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ENGINEERING ORTHOGONAL CONSTITUTIVELY INACTIVE
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cgRNA:trigger:dCas9:target complex
dCas9 ii)
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a Toehold switch cgRNA in bacteria (OFF ON logic)
Constitutively Inactive
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Figure 5.1: Constitutively inactive toehold switch cgRNAs (ON→OFF logic) with silencing dCas9 inE. coli. (a) Conditional logic: if X, then not Y. (b) Schematic of cgRNA mechanism. OFF state: the toehold switch cgRNA is constitutively inactive; the target-binding region (domain “u”; orange) is initially sequestered by a 50extension to inhibit recognition of target gene Y. ON state: in the presence of RNA trigger X, hybridization of the trigger to this 50extension (reaction arrow “i”) via the toehold region (blue) is intended to desequester the target-binding region and enable cgRNA direction of dCas9 function to target gene Y (reaction arrow “ii”).
state) were characterized using time course microplate fluorescence (Figure 5.3). In comparison to the ideal ON state of the standard gRNA, we see room for improve- ment for each of the four cgRNA/trigger pairs characterized, with distinctly poorer performance of cgRNA D + trigger XD. On this basis, the three cgRNA/trigger pairs A, B, and C were selected for full experimental characterization.
Conditional response of the toehold switch mechanism was characterized by flow cytometry in E. coliexpressing silencing dCas9 and a fluorescent protein reporter (mRFP) as the target gene Y (Figure 5.4a). The toehold switch cgRNA exhibits a conditional OFF→ON response to the expression of RNA trigger X, with OFF state imperfect relative to the ideal OFF state (no-target gRNA control) and the ON state imperfect relative to the ideal ON state (standard gRNA control). For a library of three orthogonal toehold switch cgRNA/trigger pairs, we observe a median≈3-fold OFF→ON conditional response to the expression of the cognate trigger and median crosstalk of≈20% between noncognate cgRNA/trigger combinations. Recently, Siu and Chen demonstrated a median≈6.6-fold OFF→ON conditional response using
Step 0Xn Step 1n Crosstalkp,n
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cgRNA (Gn) trigger (Xn) cgRNA:trigger (Gn·Xn)
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w = 200 w = 200 w = 1
w = 50 (4nt loop) w = 100 w = 100 w = 300
w = 25
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w = 1
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w = 1 Constrained by target gene
Constrained by dCas9 Constrained by synthetic terminator Complementarity between Gn and Xn
b
Figure 5.2: Target test tubes for sequence design of orthogonal toehold switch cgR- NAs. (a) Top: Target test tube schematics. Bottom: Target test tube details. Each target test tube contains the depicted on-target complexes (each with the depicted target structure and target concentration) and the off-target complexes listed in the table (each with vanishing target concentration). The on-target structures depicted above are used in the mechanism schematic of Figure 5.1. To simultaneously de- signN orthogonal systems, the total number of target test tubes is|Ω| = N2+2N. Lmax = 2 for all tubes. Design conditions: RNA in 1 M Na+ at 37 ◦C.38 (b) Nu- cleotide defect weights for sequence design of toehold switch cgRNAs. Nucleotides in a given sequence domain within a given complex are assigned a defect weightw as depicted.
cgRNA D + trigger XD (ON state) cgRNA C + trigger XC (ON state) Standard gRNA (ideal ON) cgRNA B + trigger XB (ON state) cgRNA A + trigger XA (ON state) No-target gRNA (ideal OFF)
Time post dCas9 induction (h)
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Poor cgRNA D ON state
Figure 5.3: Characterization of ON state of four orthogonal toehold switch cgRNAs inE. coli. Fluorescence traces of cgRNAs A–C with cognate trigger are overlapping, while cgRNA D with cognate trigger produces significantly higher fluorescence (further from ideal ON standard gRNA). Time course microplate fluorescence data normalized by A600. Mean±estimated standard error over N = 3 replicate wells.
toehold switch cgRNAs with subtly different structural details in the sequestration of the target-binding region.98
In an effort to improve performance of the toehold switch mechanism, we investi- gated the effect of the cognate trigger domain length on the activity of the cgRNA ON state. The effect of trigger domain length on ON state activity was characterized by time course microplate fluorescence for strains constitutively expressing toehold switch cgRNA A, and cognate trigger XA with truncations of the strand displace- ment domain “u” (0-20 nt stem trigger, Figure 5.5a) and truncations or extension of the toehold domain “d*” (0-20 nt toehold trigger, Figure 5.5b; 20 nt extended toehold domain strain also included a 5 nt complementary extension for cgRNA toehold domain “d”; see Figure 5.1b for domain labeled mechanism schematic).
As expected, we observed a significant increase in fluorescence with expression of the cognate trigger lacking the strand displacement domain (i.e., hybridization toehold domain only is insufficient to produce the observed OFF→ON conditional response; cgRNA A + 0 nt stem trigger, Figure 5.5a). Somewhat surprisingly, a strand displacement domain of only 5 nt (cgRNA A + 5 nt stem trigger) resulted in a significant decrease in fluorescence, and an OFF→ON conditional response comparable to that of the full-length strand displacement domain (cgRNA A + 20 nt stem trigger). This suggests that the sequestration of the target-binding region by the 20 nt reverse complementary sequence of the 50 extension is marginal, and hence that the cgRNA OFF state could be improved through extension of the target-
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Figure 5.4: Programmable conditional function of three orthogonal toehold switch cgRNAs (OFF→ON logic) with silencing dCas9 inE. coli. (a) Expression of RNA trigger X toggles the cgRNA from OFF→ON, leading to a decrease in fluorescence.
Single-cell fluorescence intensities via flow cytometry. Induced expression (aTc) of silencing dCas9 and constitutive expression of mRFP target gene Y and either: no- target gRNA that lacks target-binding region (ideal OFF state), cgRNA (OFF state), cgRNA + RNA trigger X (ON state), or standard gRNA (ideal ON state). Aut- ofluorescence (AF): cells with no mRFP. (b) Programmable conditional regulation using three orthogonal cgRNAs (A, B, and C). Left: Raw fluorescence depicting OFF→ON conditional response to cognate trigger (fold change = OFF/ON = [(no trigger)−AF]/[(cognate trigger)−AF]). Right: Normalized fluorescence depicting orthogonality between noncognate cgRNA/trigger pairs (crosstalk = [(noncognate trigger)−(no trigger)]/[(cognate trigger)−(no trigger)]). Bar graphs depict mean± estimated standard error calculated based on the mean single-cell fluorescence over 20,000 cells for each ofN =3 replicate wells (fold change and crosstalk calculated with uncertainty propagation).
binding region (orange domain “u” in Figure 5.1b). Truncation of trigger strand displacement domains to 5 nt could potentially yield a significant improvement to the orthogonality of the library of cgRNAs, as the strand displacement domain “u” is shared between all triggers and may be a major contributor to crosstalk. Truncation of the toehold domain by only three nucleotides (cgRNA A + 12 nt toehold trigger, Figure 5.5b) results in a significant loss of cgRNA function, while a 5 nt extension of both trigger and cgRNA toehold (cgRNA A-20 + 20 nt toehold trigger) performs no better than the 15 nt toehold.
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cgRNA A + 0 nt stem trigger cgRNA A + 5 nt stem trigger Standard gRNA (ideal ON) cgRNA A + 15 nt stem trigger cgRNA A + 20 nt stem trigger
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cgRNA A + 0 nt toehold trigger cgRNA A + 2 nt toehold trigger Standard gRNA (ideal ON) cgRNA A + 5 nt toehold trigger cgRNA A + 8 nt toehold trigger cgRNA A + 12 nt toehold trigger cgRNA A + 15 nt toehold trigger cgRNA A-20 + 20 nt toehold trigger
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Figure 5.5: Characterization of toehold switch cgRNA with varied trigger domain dimensions. (a) Performance of cgRNA ON state with 0-20 nt strand displacement domain (truncation of domain “u”). Triggers with 0-20 nt strand displacement domain were expressed constitutively with the the previously characterized cognate cgRNA (with 15 nt toheold domain “d”, 20 nt sequestration domain “u*”). A 5 nt strand displacement domain was sufficient for achieving the observed ON state. (b) Performance of cgRNA ON state with 0-20 nt trigger toehold region (truncation of trigger domain “d*”, or extension of trigger domain “d*” and cgRNA domain “d”). Triggers with 0-15 nt toehold domains were expressed constitutively with the previously characterized cognate cgRNA A (with 15 nt cgRNA domain
“d”). Trigger with an extended 20 nt toehold domain was expressed constitutively with an extended-toehold cognate cgRNA (20 nt cgRNA domain “d”). Trigger toeholds of length 0-12 nt did not toggle the cgRNA from OFF→ON. The OFF→ON conditional response with a 20 nt cgRNA/trigger toehold is comparable to the previously characterized 15 nt toehold. Time course microplate fluorescence data normalized by A600. Mean±estimated standard error over N = 3 replicate wells.
Unlike the splinted switch mechanism for ON→OFF logic, toehold switch cgR- NAs for OFF→ON logic are not allosteric, as the cgRNA initially down-regulates cgRNA:dCas9 function by sequestering the target-binding region with a portion of the trigger-binding region (orange domain “u*” in Figure 5.1b), resulting in only partial sequence-independence between trigger X and target gene Y (as “u” is a
subsequence of both X and Y). This partial sequence dependence is not necessarily limiting for synthetic biology applications where the trigger can be rationally de- signed and expressed exogenously, but does pose a limitation in situations where X and Y are both endogenous sequences. Another potential limitation for the de- tection of endogenous sequences is the likely continued association of trigger with cgRNA in complex with dCas9 (i.e., the cgRNA is bound by trigger in its active conformation), as the presence of a long (e.g., hundreds or thousands of nucleotides for mRNA) trigger may inhibit the downstream function of the Cas protein effector.
This is of particular concern in eukaryotes, in which the active transport of mRNAs out of the nucleus will potentially sequester active cgRNA:trigger:effector complex from nuclear dsDNA targets. The relatively poor conditional response as compared to existing ON→OFF mechanisms (including the splinted switch mechanism of Chapter 4), the partial sequence dependence of trigger X and target Y, and poten- tial issues for use of the toehold switch cgRNA with mRNA triggers motivate the development of an improved constitutively inactive cgRNA with a fundamentally different mechanism. However, the library of toehold cgRNAs developed exhibited the intended OFF→ON conditional function with selectivity for cognate trigger, and, with potential improvements to orthogonality, may prove useful as regulators for synthetic biology.
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