Modular, programmable RNA sensing using ADAR editing in living cells.
Kaseniit KE, Katz N, Kolber NS, Call CC, Wengier DL, Cody WB, Sattely ES, Gao XJ
Nat Biotechnol. 2022 Oct 5. pii: 10.1038/s41587-022-01493-x. doi: 10.1038/s41587-022-01493-x.
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Plasmids from Article
| ID | Plasmid | Purpose |
|---|---|---|
| 191138 | EK0208 CMV-TO-BFPmut-stop-t70587 (FLP-IN) | Expression of Trigger 1 in 3' UTR of an inactive BFP in mammalian cells |
| 191139 | EK0211 CMV-TO-BFPmut-stop-t17d9b (FLP-IN) | Expression of Trigger 2 in 3' UTR of an inactive BFP in mammalian cells. Used as second input in OR, AND gates |
| 191140 | EK0285 SFFV-mCherry-SG(s70587)SG-EGFP (FLP-IN) | Expression of Sensor 1 (for EK0208) in mammalian cells; mCherry marker, EGFP output. |
| 191141 | EK0294 SFFV-mCherry-SG(s70587-W)SG-EGFP (FLP-IN) | Positive control for Sensor 1 (EK0285) where the TAG stop codon is replaced with TGG tryptophan codon |
| 191142 | EK0289 SFFV-mCherry-SG(s17d9b)SG-EGFP (FLP-IN) | Expression of Sensor 2 (for EK0211) in mammalian cells; mCherry marker, EGFP output. |
| 191143 | EK0290 SFFV-mCherry-SG(s70587-AND-s17d9b)SG-EGFP (FLP-IN) | Expression of Sensor for (1 AND 2) "EK0208 AND EK0211" in mammalian cells; mCherry marker, EGFP output. |
| 191144 | EK0301 SFFV-mCherry-SG(Bdnf.s1)SG-EGFP (FLP-IN) | Expression of Sensor for murine Bdnf 3' UTR in mammalian cells; mCherry marker, EGFP output; 90 bp long |
| 191145 | EK0307 CMV-TO-BFPmut-stop-3UTR(Bdnf) (FLP-IN) | Expression of a synthetic construct with 3' UTR of murine Bdnf in the 3' UTR of an inactive BFP in mammalian cells. |
| 191146 | EK0304 CMV-TO-BFPmut-stop-Bdnf.t1 (FLP-IN) | Expression of only the trigger sequence for Bdnf.s1 (EK0301) in mammalian cells |
| 191147 | EK0425 CMV-TO-BFPmut-stop-Bdnf.t+54@202 (FLP-IN) | Expression of the sequence matching the 54 extra bases in EK0362 in mammalian cells |
| 191148 | EK0312 pAAV-EF1a-DIO-EYFP-WPRE-HGHpA | AAV expression of a Cre reporter with EYFP output; derived from a gift from prof. Liqun Luo |
| 191149 | EK0313 SFFV-mCherry-SG(s70587)SG-Cre (FLP-IN) | Expression of Sensor 1 (for EK0208) in mammalian cells; mCherry marker, Cre output derived from a gift from prof. Liqun Luo |
| 191150 | EK0341 SFFV-mCherry-SG(Bdnf.s1L153)SG-EGFP (FLP-IN) | Expression of a 153 bp long sensor for murine Bdnf 3' UTR in mammalian cells |
| 191151 | EK0354 SFFV-mCherry-SG(Bdnf.s1L72)SG-EGFP (FLP-IN) | Expression of a 72 bp long sensor for murine Bdnf 3' UTR in mammalian cells |
| 191152 | EK0358 SFFV-mCherry-SG(Bdnf.s1L36)SG-EGFP (FLP-IN) | Expression of a 36 bp long sensor for murine Bdnf 3' UTR in mammalian cells |
| 191153 | EK0362 SFFV-mCherry-SG(Bdnf.s1L36+54@202)SG-EGFP (FLP-IN) | Mammalian expression of a 90 bp (36+54) long sensor for murine Bdnf 3' UTR where the trigger sequence is split |
| 191154 | EK0379 CMV-TO-EGFP-stop-t70587 (PB) | Expression of Trigger 1 in the 3' UTR of EGFP in mammalian cells; used to make a cell line to study sensors for integrated 3' UTR or CDS triggers; expression is inducible with doxycycline due to CMV-TO promoter. |
| 191155 | EK0445 SFFV-mCherry-SGc(DNAJB1.s1)cSG-EGFP-(3xMS2) (FLP-IN) | Expression of a sensor for human DNAJB1 (hsp40) 3' UTR in mammalian cells; mCherry marker, EGFP output, three MS2 sequences in 3' UTR |
| 191156 | EK0493 SFFV-mCherry-SGc(GAPDH.s1)cSG-EGFP-(3xMS2) (FLP-IN) | Expression of a sensor for GAPDH 3' UTR in mammalian cells; mCherry marker, EGFP output, three MS2 sequences in 3' UTR |
| 191157 | EK0387 SFFV-mTagBFP2-SGc(Bdnf.s1)cSG-mCherry (FLP-IN) | Expression of a sensor for murine Bdnf 3' UTR in mammalian cells; mTagBFP2 marker, mCherry output; 90 bp long |
| 191158 | EK0344 SFFV-mCherry-SG(Bdnf.s1)SG-Cre (FLP-IN) | Expression of a sensor for murine Bdnf 3' UTR in mammalian cells; mCherry marker, Cre output; 90 bp long |
| 191159 | EK0393 SFFV-mTagBFP2-SGc(EGFP.s2)cSG-mCherry (FLP-IN) | Expression of a sensor for EGFP CDS in mammalian cells; mTagBFP2 marker, mCherry output |
| 191160 | EK0325 SFFV-mCherry-SG(EGFP.s2)SG-Cre (FLP-IN) | Expression of a sensor for EGFP CDS in mammalian cells; mCherry marker, Cre output |
| 191161 | EK0441 CMV-TO-BFPmut-stop-EGFP.t2 (FLP-IN) | Expression of a trigger sequence from EGFP CDS in 3' UTR context in mammalian cells |
| 191162 | EK0423 SFFV-mTagBFP2-SGc(s70587)cSG-mCherry (FLP-IN) | Expression of a sensor for synthetic sequence 1 (EK0208) in mammalian cells; mTagBFP2 marker, mCherry output |
| 191163 | EK0438 SFFV-mCherry-SGc(s70587)cSG-EGFP-(3xMS2) (FLP-IN) | Expression of a sensor for synthetic sequence 1 (EK0208) with three MS2 sequences in the 3' UTR in mammalian cells. Compared to EK0285, also has additional restriction sites around the sensor sequence. Recommended for the basis for cloning new sensors for use with MCP-ADAR(DD). HindIII & MluI can be used to swap out marker (mCherry). (KpnI or BamHI) and (BshTI or BcuI) can be used to swap out sensor sequence (s70587). XhoI and ApaI can be used to swap out output (EGFP). |
| 191164 | EK0409 SFFV-mCherry-SGc(s70587)cSG-EGFP (FLP-IN) | Similar to EK0285 but has additional restriction sites around the sensor sequence. Recommended for cloning new sensors when the presence of MS2 sequences are not relevant (use EK0438 if MS2 sequences |
| 191165 | NK10 SFFV-mCherry-SG(s70587-3xMS2)SG-EGFP (FLP-IN) | Expression of a sensor for synthetic sequence 1 (EK0208) with three MS2 sequences in the coding sequence in mammalian cells. Similar to EK0438, but with MS2 sequences directly after the sensor sequence, rather than 3' UTR |
| 191166 | NSK025 CMV-TO-EGFP:c.637A>G(N213D; CCA>CCG)-stop-t70587 (PB) | Mammalian expression of a EGFP mutant N213D derived from EK0379. |
| 191167 | NSK021 CMV-TO-p53R248Q (FLP-IN) | Expression of human p53 mutant R248Q in mammalian cells |
| 191168 | NSK026 CMV-TO-p53R248W (FLP-IN) | Expression of human p53 mutant R248W in mammalian cells |
| 191169 | NSK024 SFFV-mCherry-SG(p53R248Q.s2)SG-EGFP (FLP-IN) | Expression of a sensor for p53 mutant R248Q in mammalian cells; mCherry marker, EGFP output |
| 191170 | EK0395 mCherry-SG(s70587)SG-EGFP (pEAQ) | EK0285 in plant-expressable format: Sensor 1 (for EK0208); mCherry marker, EGFP output. |
| 191171 | EK0396 BFPmut-stop-t70587 (pEAQ) | EK0208 in plant-expressable format; Trigger 1 in 3' UTR of an inactive BFP |
| 191172 | EK0397 3FLAG-ADAR1-p150-HIS (pEAQ) | Human ADAR1, p150 isoform in plant-expressable format. |
| 191173 | CC0101 BFPmut-stop-Bdnf.t1 (pEAQ) | An orthogonal trigger sequence used in plant experiments, derived from the 3' UTR of murine Bdnf |
| 191174 | EK0209 CMV-TO-mCherry-SG(s70587)SG-EGFP (FLP-IN) | Mammalian expression of EK0285 with CMV-tetO promoter instead of SFFV. |
| 191175 | EK0261 CMV-TO-mCherry-SG(s70587)SG-fs(EGFP) (FLP-IN) | Mammalian expression of EK0209 with frameshift mutation (EGFP is frameshifted). |
| 191176 | EK0544 CMV-TO-mCherry-SG(s70587-dblstop)SG-EGFP (FLP-IN) | Mammalian expression of EK0209 with a second stop codon. |
| 191177 | EK0545 SFFV-mCherry-SGc(GAPDH.s1)cSG-fs(EGFP)-(3xMS2) (FLP-IN) | Mammalian expression of EK0493 with frameshift mutation (EGFP is frameshifted). |
| 191178 | EK0546 SFFV-mCherry-SGc(GAPDH.s1-dblstop)cSG-EGFP-(3xMS2) (FLP-IN) | Mammalian expression of EK0493 with second stop codon. |
| 191179 | EK0302 SFFV-mCherry-SG(Bdnf.s2)SG-EGFP (FLP-IN) | Negative control sensor in human cells. |
| 191180 | EK0303 SFFV-mCherry-SG(Bdnf.s3)SG-EGFP (FLP-IN) | Negative control sensor in human cells. |
| 191181 | EK0494 SFFV-mCherry-SGc(CFL1.s1)cSG-EGFP-(3xMS2) (FLP-IN) | Expression of CFL1 sensor in mammalian cells |
| 191182 | EK0498 SFFV-mCherry-SGc(ACTB.s1)cSG-EGFP-(3xMS2) (FLP-IN) | Expression of EACTB sensor in mammalian cells |
| 191183 | EK0499 SFFV-mCherry-SGc(PPIB.s1)cSG-EGFP-(3xMS2) (FLP-IN) | Expression of PPIB sensor in mammalian cells |
| 191184 | EK0500 SFFV-mCherry-SGc(RPLP1.s1)cSG-EGFP-(3xMS2) (FLP-IN) | Expression of RPLP1 sensor in mammalian cells |
| 191185 | EK0501 SFFV-mCherry-SGc(MYC.s1)cSG-EGFP-(3xMS2) (FLP-IN) | Expression of MYC sensor in mammalian cells |