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GenScript corporation oligonucleotides, primers, and synthetic genes
Oligonucleotides, Primers, And Synthetic Genes, supplied by GenScript corporation, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/oligonucleotides%2C+primers%2C+and+synthetic+genes/oligonucleotides+and+primers/pm37480847-256-231-251
Average 90 stars, based on 1 article reviews
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Virus:

Article Title: Prokaryotic Gabija complex senses and executes nucleotide depletion and DNA cleavage for antiviral defense.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains E. coli DH5a Sangon Biotech Cat#B528413 E. coli BL21(DE3) Yeasen Cat#11804ES80 E. coli B (ATCC 11303 ) American Type Culture Collection (ATCC) ATCC 11303 Bacillus subtilis (ATCC 6051 ) American Type Culture Collection (ATCC) ATCC 6051 Phage T4 China Center For Type Culture Collection (CCTCC) Genbank: AF158101.6 Phage T5 China Center For Type Culture Collection (CCTCC) Genbank: AY543070.1 Phage T7 China Center For Type Culture Collection (CCTCC) Genbank: NC_001604.1 Chemicals, peptides, and recombinant proteins Kanamycin Sigma Cat#K0254 Ampicillin Sigma Cat#A9518 NTPs (ATP, GTP, UTP, CTP) New England Biolabs Cat#N0450S DNA stain DAPI Sangon Biotech Cat#E607303 Membrane stain FM4-64 Thermo Fisher Scientific Cat#T3166 Ni-NTA Agarose QIAGEN Cat#30250 Preparative Superdex S200 column GE Healthcare Cat#17-1043-01 Silica Gel-60 F254 glass-backed TLC plate MilliporeSigma Cat#M1057290001 30% Acrylamide/Bis Solution, 37.5:1 Bio-Rad Cat#1610158 Tris base Roche Cat#10708976001 Imidazole Sigma-Aldrich Cat#IX0005 Dithiothreitol (DTT) Sigma-Aldrich Cat#D0632 Chloroform Sigma Cat#C2432 IPTG (Isopropyl-b-D-thiogalactoside) Sigma Cat#10724815001 GajA recombinant protein, and mutants as described This paper N/A GajB recombinant protein, and mutants as described This paper N/A Critical commercial assays QIAquick PCR Purification Kit QIAGEN Cat#28106 PiColorLock phosphate detection system kit Expedeon Cat#303-0030 DNeasy blood and tissue kit QIAGEN Cat#69504 RNase A QIAGEN Cat#27106 DNase-I New England Biolabs Cat#M0303 Gibson assembly kit New England Biolabs Cat#E2611 RNA purification kit New England Biolabs Cat#E2611 PrimeSTAR Max DNA Polymerase TaKaRa Cat#R045A Deposited data RNA-Seq data This paper SRA: PRJNA961899 Oligonucleotides, primers, and synthetic genes The sequences are listed in Tables S1, S2, and S5 This paper, Genscript Corp. N/A (Continued on next page) Cell Host & Microbe 31, 1331–1344.e1–e5, August 9, 2023 e1

Recombinant:

Article Title: Prokaryotic Gabija complex senses and executes nucleotide depletion and DNA cleavage for antiviral defense.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains E. coli DH5a Sangon Biotech Cat#B528413 E. coli BL21(DE3) Yeasen Cat#11804ES80 E. coli B (ATCC 11303 ) American Type Culture Collection (ATCC) ATCC 11303 Bacillus subtilis (ATCC 6051 ) American Type Culture Collection (ATCC) ATCC 6051 Phage T4 China Center For Type Culture Collection (CCTCC) Genbank: AF158101.6 Phage T5 China Center For Type Culture Collection (CCTCC) Genbank: AY543070.1 Phage T7 China Center For Type Culture Collection (CCTCC) Genbank: NC_001604.1 Chemicals, peptides, and recombinant proteins Kanamycin Sigma Cat#K0254 Ampicillin Sigma Cat#A9518 NTPs (ATP, GTP, UTP, CTP) New England Biolabs Cat#N0450S DNA stain DAPI Sangon Biotech Cat#E607303 Membrane stain FM4-64 Thermo Fisher Scientific Cat#T3166 Ni-NTA Agarose QIAGEN Cat#30250 Preparative Superdex S200 column GE Healthcare Cat#17-1043-01 Silica Gel-60 F254 glass-backed TLC plate MilliporeSigma Cat#M1057290001 30% Acrylamide/Bis Solution, 37.5:1 Bio-Rad Cat#1610158 Tris base Roche Cat#10708976001 Imidazole Sigma-Aldrich Cat#IX0005 Dithiothreitol (DTT) Sigma-Aldrich Cat#D0632 Chloroform Sigma Cat#C2432 IPTG (Isopropyl-b-D-thiogalactoside) Sigma Cat#10724815001 GajA recombinant protein, and mutants as described This paper N/A GajB recombinant protein, and mutants as described This paper N/A Critical commercial assays QIAquick PCR Purification Kit QIAGEN Cat#28106 PiColorLock phosphate detection system kit Expedeon Cat#303-0030 DNeasy blood and tissue kit QIAGEN Cat#69504 RNase A QIAGEN Cat#27106 DNase-I New England Biolabs Cat#M0303 Gibson assembly kit New England Biolabs Cat#E2611 RNA purification kit New England Biolabs Cat#E2611 PrimeSTAR Max DNA Polymerase TaKaRa Cat#R045A Deposited data RNA-Seq data This paper SRA: PRJNA961899 Oligonucleotides, primers, and synthetic genes The sequences are listed in Tables S1, S2, and S5 This paper, Genscript Corp. N/A (Continued on next page) Cell Host & Microbe 31, 1331–1344.e1–e5, August 9, 2023 e1

Staining:

Article Title: Prokaryotic Gabija complex senses and executes nucleotide depletion and DNA cleavage for antiviral defense.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains E. coli DH5a Sangon Biotech Cat#B528413 E. coli BL21(DE3) Yeasen Cat#11804ES80 E. coli B (ATCC 11303 ) American Type Culture Collection (ATCC) ATCC 11303 Bacillus subtilis (ATCC 6051 ) American Type Culture Collection (ATCC) ATCC 6051 Phage T4 China Center For Type Culture Collection (CCTCC) Genbank: AF158101.6 Phage T5 China Center For Type Culture Collection (CCTCC) Genbank: AY543070.1 Phage T7 China Center For Type Culture Collection (CCTCC) Genbank: NC_001604.1 Chemicals, peptides, and recombinant proteins Kanamycin Sigma Cat#K0254 Ampicillin Sigma Cat#A9518 NTPs (ATP, GTP, UTP, CTP) New England Biolabs Cat#N0450S DNA stain DAPI Sangon Biotech Cat#E607303 Membrane stain FM4-64 Thermo Fisher Scientific Cat#T3166 Ni-NTA Agarose QIAGEN Cat#30250 Preparative Superdex S200 column GE Healthcare Cat#17-1043-01 Silica Gel-60 F254 glass-backed TLC plate MilliporeSigma Cat#M1057290001 30% Acrylamide/Bis Solution, 37.5:1 Bio-Rad Cat#1610158 Tris base Roche Cat#10708976001 Imidazole Sigma-Aldrich Cat#IX0005 Dithiothreitol (DTT) Sigma-Aldrich Cat#D0632 Chloroform Sigma Cat#C2432 IPTG (Isopropyl-b-D-thiogalactoside) Sigma Cat#10724815001 GajA recombinant protein, and mutants as described This paper N/A GajB recombinant protein, and mutants as described This paper N/A Critical commercial assays QIAquick PCR Purification Kit QIAGEN Cat#28106 PiColorLock phosphate detection system kit Expedeon Cat#303-0030 DNeasy blood and tissue kit QIAGEN Cat#69504 RNase A QIAGEN Cat#27106 DNase-I New England Biolabs Cat#M0303 Gibson assembly kit New England Biolabs Cat#E2611 RNA purification kit New England Biolabs Cat#E2611 PrimeSTAR Max DNA Polymerase TaKaRa Cat#R045A Deposited data RNA-Seq data This paper SRA: PRJNA961899 Oligonucleotides, primers, and synthetic genes The sequences are listed in Tables S1, S2, and S5 This paper, Genscript Corp. N/A (Continued on next page) Cell Host & Microbe 31, 1331–1344.e1–e5, August 9, 2023 e1

Membrane:

Article Title: Prokaryotic Gabija complex senses and executes nucleotide depletion and DNA cleavage for antiviral defense.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains E. coli DH5a Sangon Biotech Cat#B528413 E. coli BL21(DE3) Yeasen Cat#11804ES80 E. coli B (ATCC 11303 ) American Type Culture Collection (ATCC) ATCC 11303 Bacillus subtilis (ATCC 6051 ) American Type Culture Collection (ATCC) ATCC 6051 Phage T4 China Center For Type Culture Collection (CCTCC) Genbank: AF158101.6 Phage T5 China Center For Type Culture Collection (CCTCC) Genbank: AY543070.1 Phage T7 China Center For Type Culture Collection (CCTCC) Genbank: NC_001604.1 Chemicals, peptides, and recombinant proteins Kanamycin Sigma Cat#K0254 Ampicillin Sigma Cat#A9518 NTPs (ATP, GTP, UTP, CTP) New England Biolabs Cat#N0450S DNA stain DAPI Sangon Biotech Cat#E607303 Membrane stain FM4-64 Thermo Fisher Scientific Cat#T3166 Ni-NTA Agarose QIAGEN Cat#30250 Preparative Superdex S200 column GE Healthcare Cat#17-1043-01 Silica Gel-60 F254 glass-backed TLC plate MilliporeSigma Cat#M1057290001 30% Acrylamide/Bis Solution, 37.5:1 Bio-Rad Cat#1610158 Tris base Roche Cat#10708976001 Imidazole Sigma-Aldrich Cat#IX0005 Dithiothreitol (DTT) Sigma-Aldrich Cat#D0632 Chloroform Sigma Cat#C2432 IPTG (Isopropyl-b-D-thiogalactoside) Sigma Cat#10724815001 GajA recombinant protein, and mutants as described This paper N/A GajB recombinant protein, and mutants as described This paper N/A Critical commercial assays QIAquick PCR Purification Kit QIAGEN Cat#28106 PiColorLock phosphate detection system kit Expedeon Cat#303-0030 DNeasy blood and tissue kit QIAGEN Cat#69504 RNase A QIAGEN Cat#27106 DNase-I New England Biolabs Cat#M0303 Gibson assembly kit New England Biolabs Cat#E2611 RNA purification kit New England Biolabs Cat#E2611 PrimeSTAR Max DNA Polymerase TaKaRa Cat#R045A Deposited data RNA-Seq data This paper SRA: PRJNA961899 Oligonucleotides, primers, and synthetic genes The sequences are listed in Tables S1, S2, and S5 This paper, Genscript Corp. N/A (Continued on next page) Cell Host & Microbe 31, 1331–1344.e1–e5, August 9, 2023 e1

Thin Layer Chromatography:

Article Title: Prokaryotic Gabija complex senses and executes nucleotide depletion and DNA cleavage for antiviral defense.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains E. coli DH5a Sangon Biotech Cat#B528413 E. coli BL21(DE3) Yeasen Cat#11804ES80 E. coli B (ATCC 11303 ) American Type Culture Collection (ATCC) ATCC 11303 Bacillus subtilis (ATCC 6051 ) American Type Culture Collection (ATCC) ATCC 6051 Phage T4 China Center For Type Culture Collection (CCTCC) Genbank: AF158101.6 Phage T5 China Center For Type Culture Collection (CCTCC) Genbank: AY543070.1 Phage T7 China Center For Type Culture Collection (CCTCC) Genbank: NC_001604.1 Chemicals, peptides, and recombinant proteins Kanamycin Sigma Cat#K0254 Ampicillin Sigma Cat#A9518 NTPs (ATP, GTP, UTP, CTP) New England Biolabs Cat#N0450S DNA stain DAPI Sangon Biotech Cat#E607303 Membrane stain FM4-64 Thermo Fisher Scientific Cat#T3166 Ni-NTA Agarose QIAGEN Cat#30250 Preparative Superdex S200 column GE Healthcare Cat#17-1043-01 Silica Gel-60 F254 glass-backed TLC plate MilliporeSigma Cat#M1057290001 30% Acrylamide/Bis Solution, 37.5:1 Bio-Rad Cat#1610158 Tris base Roche Cat#10708976001 Imidazole Sigma-Aldrich Cat#IX0005 Dithiothreitol (DTT) Sigma-Aldrich Cat#D0632 Chloroform Sigma Cat#C2432 IPTG (Isopropyl-b-D-thiogalactoside) Sigma Cat#10724815001 GajA recombinant protein, and mutants as described This paper N/A GajB recombinant protein, and mutants as described This paper N/A Critical commercial assays QIAquick PCR Purification Kit QIAGEN Cat#28106 PiColorLock phosphate detection system kit Expedeon Cat#303-0030 DNeasy blood and tissue kit QIAGEN Cat#69504 RNase A QIAGEN Cat#27106 DNase-I New England Biolabs Cat#M0303 Gibson assembly kit New England Biolabs Cat#E2611 RNA purification kit New England Biolabs Cat#E2611 PrimeSTAR Max DNA Polymerase TaKaRa Cat#R045A Deposited data RNA-Seq data This paper SRA: PRJNA961899 Oligonucleotides, primers, and synthetic genes The sequences are listed in Tables S1, S2, and S5 This paper, Genscript Corp. N/A (Continued on next page) Cell Host & Microbe 31, 1331–1344.e1–e5, August 9, 2023 e1

Polymerase Chain Reaction:

Article Title: Prokaryotic Gabija complex senses and executes nucleotide depletion and DNA cleavage for antiviral defense.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains E. coli DH5a Sangon Biotech Cat#B528413 E. coli BL21(DE3) Yeasen Cat#11804ES80 E. coli B (ATCC 11303 ) American Type Culture Collection (ATCC) ATCC 11303 Bacillus subtilis (ATCC 6051 ) American Type Culture Collection (ATCC) ATCC 6051 Phage T4 China Center For Type Culture Collection (CCTCC) Genbank: AF158101.6 Phage T5 China Center For Type Culture Collection (CCTCC) Genbank: AY543070.1 Phage T7 China Center For Type Culture Collection (CCTCC) Genbank: NC_001604.1 Chemicals, peptides, and recombinant proteins Kanamycin Sigma Cat#K0254 Ampicillin Sigma Cat#A9518 NTPs (ATP, GTP, UTP, CTP) New England Biolabs Cat#N0450S DNA stain DAPI Sangon Biotech Cat#E607303 Membrane stain FM4-64 Thermo Fisher Scientific Cat#T3166 Ni-NTA Agarose QIAGEN Cat#30250 Preparative Superdex S200 column GE Healthcare Cat#17-1043-01 Silica Gel-60 F254 glass-backed TLC plate MilliporeSigma Cat#M1057290001 30% Acrylamide/Bis Solution, 37.5:1 Bio-Rad Cat#1610158 Tris base Roche Cat#10708976001 Imidazole Sigma-Aldrich Cat#IX0005 Dithiothreitol (DTT) Sigma-Aldrich Cat#D0632 Chloroform Sigma Cat#C2432 IPTG (Isopropyl-b-D-thiogalactoside) Sigma Cat#10724815001 GajA recombinant protein, and mutants as described This paper N/A GajB recombinant protein, and mutants as described This paper N/A Critical commercial assays QIAquick PCR Purification Kit QIAGEN Cat#28106 PiColorLock phosphate detection system kit Expedeon Cat#303-0030 DNeasy blood and tissue kit QIAGEN Cat#69504 RNase A QIAGEN Cat#27106 DNase-I New England Biolabs Cat#M0303 Gibson assembly kit New England Biolabs Cat#E2611 RNA purification kit New England Biolabs Cat#E2611 PrimeSTAR Max DNA Polymerase TaKaRa Cat#R045A Deposited data RNA-Seq data This paper SRA: PRJNA961899 Oligonucleotides, primers, and synthetic genes The sequences are listed in Tables S1, S2, and S5 This paper, Genscript Corp. N/A (Continued on next page) Cell Host & Microbe 31, 1331–1344.e1–e5, August 9, 2023 e1

Purification:

Article Title: Prokaryotic Gabija complex senses and executes nucleotide depletion and DNA cleavage for antiviral defense.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains E. coli DH5a Sangon Biotech Cat#B528413 E. coli BL21(DE3) Yeasen Cat#11804ES80 E. coli B (ATCC 11303 ) American Type Culture Collection (ATCC) ATCC 11303 Bacillus subtilis (ATCC 6051 ) American Type Culture Collection (ATCC) ATCC 6051 Phage T4 China Center For Type Culture Collection (CCTCC) Genbank: AF158101.6 Phage T5 China Center For Type Culture Collection (CCTCC) Genbank: AY543070.1 Phage T7 China Center For Type Culture Collection (CCTCC) Genbank: NC_001604.1 Chemicals, peptides, and recombinant proteins Kanamycin Sigma Cat#K0254 Ampicillin Sigma Cat#A9518 NTPs (ATP, GTP, UTP, CTP) New England Biolabs Cat#N0450S DNA stain DAPI Sangon Biotech Cat#E607303 Membrane stain FM4-64 Thermo Fisher Scientific Cat#T3166 Ni-NTA Agarose QIAGEN Cat#30250 Preparative Superdex S200 column GE Healthcare Cat#17-1043-01 Silica Gel-60 F254 glass-backed TLC plate MilliporeSigma Cat#M1057290001 30% Acrylamide/Bis Solution, 37.5:1 Bio-Rad Cat#1610158 Tris base Roche Cat#10708976001 Imidazole Sigma-Aldrich Cat#IX0005 Dithiothreitol (DTT) Sigma-Aldrich Cat#D0632 Chloroform Sigma Cat#C2432 IPTG (Isopropyl-b-D-thiogalactoside) Sigma Cat#10724815001 GajA recombinant protein, and mutants as described This paper N/A GajB recombinant protein, and mutants as described This paper N/A Critical commercial assays QIAquick PCR Purification Kit QIAGEN Cat#28106 PiColorLock phosphate detection system kit Expedeon Cat#303-0030 DNeasy blood and tissue kit QIAGEN Cat#69504 RNase A QIAGEN Cat#27106 DNase-I New England Biolabs Cat#M0303 Gibson assembly kit New England Biolabs Cat#E2611 RNA purification kit New England Biolabs Cat#E2611 PrimeSTAR Max DNA Polymerase TaKaRa Cat#R045A Deposited data RNA-Seq data This paper SRA: PRJNA961899 Oligonucleotides, primers, and synthetic genes The sequences are listed in Tables S1, S2, and S5 This paper, Genscript Corp. N/A (Continued on next page) Cell Host & Microbe 31, 1331–1344.e1–e5, August 9, 2023 e1



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A. Representative micrograph of the NusG- ops EC in vitreous ice. B. The fifteen most populated classes from 2D classification. C. Angular distribution for NusG- ops EC particle projections. D. Gold-standard FSC of the NusG- ops EC. The gold-standard FSC was calculated by comparing the two independently determined half-maps from RELION. The dotted line represents the 0.143 FSC cutoff, which indicates a nominal resolution of 3.7 Å. E. FSC calculated between the refined structure and the half map used for refinement (work), the other half map (free), and the full map. F. (top) The 3.7-Å resolution cryo-EM density map of the NusG- ops EC is colored as follows: αI, αII, ω subunits, gray; β, cyan; β’, pink; NusG, green; <t>t-DNA,</t> dark blue; nt-DNA, <t>yellow;</t> <t>RNA,</t> red. The rightmost view is sliced as indicated in the leftmost view. (bottom) Same views as (top) but colored by local resolution .
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Image Search Results


A. Representative micrograph of the NusG- ops EC in vitreous ice. B. The fifteen most populated classes from 2D classification. C. Angular distribution for NusG- ops EC particle projections. D. Gold-standard FSC of the NusG- ops EC. The gold-standard FSC was calculated by comparing the two independently determined half-maps from RELION. The dotted line represents the 0.143 FSC cutoff, which indicates a nominal resolution of 3.7 Å. E. FSC calculated between the refined structure and the half map used for refinement (work), the other half map (free), and the full map. F. (top) The 3.7-Å resolution cryo-EM density map of the NusG- ops EC is colored as follows: αI, αII, ω subunits, gray; β, cyan; β’, pink; NusG, green; t-DNA, dark blue; nt-DNA, yellow; RNA, red. The rightmost view is sliced as indicated in the leftmost view. (bottom) Same views as (top) but colored by local resolution .

Journal: bioRxiv

Article Title: Structural basis for transcript elongation control by NusG/RfaH universal regulators

doi: 10.1101/324400

Figure Lengend Snippet: A. Representative micrograph of the NusG- ops EC in vitreous ice. B. The fifteen most populated classes from 2D classification. C. Angular distribution for NusG- ops EC particle projections. D. Gold-standard FSC of the NusG- ops EC. The gold-standard FSC was calculated by comparing the two independently determined half-maps from RELION. The dotted line represents the 0.143 FSC cutoff, which indicates a nominal resolution of 3.7 Å. E. FSC calculated between the refined structure and the half map used for refinement (work), the other half map (free), and the full map. F. (top) The 3.7-Å resolution cryo-EM density map of the NusG- ops EC is colored as follows: αI, αII, ω subunits, gray; β, cyan; β’, pink; NusG, green; t-DNA, dark blue; nt-DNA, yellow; RNA, red. The rightmost view is sliced as indicated in the leftmost view. (bottom) Same views as (top) but colored by local resolution .

Article Snippet: Synthetic DNA oligonucleotides were obtained from Integrated DNA Technologies (Coralville, IA), RNA oligonucleotides from GE Healthcare Dharmacon (Lafayette, CO).

Techniques: Cryo-EM Sample Prep

A. Representative micrograph of the RfaH- ops E in vitreous ice. B. The fifteen most populated classes from 2D classification. C. Angular distribution for RfaH- ops EC particle projections. D. Gold-standard FSC of the RfaH- ops EC. The gold-standard FSC was calculated by comparing the two independently determined half-maps from RELION. The dotted line represents the 0.143 FSC cutoff, which indicates a nominal resolution of 3.5 Å. E. RfaH-NGN- ops EC: FSC calculated between the refined structure and the half map used for refinement (work), the other half map (free), and the full map. F. RfaH-full-length- ops EC: FSC calculated between the refined structure and the half map used for refinement (work), the other half map (free), and the full map. G. (top) The 3.5-Å resolution cryo-EM density map of the RfaH- ops EC is colored as follows: αI, αII, ω subunits, gray; β, cyan; β’, pink; RfaH, orange; t-DNA, dark blue; nt-DNA, yellow; RNA, red. The rightmost view is sliced as indicated in the leftmost view. (bottom) Same views as (top) but colored by local resolution .

Journal: bioRxiv

Article Title: Structural basis for transcript elongation control by NusG/RfaH universal regulators

doi: 10.1101/324400

Figure Lengend Snippet: A. Representative micrograph of the RfaH- ops E in vitreous ice. B. The fifteen most populated classes from 2D classification. C. Angular distribution for RfaH- ops EC particle projections. D. Gold-standard FSC of the RfaH- ops EC. The gold-standard FSC was calculated by comparing the two independently determined half-maps from RELION. The dotted line represents the 0.143 FSC cutoff, which indicates a nominal resolution of 3.5 Å. E. RfaH-NGN- ops EC: FSC calculated between the refined structure and the half map used for refinement (work), the other half map (free), and the full map. F. RfaH-full-length- ops EC: FSC calculated between the refined structure and the half map used for refinement (work), the other half map (free), and the full map. G. (top) The 3.5-Å resolution cryo-EM density map of the RfaH- ops EC is colored as follows: αI, αII, ω subunits, gray; β, cyan; β’, pink; RfaH, orange; t-DNA, dark blue; nt-DNA, yellow; RNA, red. The rightmost view is sliced as indicated in the leftmost view. (bottom) Same views as (top) but colored by local resolution .

Article Snippet: Synthetic DNA oligonucleotides were obtained from Integrated DNA Technologies (Coralville, IA), RNA oligonucleotides from GE Healthcare Dharmacon (Lafayette, CO).

Techniques: Cryo-EM Sample Prep

A. On most bacterial operons, NusG (G, green ) associates with RNAP weakly until RNAP enters a protein-coding gene and NusG-KOW interaction with 30S is possible (during initiation or slight uncoupling of transcription and translation). Weak NusG interaction is sufficient to inhibit backtracking but not to inhibit PH-induced RNAP swiveling. When transcription and translation become significantly uncoupled, NusG activates Rho-dependent termination via NusG-KOW-Rho interaction. B. On ops -containing operons, RfaH (H, magenta ) is recruited by contacts to the ops hairpin in the exposed nt-DNA ( yellow ; ). The refolded RfaH-KOW domain interacts with RNAP and the tightly bound RfaH excludes NusG, inhibits backtracking, and inhibits PH stimulation of pausing by preventing RNAP swiveling . RfaH associates with 30S similarly to NusG, but inhibits Rho indirectly upon significant transcription-translation uncoupling by excluding NusG. C. Spt4/5 (4 and 5, orange ) associates with RNAPII in the promoter-proximal region though NusG homologous contacts of its NGN and of 5 of its 7 KOWs ( ; ). Bound Spt5 inhibits backtracking, may inhibit swiveling and formation of nascent RNA structures, and mediates the regulatory switch between promoter-proximal pausing/attenuation and productive elongation in part by affecting actions of NELF and P-TEFb ( ; ). The full set of Spt5 interactions involved in this switch as well as in downstream roles in mediating RNA maturation, chromatin modifications, recruiting of DNA repair factors, cell-cycle control, polyadenylation, and termination remains incompletely defined ( ; ; ).

Journal: bioRxiv

Article Title: Structural basis for transcript elongation control by NusG/RfaH universal regulators

doi: 10.1101/324400

Figure Lengend Snippet: A. On most bacterial operons, NusG (G, green ) associates with RNAP weakly until RNAP enters a protein-coding gene and NusG-KOW interaction with 30S is possible (during initiation or slight uncoupling of transcription and translation). Weak NusG interaction is sufficient to inhibit backtracking but not to inhibit PH-induced RNAP swiveling. When transcription and translation become significantly uncoupled, NusG activates Rho-dependent termination via NusG-KOW-Rho interaction. B. On ops -containing operons, RfaH (H, magenta ) is recruited by contacts to the ops hairpin in the exposed nt-DNA ( yellow ; ). The refolded RfaH-KOW domain interacts with RNAP and the tightly bound RfaH excludes NusG, inhibits backtracking, and inhibits PH stimulation of pausing by preventing RNAP swiveling . RfaH associates with 30S similarly to NusG, but inhibits Rho indirectly upon significant transcription-translation uncoupling by excluding NusG. C. Spt4/5 (4 and 5, orange ) associates with RNAPII in the promoter-proximal region though NusG homologous contacts of its NGN and of 5 of its 7 KOWs ( ; ). Bound Spt5 inhibits backtracking, may inhibit swiveling and formation of nascent RNA structures, and mediates the regulatory switch between promoter-proximal pausing/attenuation and productive elongation in part by affecting actions of NELF and P-TEFb ( ; ). The full set of Spt5 interactions involved in this switch as well as in downstream roles in mediating RNA maturation, chromatin modifications, recruiting of DNA repair factors, cell-cycle control, polyadenylation, and termination remains incompletely defined ( ; ; ).

Article Snippet: Synthetic DNA oligonucleotides were obtained from Integrated DNA Technologies (Coralville, IA), RNA oligonucleotides from GE Healthcare Dharmacon (Lafayette, CO).

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