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. Author manuscript; available in PMC: 2024 Jun 1.
Published in final edited form as: Mol Cell. 2023 Jun 1;83(11):1827–1838.e6. doi: 10.1016/j.molcel.2023.05.005

Key resources table

REAGENT or RESOURCE SOURCE IDENTIFIER
Bacterial and virus strains
Escherichia coli DH5α J. Peters Lab N/A
Escherichia coli BW27783 attTn7::miniTn7(miniTn6900(kanR)) J. Peters Lab, Pettasi et al., 2020 MTP997
Escherichia coli BL21-AI Invitrogen Cat# C607003
Escherichia coli CW51 J. Peters Lab JP606
T7 Express Competent Escherichia coli NEB Cat# C2566H
Critical commercial assays
Q5® High-Fidelity DNA polymerase NEB Cat# M0491L
NEBuilder® HiFi DNA Assembly Master Mix NEB Cat# E2621L
His-Pur™ Ni-NTA resin ThermoFisher Cat# 88221
CloneJET PCR Cloning Kit ThermoFisher Cat# K1231
GeneJET Gel Extraction Kit ThermoFisher Cat# K0691
T4 DNA Ligase ThermoFisher Cat# EL0011
Deposited data
Full R-loop Cascade-TniQ complex This paper PDB: 7U5D EMDB: 26348
Partial R-loop Cascade-TniQ complex This paper PDB: 7U5E EMDB: 26349
Custom code for Rosetta simulations and PAM analyses and plots This paper Mendeley Data DOI: 10.17632/gjgspgnxvy.1
NGS data for PAM analysis This paper, NCBI Sequence Read Archive Bioproject: PRJNA935286
Oligonucleotides
Oligo_cryo1, CCGCAAGAGGATGATTCGGGTGCTTACCTCCTGACCTTCTTTAGTAGGTTCAACCCCTGATCGAGTGCCGGGATGT This paper N/A
Oligo_cryo2, TGGCCCCATCAGCCACATCCCGGCACTCGAAGTCCCCAACTTGGATGATTTCTTCCAGTCCTGGTAAGCACCCGAATCATCCTCTTGCGG This paper N/A
Oligo_cryo3, GGCTGATGGGGCCACCACCTTGCGCTCGTTCGCCAGCCAG This paper N/A
Oligo_cryo4, CTGGCTGGCGAACGAGCGCAAGGTGG This paper N/A
F_EMSA, ACCTGCAGGCATGCAAG This paper N/A
R_EMSA, /Cy5/GCAGTTAAGTGCCTGCTGGCGAGGAAGCGGAAGAG This paper N/A
DNA substrate for EMSA, Top_ffs_bubble_EMSA Cy3/GCGGCACAGGTCTCACGCGTTCGTCACTACCAGGACTGGAAGAAATCATCCAAGTTGGGGACTTCGAGTGCCGGGATGTGGCTGATGGGGCCACCACCTGTTTCTGCACTTCAACCAGTTAGCCTCCAGAGCAACCGAGACCCGCTGCTG This paper N/A
DNA substrate for EMSA, Bottom_ffs_bubble_EMSA CAGCAGCGGGTCTCGGTTGCTCTGGAGGCTAACTGGTTGAAGTGCAGAAACAGGTGGTGGCCCCATCAGCCACATCCCGGCACTCGATTATTTTTTTAATTTATTAAATAATTTTATTAGGTAGTGACGAACGCGTGAGACCTGTGCCGC This paper N/A
Recombinant DNA
All plasmids used and constructed in this study This paper See Table S2
Software and algorithms
Warp Tegunov et al., 201935 http://www.warpem.com/warp/
cryoSPARC Punjani et al., 201736 https://cryosparc.com/
Topaz Bepler et al., 201937 https://cb.csail.mit.edu/cb/topaz/
RELION Scheres, 201238 https://relion.readthedocs.io/en/release-4.0/
cryoSPARC 3DVA Punjani et al., 202139 https://cryosparc.com/
UCSF Chimera Pettersen et al., 200442 https://www.cgl.ucsf.edu/chimera/
UCSF ChimeraX Goddard et al., 201843 https://www.cgl.ucsf.edu/chimerax/
I-TASSER Yang et al., 201545 https://zhanggroup.org/I-TASSER/
Coot Emsley et al., 201046 https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/
RosettaES Frenz et al., 201747 https://dimaiolab.ipd.uw.edu/software/
MolProbity Williams et al., 201848 http://molprobity.biochem.duke.edu/
Phenix Afonine et al., 201849 https://phenix-online.org/
Biopython Cock et al., 200962 https://biopython.org/
Matplotlib Hunter, 200763 https://matplotlib.org/
Seaborn Waskom, 202164 https://seaborn.pydata.org/
Krona Ondov et al., 201165 https://github.com/marbl/Krona/wiki
WebLogo 3 Crooks et al., 200467 http://weblogo.threeplusone.com/
Cd-hit Li et al., 200668 https://github.com/weizhongli/cdhit
MUSCLE Edgar, 200470 http://www.drive5.com/muscle