Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Bacterial and virus strains | ||
| Escherichia coli DH5 | NEB | Cat# C2987H |
| Escherichia coli BL21(DE3) | NEB | Cat# C2527H |
| Chemicals, peptides, and recombinant proteins | ||
| T7 RNA polymerase | This study; purified as in (Butler and Chamberlin, 1982; Davanloo et al., 1984) | N/A |
| E. coli RNA polymerase holoenzyme | NEB | Cat# M0551 |
| NTP set | Thermo Fisher | Cat# R0481 |
| Dichlorodimethylsilane (DDS) | Sigma | Cat# 440272 |
| Biotin-conjugated bovine serum albumin | Sigma | Cat# A8549 |
| Tween-20 | Fisher BioReagents | Cat# BP337 |
| Neutravidin | Thermo Fisher | Cat# 31000 |
| Trolox | ACROS Organics | Cat# AC218940010 |
| Glucose oxidase | Sigma | Cat# G2133 |
| Catalase | Sigma | Cat# C9322 |
| Glucose | Sigma | Cat#G8270 |
| RNasin plus | Promega | Cat# N2611 |
| ATP, [gamma-32P]-6000Ci/mmol | Perkin Elmer | Cat# BLU502Z500UC |
| UTP, [alpha-32P]-6000Ci/mmol | Perkin Elmer | Cat# BLU007H250UC |
| Sulfo-Cyanine3 NHS ester | Lumiprobe | Cat# 21320 |
| Sulfo-Cyanine5 NHS ester | Lumiprobe | Cat# 23320 |
| Q5 DNA polymerase | NEB | Cat# M0491 |
| Q5U DNA polymerase | NEB | Cat# M0515 |
| HiFi Taq Ligase | NEB | Cat# M0647 |
| USER enzyme | NEB | Cat# M5505 |
| Rifampicin | Sigma | Cat# R3501 |
| Heparin Sodium Salt | Sigma | Cat#H3393 |
| 3'-O-Methyluridine-5'-Triphosphate | TriLink | Cat# N-1059-1 |
| 3'-O-Methylcytidine-5'-Triphosphate | TriLink | Cat# N-1057-1 |
| 3'-O-Methylguanosine-5'-Triphosphate | TriLink | Cat# N-1058-1 |
| 3'-O-Methyladenosine-5'-Triphosphate | TriLink | Cat# N-1056-1 |
| Critical commercial assays | ||
| NucleoSpin Gel and PCR Clean-up | Takara | Cat# 740609 |
| Deposited data | ||
| Raw microscopy movies | This paper | https://doi.org/10.7281/T1/AVEV7M |
| Figure source data | This paper | https://doi.org/10.7281/T1/AVEV7M |
| Oligonucleotides | ||
| Tether_T3_33nts_3’ BIO: 5’ – CTAACTCTCTACCCA TCCATCTCTCACTCACCC /3BIO/ – 3’ | (Rodgers and Woodson, 2019) | N/A |
| SA5_aadU35: 5’ –CCTGTGTCCTGTGTGTCCTGTCCAAAGTGTGTCG/iAmMC6T/CC – 3’ | (Rodgers and Woodson, 2019) | N/A |
| T7Pro_Tether_FOR: 5’ –GATCCTAATACGACTCACTATAGGGTGAGTGAGAGATGGATGGGTAGAGAGTTAGTAGTA – 3’ | (Rodgers and Woodson, 2019) | N/A |
| T7A1_FOR: 5’ – TATCAAAAAGAGTATTGACTTAAAGTCTAACCTATAGGATACTTACAGCC – 3’ | This study | N/A |
| Term_REV_29_aadT25: 5’ – CAAAAAACCCCTCAAGACCCGTT/iAmMC6T/AGAGG – 3’ | This study | N/A |
| rpoSREV2_dT180_dUx2: 5’ – AAA/ideoxyU/AACGCAGCGGG/ideoxyU/T/iAmMC6T/ACGGATTTCC – 3’ | This study | N/A |
| rpoSFOR2_dUx2_197: 5’ – ACCCGC/ideoxyU/GCGTTATT/ideoxyU/GCCGCAGCGATAAATCG – 3’ | This study | N/A |
| RpoS301_REV_aadT121_dU130: 5’ – ATGCAAGCGTGTTGAACTGG/ideoxyU/TCCGGTGC/iAmMC6T/ACCC – 3’ | This study | N/A |
| RpoS301_FOR_dU150: 5’ – ACCAGTTCAACACGCTTGCA/ideoxyU/UTTTGAAATTCG – 3’ | This study | N/A |
| RpoS_REV_SA5_nt432: 5’ – GTGTCCTGTCCAAAGTGTGTCGTCCTGCAAGCGTGTTGAACTGGTTCCGGTGCTACCC – 3’ | This study | N/A |
| RpoS_REV2_SA5_NIS_nt562: 5’ – GTGTCCTGTCCAAAGTGTGTCGTCCGACGGAACATTCAAGCAAAAGCCTGGTTCC – 3’ | This study | N/A |
| Recombinant DNA | ||
| pET21b-EcHfq | (Zhang et al., 2002) | N/A |
| pAR1219-T7RNAP | (Davanloo et al., 1984) | N/A |
| Sequences for linear DNA templates listed in Table S2 | This study | N/A |
| Software and algorithms | ||
| Single-molecule fluorescence acquisition software (smCamera) | Ha Lab, Custom made | https://github.com/Ha-SingleMoleculeLab/Data-Aquisition |
| MATLAB | Mathworks | R2022a |
| GLIMPSE/IMSCROLL | (Friedman and Gelles, 2015) | N/A |
| FIJI | (Schindelin et al., 2012) | N/A |