps between the DNA fragments to ensure that the fragments are assembled in the right order.
This game can be played from Peccoud Lab’s website at http://peccoud.vbi.vt.edu/dnafactory
The game includes two levels of puzzles.
The Synthesis level introduces the main notions supporting gene synthesis:
- complementarity of DNA bases and melting temperatures
- extension of primers using a DNA polymerase
- notion of supply expenses and labor costs related to speed of execution. It should be noted that the user has to “pay” for materials and labor from the money they have in their “bank”; the user starts out with $15 in their “account”. Materials are paid for as soon as the user clicks on the “Create” button; if the user does not have enough money in his or her bank, then they can replay the Synthesis Game #1 to augment their funds. Labor is debited from the bank as the user assembles the DNA fragments, so it is to your advantage to work fast!
In the “Design” level, puzzles allow the users are placed in the position of a gene synthesis company receiving orders from customers. They need to split the DNA sequences provided by the customer into oligos, smaller fragments that can be synthesized chemically. This is achieve by using the mouse to indicate the start and ending point of each oligo. After all the oligos have been designed, the user clicks the “Create” to get the oligos synthesized. Then the user needs to put them back together using the same techniques employed in the “Synthesis” puzzles. The notions introduced at this level include:
- the design of DNA sequences
- possible problems in gene synthesis resulting from specific features of DNA sequences like repeats
- finding an optimal compromise between reducing cost of supplies without jeopardizing the probability of a successful assembly
- notion of cash flow
Development of DNAFactory was funded under National Science Foundation (NSF) Grant #1241328, “INSPIRE: Modeling and optimization of DNA manufacturing processes”. The game was developed by Blair Lyons of DynamoidApps.