| Bacterial and Virus Strains |
| MG1655 |
ATCC |
47076 |
| ElectroMax DH10B-T1R electrocompetent cells |
ThermoFisher |
1521050 |
| Chemicals, Peptides, and Recombinant Proteins |
| Nuclease-free water (not DEPC-treated) |
ThermoFisher |
AM9932 |
| Bacto agar |
VWR |
90000-760 |
| Bacto tryptone |
VWR |
90000-286 |
| Bacto yeast extract |
VWR |
90000-726 |
| Chloramphenicol |
Gold Biotech |
C-105-25 |
| Spectinomycin |
Gold Biotech |
S0188-25 |
| SOC Outgrowth Medium |
NEB |
B9020S |
| dNTP solution mix, 10 mM of each NTP |
NEB |
N0447S |
| NTP set (ultra-pure), 100 mM solutions |
GE Healthcare |
27-2025-01 |
| NAD+
|
Roche |
10127965001 |
| NADH |
Roche |
10107735001 |
| desphospho-CoA |
Sigma-Aldrich |
D3385 |
| FAD |
Sigma-Aldrich |
F6625 |
| Tris base (Amresco) |
VWR |
97061-800 |
| Boric Acid (ACS grade) |
VWR |
97061-980 |
| EDTA disodium salt dyhydrate |
VWR |
97061-018 |
| 0.5 M EDTA pH 8 |
ThermoFisher |
AM9260G |
| Sodium Chloride |
EMD Milipore |
SX0420-3 |
| Potassium Chloride |
EMD Milipore |
7300-500GM |
| Sodium Acetate, trihydrate |
VWR |
MK736406 |
| Formamide, deionized |
VWR |
EM-4610 |
| Sodium dodecylsulfate (SDS) |
VWR |
97064-470 |
| Magnesium chloride hexahydrate |
VWR |
EM-5980 |
| Glycerol (ACS grade) |
VWR |
EMGX0185-5 |
| Bovine Serum Albumin (BSA) fraction V |
VWR |
101174-932 |
| Bromophenol Blue |
VWR |
EM-BX1410-7 |
| Xylene Cyanol |
Sigma-Aldrich |
X4126-10G |
| Amaranth Dye |
VWR |
200030-400 |
| Temed (JT Baker) |
VWR |
JT4098-1 |
| Ammonium Persulfate |
VWR |
97064-594 |
| Dithiothreitol (DTT) |
Gold Bio |
DTT50 |
| Glycogen from Oyster (type II) |
Sigma-Aldrich |
G8751 |
| Hydrochloric Acid (ACS plus) |
Fisher Scientific |
A144-212 |
| Ethyl Alcohol |
Pharmco-AAPER |
111000200 |
| Isopropyl Alcohol |
BDH |
BDH1133-1LP |
| Heparin sulfate |
Sigma-Aldrich |
H-3393 |
| GeneMate LE Quick Dissolve agarose |
BioExpress |
E-3119-500 |
| SequaGel sequencing system |
National Diagnostics |
EC833 |
| 10% TBE-Urea gels, 1mm x 10 wells |
ThermoFisher |
EC6875Box |
| 10% TBE gels, 1mm x 10 wells |
ThermoFisher |
EC6275Box |
| α-32P CTP EasyTide 250 uCi |
Perkin Elmer |
BLU508H250UC |
| α-32P GTP EasyTide 250 uCi |
Perkin Elmer |
BLU506H250UC |
| α-32P UTP EasyTide 250 uCi |
Perkin Elmer |
BLU507H250UC |
| Low Range ssRNA Ladder |
NEB |
N0364S |
| O’Gene Ruler Ultra Low Range DNA Ladder |
ThermoFisher |
SM1223 |
| 6X Orange DNA Loading Dye |
ThermoFisher |
R0631 |
| SYBR Gold nucleic acid gel stain |
ThermoFisher |
S11494 |
| TRI Reagent |
Molecular Research Center |
TR118 |
| Acid phenol:chloroform (CHCl3) pH 4.5 |
ThermoFisher |
AM9720 |
| TURBO DNAse |
ThermoFisher |
AM2238 |
| DNase I |
Zymo Research |
E1009A |
| RNaseOUT, Recombinant Ribonuclease Inhibitor |
ThermoFisher |
10777-019 |
| Calf Intestine Alkaline Phosphatase |
NEB |
M0290S |
| RNA 5′ Polyphosphatase |
Lucigen (Epicentre) |
RP8092H |
| NudC |
(Cahova et al., 2015) |
|
| Rai1 |
(Xiang et al., 2009) |
|
| T4 RNA Ligase 1 (ssRNA Ligase) |
NEB |
M0204L |
| Superscript III Reverse Transcriptase |
ThermoFisher |
18080-044 |
| RNAse H |
ThermoFisher |
AM2293 |
| Phusion HF DNA Polymerase |
ThermoFisher |
F-530L |
| 5X Detergent-free Phusion HF Buffer Pack |
NEB |
B0520S |
| Phusion Flash HF master mix |
ThermoFisher |
F-548L |
|
E. coli RNA polymerase core (β′-6xHis) |
(Artsimovitch et al., 2003) |
|
|
E. coli σ70-6xHis |
(Marr and Roberts, 1997) |
|
| Critical Commercial Assays |
| Direct-zol RNA MiniPrep |
Zymo Research |
R2051 |
| MICROBExpress Bacterial mRNA purification Kit |
ThermoFisher |
AM1905 |
| QIAprep Spin Miniprep Kit |
Qiagen |
27106 |
| Qubit dsDNA HS assay kit |
ThermoFisher |
Q32851 |
| Qubit ssDNA Assay kit |
ThermoFisher |
Q10212 |
| Micellula DNA Emulsion PCR Kit |
Chimerx |
3600-02 |
| QIAquick PCR purification kit |
Qiagen |
28104 |
| Deposited Data |
| Sequencing data |
NIH Sequence Read |
accession number |
| Unprocessed gel images |
Archive |
PRJNA411835 |
|
Mendeley Data |
http://dx.doi.org/10.17632/kjc9rypnzr.2 |
| Oligonucleotides (sequences provided 5′ to 3′) |
| Sequences of the DNA and RNA primers used in this work are provided in Table S1
|
Integrated DNA Technologies (IDT) |
|
| Recombinant DNA |
| pIA900 |
Gift of I. Artsimovitch |
|
| pσ70–His |
Gift of J. Roberts |
|
| pET NudC-His |
(Bird et al., 2016) |
|
| pMASTER-lacCONS-N7
|
(Vvedenskaya et al., 2015) |
|
| Software and Algorithms |
| Excel |
Microsoft |
2011 |
| ImageQuant |
GE Healthcare |
TL 5.1 |
| SigmaPlot |
Systat Software Inc. |
Ver. 10 |
| MASTER-EX-CLT |
Nickels Lab, Rutgers University |
https://github.com/NickelsLabRutgers/MASTER-EX-CLT |
| R programming language |
R Core Team |
http://www.R-project.org/ |
| ggplot2 |
(Wickham, 2016) |
http://www.springer.com/us/book/9780387981413 |
| Dplyr |
(Wickham and Francois, 2016) |
https://CRAN.R-project.org/package=dplyr |
| ViennaRNA package (RNAfold) |
(Lorenz et al., 2011) |
Version 2.4.3 https://www.tbi.univie.ac.at/RNA/index.html
|
| Pymol |
Schrodinger, LLC |
http://www.pymol.org |
| Illustrator |
Adobe |
Ver. CS6 |
| Other |
| Bench protocol |
|
Methods S1 |
| Illumina high-throughput sequencing |
RUCDR, Rutgers University |
www.rucdr.org |
| Illumina high-throughput sequencing |
Waksman Genomics Core Facility, Rutgers University |
ngs.lab@rutgers.edu |
| Molecular Dynamics PhosphorImager |
GE Healthcare |
Typhoon 9400 |
