Project Description
Current biosensors are limited in the sense that they produce digital outputs (either 0 or 1 output) in the presence of an inducer. In order to create a more useful biosensor, analog devices with wider ranges of outputs are necessary. In contrast to digital sensors, an analog device can measure an inducer across a spectrum; for example, an analog device could be used to pinpoint the concentration of iron in groundwater, whereas digital devices could only register whether the concentration exceeded a pre-defined threshold amount.
Our device, the bacterial tape recorder, will generate such analog outputs by converting chemical inputs into DNA based memory. Using the SCRIBE (Synthetic Cellular Recorders Integrating Biological Events) system developed by Timothy Lu’s lab at MIT, we aim to standardize a device that can characterize the intensity of and duration of events and store them for later retrieval. The SCRIBE system works by integrating plasmid DNA, later becoming specifically ssDNA into genomic DNA upon stimulation. By population analysis of cells that express the analog marker, we will use this system to monitor hazardous environmental factors such as heavy metals, which are known to be detrimental to groundwater in urban areas and developing countries.
We aim to introduce a degree of modularity that will allow future synthetic biologists to choose what inputs are the stimulus for analog recording.
Project motivation
When brainstorming project ideas, we went over what typically motivates an iGEMmer: Saving the world, making food available to all, fixing the environment, making really cool looking plates with an array of different chromoproteins. But we realized a central theme in all of our projects, there was no concrete way of telling whether or not a cell carried the memory of being manipulated to perform such tasks. An advisor suggested that we look into a new analog way to store cellular memory: SCRIBE. We didn’t really contemplate any other project after that, all we could think about is how we could manifest all of our project ideas using SCRIBE. After researching different storage capabilities using synbio, we realized that SCRIBE truly did have merit, and could possibly be a tool that our iGEM progeny could use!
Defining the Problem
We are all comfortable with how modern memory works using computers. Memory is stored as binary bits: 0’s and 1’s. We call this digital memory, and biologists can implement synthetic digital memory to store bits of information. Two main methods are epigenetic-based devices and recombinase-based devices. Both incorporate digital information, however we aim to introduce an analog set up for “tape-recording” memories.
Epigenetic switches
Epigenetic switches typically record binary bits through expression levels - 0 referring to no expression and 1 referring to expression. Epigenetic memory devices have a few problems however. They require orthogonal transcription factors, and they can lose their state due to fluctuations in the environment or because the cell dies
Recombinase
Recombinase-based switches are different than epigenetic switches in that they are able to record data directly into the DNA of the cell. Binary bits are represented by the orientation of large stretches of DNA. However, recombinase-based switches fail to utilize the full recording power of DNA, because they require tedious engineering of these recombination sites in advance, and hundreds of basepairs are used to record a single bit. We see that the recording capacity of these devices is exhausted within a few hours. Furthermore, the scalability of these devices is limited by the number of orthogonal recombinases that exist as well.
Enter SCRIBE
In an attempt to address the current limitations in current biological systems, Dr. Fahim Farzadfard and Dr. Timothy Lu from MIT developed SCRIBE: an inducible process for creating and inserting single-stranded DNA into a host’s genome.
