Background and Motivation
In the near future, biological circuits will be much more
modular and
sophisticated than they are now, with a ten-fold
smaller nucleotide footprint.
The Enabling Technology: Toehold-Mediated Strand Displacement
A
gate strand and
output strand exist as a complex that is
partially bound through complementary Watson-Crick base-pairing within the S2 binding domain. The gate strand also contains an
open, unbound domain called a
toehold region, T*. An input strand with a free complementary toehold region, T, can bind to the toehold region on the gate strand, and subsequently displace the output strand to yield an input-gate complex. This is called a
toehold-mediated strand displacement reaction. The output strand is used as an input for a downstream gate-output complex.
Background
Qian and Winfree (
Science 2011) utilized DNA computation to create AND and OR logic gates
in vitro. They constructed a sophisticated binary square root circuit using these gates:
Each of these:
undergoes the same
toehold-mediated strand displacement reaction. These reactions are fully modular and can be scaled to circuits of any degree of sophistication.
Motivation for Bringing Strand Displacement to Mammalian Synthetic Biology
- More sophisticated circuits with smaller nucleotide footprint
A traditional NOT gate is ~1000 bp, whereas our strand displacement NOT gate is ~ gate is ~100 bp.
- Simple combinatorial design space
With 4 bases, we can create a nearly infinite number of orthogonal sequences leading to orthogonal parts.
- Ease of composition
The input motif matches the output motif allowing for modular cascading reactions.
- Tunability
We can set arbitrary digital signal thresholds by varying the concentration of circuit species. We can also achieve signal amplification by including a fuel molecule.
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