Research ArticleSYNTHETIC BIOLOGY

BioBits™ Explorer: A modular synthetic biology education kit

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Science Advances  01 Aug 2018:
Vol. 4, no. 8, eaat5105
DOI: 10.1126/sciadv.aat5105
  • Fig. 1 BioBits™ kits: Freeze-dried educational kits.

    (A) FD-CF demonstrations require only the addition of water to the supplied reactions and incubation for 1 to 20 hours at 25° to 37°C for observation and analysis by students. In contrast, traditional biology experiments require substantial time, resources, and specialized equipment. (B) With the DNA template and any substrate molecules provided with the FD-CF reaction, the students just have to add water to run a number of bioscience activities and demonstrations.

  • Fig. 2 Fluorescent proteins as visual outputs.

    (A) A set of fluorescent proteins were expressed by FD-CF expression in crude extract and visualized with (i) a laboratory transilluminator (Safe Imager at 470-nm excitation), (ii) white light epi-illumination, (iii) a portable, inexpensive (<US$15) 450-nm classroom illuminator with an orange acrylic filter, or (iv) a yellow acrylic filter. (B) sfGFP and eforRed fluorescent proteins were expressed at a range of different combinations (by ratio of template DNA added) in FD-CF crude extract and visualized with (i) the Safe Imager, (ii) white light, and (iii) the classroom illuminator with the orange acrylic filter to demonstrate tunable protein expression.

  • Fig. 3 Fragrance-generating enzymes as olfactory outputs.

    (A) Using FD-CF reactions, we manufactured enzymes that can generate various smells from the Saccharomyces cerevisiae acetyltransferase ATF1. (B) Production of fragrance molecules after substrate addition to overnight FD-CF reactions of ATF1, as detected by headspace GC-MS. Values represent averages, and error bars represent SDs of n = 3 biological replicates.

  • Fig. 4 Hydrogel-generating enzymes as tactile outputs.

    (A) Schematic of fibrin hydrogels created from FD-CF–generated batroxobin/ecarin proteases that activate fibrinogen by cleavage or PEG-peptide hydrogels cross-linked by FD-CF–generated sortase enzymes that induce cross-linking by transpeptidase activity. (B) Inverted glass tubes to demonstrate formation of hydrogels. (C) Close-up images of the formed hydrogels that can be manipulated by hand. (D) Tuning the mechanical properties of the hydrogel by varying the % PEG to create a range of materials with varying viscosities. (E) An 8% crude FD-CF PEG hydrogel is highly elastic. (F) Casting the hydrogels into shapes using molds and mixing with crude FD-CF fluorescent protein reactions to obtain shaped fluorescent hydrogels. Scale bar, 1 cm.

  • Fig. 5 Toehold-based environmental sensing demonstrations.

    (A) Schematic of a toehold switch sensor. Upon the presence of a trigger RNA, strand invasion melts the secondary structure, allowing ribosomal translation to occur. (B) Schematic of activity that allows extracted DNA from banana or kiwi fruit to be processed and detected by a toehold switch sensor in FD-CF. (C) The banana toehold switch sensor or (D) the kiwi toehold switch sensor produces a clear fluorescence output (sfGFP) when exposed to extracted and amplified DNA of the relevant fruit but not when exposed to DNA sequences from other fruits. Images shown are from a custom-built 450-nm handheld imager with a yellow acrylic filter and quantified by a plate reader at 485-nm excitation and 520-nm emission. Values represent averages, and error bars represent SDs of n = 3 biological replicates.

Supplementary Materials

  • Supplementary material for this article is available at http://advances.sciencemag.org/cgi/content/full/4/8/eaat5105/DC1

    Fig. S1. Quantification of all proteins expressed in FD-CF.

    Fig. S2. Fluorescent proteins expressed in the PURE and crude extract systems.

    Fig. S3. Quantitative analysis of fluorescent proteins.

    Fig. S4. Representative scanning electron microscopy images of hydrogel ultrastructures generated with FD-CF enzymes.

    Fig. S5. Schematic of RPA reaction.

    Fig. S6. Detailed steps for isolating genomic DNA from fruits for environmental sensing activity.

    Table S1. Library of proteins and toehold switches that enable visual, olfactory, and tactile outputs for educational engagement.

    Table S2. FD-CF reactions allow for inexpensive classroom synthetic biology education kits.

  • Supplementary Materials

    This PDF file includes:

    • Fig. S1. Quantification of all proteins expressed in FD-CF.
    • Fig. S2. Fluorescent proteins expressed in the PURE and crude extract systems.
    • Fig. S3. Quantitative analysis of fluorescent proteins.
    • Fig. S4. Representative scanning electron microscopy images of hydrogel ultrastructures generated with FD-CF enzymes.
    • Fig. S5. Schematic of RPA reaction.
    • Fig. S6. Detailed steps for isolating genomic DNA from fruits for environmental sensing activity.
    • Table S1. Library of proteins and toehold switches that enable visual, olfactory, and tactile outputs for educational engagement.
    • Table S2. FD-CF reactions allow for inexpensive classroom synthetic biology education kits.

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