KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-digoxigenin (from sheep) | Roche | Cat# 11333089001, RRID:AB_514496 |
| Bacterial and Virus Strains | ||
| NEB 5-alpha Competent E. coli (High Efficiency) | NEB | Cat# C2987H |
| NEB Stable Competent E. coli (High Efficiency) | NEB | Cat# C3040H |
| Biological Samples | ||
| Topoisomerase yeast strain MATa pep4::HIS3 prb1::LEU2 bar1::HISG lys2::GAL1/10-GAL4 can1 ade2 trp1 ura3 his3 leu2-3112 | J. C. Wang Lab (Harvard University) | N/A |
| HeLa-S3 cells | National Cell Culture Center | HA.48 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Collodion solution | Sigma-Aldrich | Cat# 09986 |
| Silicone high-vacuum grease | Dow Corning | Part # 146355 D |
| Biotin-14-dATP | Invitrogen | Cat# 19524016 |
| Digoxigenin-11-dUTP | Roche | Cat# 11093088910 |
| dNTP Set 100 mM Solutions | Thermo Scientific | Cat# R0181 |
| ATP | Roche | Cat# 11140965001 |
| T4 DNA ligase | NEB | Cat# M0202S |
| Taq DNA Polymerase | NEB | Cat# M0273S |
| FastDigest BglI | Thermo Scientific | Cat# FD0074 |
| FastDigest BstXI | Thermo Scientific | Cat# FD1024 |
| Nt.BsmAI | NEB | Cat# R0121S |
| Beta-casein from bovine milk | Sigma-Aldrich | Cat# C6905 |
| Hela histone core | Brennan et al., 2016 | N/A |
| S. Cerevisiae topoisomerase II | This study | N/A |
| Oligonucleotides | ||
| Forward primer for making the biotin-labeled and digoxigenin-labeled adapters pUC57-F: GTAAAACGACGGCCAGTG |
IDT | N/A |
| Reverse primer for making the biotin-labeled and digoxigenin-labeled adapters pUC57-R: GGAAACAGCTATGACCATG |
IDT | N/A |
| The 197-bp repeat sequence of p197NRL-64ex with the 601 sequence underlined: GGGCGCCGCCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTGCATGTATTGAACACACCCCCTAACACACTACGACACCCC |
This study | N/A |
| The 482-bp low nucleosome affinity sequence of pNFRTC: GCCTGGGTGGCTTCATTCGTTCTTTTGTTCCTTATTTTGTTC CTTACTTAGTTGGTTATTTGCTTGTTTGGTTATTTATTTCGT TGGTTATTTGGTTAATTCCTT CTTTGCTTTCTTCATTCCTTT CTTGCTTTATTCCTTGTTTTTTTGGTTTCTTAGTTTCCTTTTC CCTAGAGGTAGCCAAAGTCTTTGCAACTAT ACTTTCAGCT CTGACAAATTTGTTCTTATTACIICICIIIIIIIIGATTTGT TCTTCCCTCTTTTTCTTAGCTAATTCTTGTCTTTCGATTCTA GTTCTATCAGCATTTCTTTATAAATCTATTTTTTTTTTTTTTT CGACACAAAATGTCTATTTCTTGGAGTGCTTACTCTTCTTT TTGTTTTTACCTTGTTTCAACTCGTTTAATCTATCAACTTTT TCCTTGATCCTTTCCAAAGATAATTTGACATCACCTTTTTG GCACTAGGTGCCACCGATGTGG |
This study | N/A |
| Recombinant DNA | ||
| p197NRL-64ex containing the 64 repeats of the Widom 601 sequence | This study | N/A |
| pNFRTC for making the multiple-label DNA end adapters | This study | N/A |
| pUC19 | New England Biolabs | Cat# N3041S |
| Software and Algorithms | ||
| LabVIEW VIs for instrument control, data acquisition, and data analysis | This study | N/A |
| MATLAB scripts for data analysis | This study | N/A |
| SeqBuilder (for DNA primer design) | DNASTAR | Version 11.2.1 (29) |
| Other | ||
| Microscope cover glass | Fisher Scientific | Cat# 12–544-B |
| Microscope slides | Fisher Scientific | Cat# 12-550-10 |
| Angular optical trap setup | Deufel et al., 2007 | N/A |
| Magnetic tweezers setup | This study | N/A |
| Dynabeads MyOne Streptavidin T1 | Invitrogen | Cat# 65601 |
| Streptavidin-coated quartz cylinder | Deufel et al., 2007 and this study | N/A |
| 4” Quartz Wafer | Precision MicroOptics | Cat# PWQB-131332 |
| PureLink Quick PCR Purification Kit | Invitrogen | Cat# K310001 |