REAGENT or RESOURCE | SOURCE | IDENTIFIER |
---|---|---|
Bacterial and virus strains | ||
E.coli: BL21(DE3) Competent cells | Novagen | Cat#69450–3 |
E.coli: DH5α Competent cells | ThermoFisher | Cat#18265017 |
E.coli: Turbo Competent cells | Weidi | Cat#DL1081 |
Chemicals, peptides, and recombinant proteins | ||
ULP1 | Home-made | N/A |
T7 RNA polymerase | Home-made | N/A |
Urea | Sangon Biotech | CAS: 57-13-6 Cat#A610148-0500 |
Diethyl pyrocarbonate | Sangon Biotech | CAS: 1609-47-8 Cat#B600154-0100 |
40% acrylamide and bis-acrylamide solution, 29:1 | Sangon Biotech | Cat#B546013–0500 |
Critical commercial assays | ||
PureLink HiPure Plasmid Megaprep Kit | ThermoFisher | Cat#K210008 |
Deposited data | ||
Coordinate of LshCas13a-crRNA-anti-tag RNA ternary complex | This paper | PDB: 7DMQ |
Density map of LshCas13a-crRNA-anti-tag RNA ternary complex | This paper | EMDB: EMD-30767 |
Recombinant DNA | ||
pRSF-Duet-1-His6-SUMO-LshCas13a, wild-type and various mutants | This paper | N/A |
pRSF-Duet-1-His6-SUMO-LbuCas13a, wild-type and various mutants | This paper | N/A |
pUT7-LshCas13a crRNA, wild-type and mutant | This paper | N/A |
pUT7-LbuCas13a crRNA, wild-type and mutant | This paper | N/A |
pUT7-target RNA (RNA1–6, 21-spacer RNA) | This paper | N/A |
pUT7-non-target RNA | This paper | N/A |
pCDF-Duet-1-LshCas13a-CRISPR, wild-type and various mutants | This paper | N/A |
pRSF-Duet-1-LbuCas13a-CRISPR, wild-type and various mutants | This paper | N/A |
pBR322-EYFP, with or without anti-tag sequence | This paper | N/A |
Oligonucleotides | ||
56-nt LshCas13a crRNA: GGCCACCCCAAUAUCGAAGGGGACUAAAACUAGAUUGCUGUUCUACCAAGUAAUCCAU | This paper | N/A |
57-nt LbuCas13a crRNA: GGACCACCCCAAAAAUGAAGGGGACUAAAACUAGAUUGCUGUUCUACCAAGUAAUCCAU | This paper | N/A |
50-nt LbuCas13a crRNA: GGACCACCCCAAAAAUGAAGGGGACUAAAACUAGAUUGCUGUUCUACCAAGU | This paper | N/A |
Target RNA1: GGGAAGUUCAACUCUUUAUGUAUUGAUCUUCCAAAAUauggauuacuugguagaacagcaaucuaCUC | This paper | N/A |
Target RNA2: GGGAAGUUCAACUCUUUAUGUAUUGAUCUUCCAAAAUauggauuacuugguagaacagcaaucuaGUUUUCUC | This paper | N/A |
Target RNA3: GGGAAGUUCAACUCUUUAUGUAUUGAUCUUCCAAAAUauggauuacuugguagaacagcaaucuaGUUUUAGUCUC | This paper | N/A |
Target RNA4: GauggauuacuugguagaacagcaaucuaCAAAAUCA | IDT | N/A |
Target RNA5: GauggauuacuugguagaacagcaaucuaGUUUUUCA | IDT | N/A |
Target RNA6: GauggauuacuugguagaacagcaaucuaGUUUUAGU | IDT | N/A |
21-nt Target RNA without anti-tag: GacuugguagaacagcaaucuaCAAAAUCA | IDT | N/A |
21-nt Target RNA with anti-tag: GacuugguagaacagcaaucuaGUUUUAGU | IDT | N/A |
102-nt non-target RNA: GGAUAACUCAAUUUGUAAAAAAGUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUC | This paper | N/A |
Software and algorithms | ||
Coot | Emsley et al., 2010 |
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot; RRID:SCR_014222 |
Phenix | Adams et al., 2010 |
https://www.phenix-online.org; RRID: SCR_014224 |
SerialEM data collection software | Mastronarde, 2005 |
https://bio3d.colorado.edu/SerialEM/; RRID: SCR_017293 |
MotionCor2 | Zheng et al., 2017 |
https://msg.ucsf.edu/em/software/motioncor2.html; RRID: SCR_016499 |
CTFFIND4 | Rohou and Grigorieff, 2015 |
https://grigoriefflab.janelia.org/ctffind4/; RRID: SCR_016732 |
RELION | Scheres, 2012 |
https://www3.mrc-lmb.cam.ac.uk/relion//index.php?title=Main_Page%2F; RRID: SCR_016274 |
ResMap | Kucukelbir et al., 2014 | http://resmap.sourceforge.net/ |
USCF Chimera | Pettersen et al., 2004 |
https://www.cgl.ucsf.edu/chimera/; RRID: SCR_004097 |
PyMOL | The PyMOL Molecular Graphics System, Version 2.2.3, Schrodinger, LLC |
https://pymol.org/2/; RRID: SCR_000305 |
CueMol | Version 2.2.3.434 |
http://www.cuemol.org; RRID: SCR_019052 |
Clustal Omega | Madeira et al., 2019 |
https://www.ebi.ac.uk/Tools/msa/clustalo/; RRID: SCR_001591 |
PRISM | Version 7.0 |
https://www.graphpad.com/scientific-software/prism/; RRID: SCR_002798 |
Other | ||
Amicon concentrators (30K) | Millipore | Cat#UFC903024 |
HisTrap FF (5 ml) | GE Healthcare | Cat#17-5255-01 |
HiTrap Heparin HP (5 ml) | GE Healthcare | Cat#17-0407-03 |
HiLoad 16/600 Superdex 200 pg | GE Healthcare | Cat#28989335 |
Superdex 200 10/300 GL | GE Healthcare | Cat#17517501 |
UltrAufoil R1.2/1.3 300 mesh grids | Quantifoil | Cat# BQRU1.2/1.3–3A-B |
Whatman Elutrap electroelution system | Sigma-Aldrich | Cat#WHA10447700 |