Key resources table.
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Gene (Methanosarcina mazei) | Top6A | Gift from James Berger, Johns Hopkins University |
NCBI Gene ID: 1480760 | |
| Gene (Methanosarcina mazei) | Top6B | Gift from James Berger, Johns Hopkins University |
NCBI Gene ID: 1480759 | |
| Strain, strain background (E. coli) | Rosetta 2 (pLysS) | Novagen | ||
| Genetic reagent (E. coli) | pBR322* | Inspiralis | ||
| Genetic reagent (E. coli) | pET28a | EMD Millipore | CAT#:69,865 | |
| Genetic reagent (E. coli) | pBlueScript II KS(+) | Agilent | CAT#:212,207 | |
| Recombinant DNA reagent | Top6AB dual expression vector | PMID:17603498 | Corbett et al., 2007 | |
| Antibody | Anti-digoxigenin(SheepPolyclonal) | Roche | Roche Cat# 11333089001, RRID:AB_514496 | Reconstituted in 1 x Phosphatebuffered saline (0.6 µg) |
| Commercial assay or kit | PCR DNA purification kit | Qiagen | Qiagen Cat. #: 28,104 | |
| Other | Streptavidin coated magnetic beads (ø: 1 and 2.8 µm) | Invitrogen | Invitrogen Cat. #: 65,602 and 65,305 | |
| Chemical compound, drug | Phusion high-fidelity DNA polymerase | New England Biolabs | NEB Cat. #: M0530 | |
| Chemical compound, drug | T4 DNA ligase | Promega | Promega Cat. #: M1801 | |
| Chemical compound, drug | BsaI-HF | New England Biolabs | NEB Cat. #: R3535 | |
| Chemical compound, drug | Biotin-16-dUTP | Roche | Sigma Cat#:11093070910 | |
| Chemical compound, drug | Digoxigenin-11-dUTP | Roche | Sigma Cat#:11558706910 | |
| Sequence-based reagent | 5 kb DNA supercoil primer1 | Eurofin Genomics Seol and Neuman, 2011a |
5'- GCT GGG TCT CGG TTGTTC CCT TTA GTG AGG GTT AAT TG |
|
| Sequence-based reagent | 5 kb DNA supercoil primer2 | Eurofin Genomics Seol and Neuman, 2011a |
5'- GCT GGG TCT CGT GGT TTC CCTTTA GTG AGG GTT AAT TG |
|
| Sequence-based reagent | 3 kb DNA braid primer1 | Eurofin Genomics | 5’(2 x)biotin-GCTGGGTCTCGGTTGGAACTGCGACT GGATAGG |
|
| Sequence-based reagent | 3 kb DNA braid primer 2 | Eurofin Genomics | 5' (3 x) digoxigenin-GCTGGGTCTCGGTTGGATTACGCCA GTTGTACG |
|
| Sequence-based reagent | 5 kb DNA braid primer1 | Eurofin Genomics | 5’(2 x)biotin-CTTCCGCTTCCTCGCTCACTGACTC | |
| Sequence-based reagent | 5 kb DNA braid primer 2 | Eurofin Genomics | 5' (3 x) digoxigenin-CTGTTCATCCGCGTCCAGCTCGTTG | |
| Sequence-based reagent | Bio/Dig labelledPrimer1 | Eurofin Genomics Seol and Neuman, 2011a |
5’-GGA CCT GCT TTC GTT GTG GCG TAA TCA TGG TCA TAG |
|
| Sequence-based reagent | Bio/Dig labelledPrimer2 | Eurofin Genomics Seol and Neuman, 2011a |
5'- GGG TCT CGT GGT TTA TAG TCC TGT CGG GTT TC |
|
| Software, algorithm | LabVIEW, Instrument control software | National Instruments | NI Cat. #: 776678–35 | |
| Software, algorithm | Igor Pro 7,Data analysis | WaveMetrics | PMID:28069956 | |
| Software, algorithm | ImageJ, Data analysis | National Institutes of Health | ||
| Chemical compound, drug | Adenosine triphosphate (ATP) | MilliporeSigma | A2383 | |
| Chemical compound, drug | Nicotinamide adenine dinucleotide (NADH) | MilliporeSigma | 10107735001 | |
| Chemical compound, drug | Pyruvate Kinase/Lactic Dehydrogenase (PK/LDH) | MilliporeSigma | P0294 | |
| Chemical compound, drug | Phosphoenol-pyruvate (PEP) | MilliporeSigma | 10108294001 | |
| Other | Plate reader | BMG LabTech | CLARIOstar Plus | Used for the PK/LDH-coupled ATPase assay. |
| Software, algorithm | Microsoft Excel | RRID:SCR_016137 | Used for data analysis for the PK/LDH-coupled ATPase assay. |
|
| Software, algorithm | LAMMPS | https://www.lammps.org/ | Used for Molecular Dynamics Simulations |
|
| Software, algorithm | MATLAB | MathWorks | Used for analyses of Molecular Dynamics Simulations |