Structured Review

Promega rq1 dnase
Detection of chromosomal DNA fragmentation in blastocysts by TUNEL staining. TUNEL staining was performed on blastocysts as described in Materials and Methods. Blastocysts with expanded blastocoel cavities were selected to ensure that they had entered the stage when limited apoptosis would normally occur. Bright-field microscopy (A, C, and E) and the corresponding fluorescent images of TUNEL-stained blastocysts (B, D, and F) are shown. (A and B) Wild-type blastocyst treated with <t>RQ1</t> <t>DNase</t> as a positive control. (C and D) Wild-type blastocyst showing very few stained cells. (E and F) NRF-1 −/− blastocyst showing essentially the same staining intensity as the wild-type embryos.
Rq1 Dnase, supplied by Promega, used in various techniques. Bioz Stars score: 99/100, based on 458 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Images

1) Product Images from "Mitochondrial DNA Instability and Peri-Implantation Lethality Associated with Targeted Disruption of Nuclear Respiratory Factor 1 in Mice"

Article Title: Mitochondrial DNA Instability and Peri-Implantation Lethality Associated with Targeted Disruption of Nuclear Respiratory Factor 1 in Mice

Journal: Molecular and Cellular Biology

doi: 10.1128/MCB.21.2.644-654.2001

Detection of chromosomal DNA fragmentation in blastocysts by TUNEL staining. TUNEL staining was performed on blastocysts as described in Materials and Methods. Blastocysts with expanded blastocoel cavities were selected to ensure that they had entered the stage when limited apoptosis would normally occur. Bright-field microscopy (A, C, and E) and the corresponding fluorescent images of TUNEL-stained blastocysts (B, D, and F) are shown. (A and B) Wild-type blastocyst treated with RQ1 DNase as a positive control. (C and D) Wild-type blastocyst showing very few stained cells. (E and F) NRF-1 −/− blastocyst showing essentially the same staining intensity as the wild-type embryos.
Figure Legend Snippet: Detection of chromosomal DNA fragmentation in blastocysts by TUNEL staining. TUNEL staining was performed on blastocysts as described in Materials and Methods. Blastocysts with expanded blastocoel cavities were selected to ensure that they had entered the stage when limited apoptosis would normally occur. Bright-field microscopy (A, C, and E) and the corresponding fluorescent images of TUNEL-stained blastocysts (B, D, and F) are shown. (A and B) Wild-type blastocyst treated with RQ1 DNase as a positive control. (C and D) Wild-type blastocyst showing very few stained cells. (E and F) NRF-1 −/− blastocyst showing essentially the same staining intensity as the wild-type embryos.

Techniques Used: TUNEL Assay, Staining, Microscopy, Positive Control

2) Product Images from "Characterization of Hydrogen Peroxide-Induced DNA Release by Streptococcus sanguinis and Streptococcus gordonii "

Article Title: Characterization of Hydrogen Peroxide-Induced DNA Release by Streptococcus sanguinis and Streptococcus gordonii

Journal: Journal of Bacteriology

doi: 10.1128/JB.00906-09

Characterization of eRNA. (A) Agarose gel electrophoresis (1%) of RNA stained with ethidium bromide (1 μg/ml) as described in Materials and Methods. The photograph is representative of three independent experiments with similar results. Lanes: 1, S. gordonii ; 2, S. sanguinis ; 3, S. gordonii Pox − ; 4, S. sanguinis Pox − . (B) Precipitated nucleic acids from S. gordonii were digested with DNase RQ1 and RNase A, resolved by agarose gel electrophoresis (1%), and stained with ethidium bromide (1 μg/ml). (C) Quantification of eRNA by use of an RNA-specific fluorescent dye with the Quant-iT RNA assay. Sg, S. gordonii ; Ss, S. sanguinis . (D) Relative amounts of RNA normalized to cell density measured at A 600 . Data presented are the means ± SD of results from three independent experiments done on different days. (E) eRNA degradation. Total RNA from S. mutans ). Shown are means ± SD of results from at least two independent experiments with BHI, with the 0-min arbitrary level set to 100%.
Figure Legend Snippet: Characterization of eRNA. (A) Agarose gel electrophoresis (1%) of RNA stained with ethidium bromide (1 μg/ml) as described in Materials and Methods. The photograph is representative of three independent experiments with similar results. Lanes: 1, S. gordonii ; 2, S. sanguinis ; 3, S. gordonii Pox − ; 4, S. sanguinis Pox − . (B) Precipitated nucleic acids from S. gordonii were digested with DNase RQ1 and RNase A, resolved by agarose gel electrophoresis (1%), and stained with ethidium bromide (1 μg/ml). (C) Quantification of eRNA by use of an RNA-specific fluorescent dye with the Quant-iT RNA assay. Sg, S. gordonii ; Ss, S. sanguinis . (D) Relative amounts of RNA normalized to cell density measured at A 600 . Data presented are the means ± SD of results from three independent experiments done on different days. (E) eRNA degradation. Total RNA from S. mutans ). Shown are means ± SD of results from at least two independent experiments with BHI, with the 0-min arbitrary level set to 100%.

Techniques Used: Agarose Gel Electrophoresis, Staining

3) Product Images from "A DNase from a Fungal Phytopathogen Is a Virulence Factor Likely Deployed as Counter Defense against Host-Secreted Extracellular DNA"

Article Title: A DNase from a Fungal Phytopathogen Is a Virulence Factor Likely Deployed as Counter Defense against Host-Secreted Extracellular DNA

Journal: mBio

doi: 10.1128/mBio.02805-18

C. heterostrophus secretes DNases, and secretion is induced by plant tissue. WT, nuc1 mutant, nuc2 mutant, and nuc1 nuc2 double-mutant filtrates degrade intact λ DNA in the presence of plant material. The nuc1 single mutant and nuc1 nuc2 double mutant degrade lambda DNA less well than the WT or the nuc2 single mutant. This indicates that DNase(s) are secreted by the fungus, that the nuc1 mutant secretes a DNase that is important in DNA degradation, and that secretion is induced by host material. Left, size markers in kilobases. +, addition of corn leaf (CL) fragments, lambda DNA, or purified RQ1 RNase-free DNase. Culture filtrates examined were from WT strain C4, nuc1 mutant strains 144206-3-1 and 8-1, nuc2 mutant strains 149183-2-1 and 3-1, and nuc1 nuc2 double-mutant strains 144206/149183-4-1 and 8-1. The negative-control reaction with λ DNA did not degrade the DNA, while the positive-control reaction with λ DNA plus DNase did. Also note that λ DNA was not degraded by the CL material.
Figure Legend Snippet: C. heterostrophus secretes DNases, and secretion is induced by plant tissue. WT, nuc1 mutant, nuc2 mutant, and nuc1 nuc2 double-mutant filtrates degrade intact λ DNA in the presence of plant material. The nuc1 single mutant and nuc1 nuc2 double mutant degrade lambda DNA less well than the WT or the nuc2 single mutant. This indicates that DNase(s) are secreted by the fungus, that the nuc1 mutant secretes a DNase that is important in DNA degradation, and that secretion is induced by host material. Left, size markers in kilobases. +, addition of corn leaf (CL) fragments, lambda DNA, or purified RQ1 RNase-free DNase. Culture filtrates examined were from WT strain C4, nuc1 mutant strains 144206-3-1 and 8-1, nuc2 mutant strains 149183-2-1 and 3-1, and nuc1 nuc2 double-mutant strains 144206/149183-4-1 and 8-1. The negative-control reaction with λ DNA did not degrade the DNA, while the positive-control reaction with λ DNA plus DNase did. Also note that λ DNA was not degraded by the CL material.

Techniques Used: Mutagenesis, Lambda DNA Preparation, Purification, Negative Control, Positive Control

4) Product Images from "A DNase from a Fungal Phytopathogen Is a Virulence Factor Likely Deployed as Counter Defense against Host-Secreted Extracellular DNA"

Article Title: A DNase from a Fungal Phytopathogen Is a Virulence Factor Likely Deployed as Counter Defense against Host-Secreted Extracellular DNA

Journal: mBio

doi: 10.1128/mBio.02805-18

C. heterostrophus secretes DNases, and secretion is induced by plant tissue. WT, nuc1 mutant, nuc2 mutant, and nuc1 nuc2 double-mutant filtrates degrade intact λ DNA in the presence of plant material. The nuc1 single mutant and nuc1 nuc2 double mutant degrade lambda DNA less well than the WT or the nuc2 single mutant. This indicates that DNase(s) are secreted by the fungus, that the nuc1 mutant secretes a DNase that is important in DNA degradation, and that secretion is induced by host material. Left, size markers in kilobases. +, addition of corn leaf (CL) fragments, lambda DNA, or purified RQ1 RNase-free DNase. Culture filtrates examined were from WT strain C4, nuc1 mutant strains 144206-3-1 and 8-1, nuc2 mutant strains 149183-2-1 and 3-1, and nuc1 nuc2 double-mutant strains 144206/149183-4-1 and 8-1. The negative-control reaction with λ DNA did not degrade the DNA, while the positive-control reaction with λ DNA plus DNase did. Also note that λ DNA was not degraded by the CL material.
Figure Legend Snippet: C. heterostrophus secretes DNases, and secretion is induced by plant tissue. WT, nuc1 mutant, nuc2 mutant, and nuc1 nuc2 double-mutant filtrates degrade intact λ DNA in the presence of plant material. The nuc1 single mutant and nuc1 nuc2 double mutant degrade lambda DNA less well than the WT or the nuc2 single mutant. This indicates that DNase(s) are secreted by the fungus, that the nuc1 mutant secretes a DNase that is important in DNA degradation, and that secretion is induced by host material. Left, size markers in kilobases. +, addition of corn leaf (CL) fragments, lambda DNA, or purified RQ1 RNase-free DNase. Culture filtrates examined were from WT strain C4, nuc1 mutant strains 144206-3-1 and 8-1, nuc2 mutant strains 149183-2-1 and 3-1, and nuc1 nuc2 double-mutant strains 144206/149183-4-1 and 8-1. The negative-control reaction with λ DNA did not degrade the DNA, while the positive-control reaction with λ DNA plus DNase did. Also note that λ DNA was not degraded by the CL material.

Techniques Used: Mutagenesis, Lambda DNA Preparation, Purification, Negative Control, Positive Control

5) Product Images from "TcTASV: A Novel Protein Family in Trypanosoma cruzi Identified from a Subtractive Trypomastigote cDNA Library"

Article Title: TcTASV: A Novel Protein Family in Trypanosoma cruzi Identified from a Subtractive Trypomastigote cDNA Library

Journal: PLoS Neglected Tropical Diseases

doi: 10.1371/journal.pntd.0000841

The TcT-E element (TcT-E elem ) is present in multiple copies in the T. cruzi genome and is associated with different coding regions. (A) Identification of an enriched 280-bp element in the TcT-E library. In silico screening of the TcT-E library using the FL-160-2 3′ UTR as bait depicted a large number of clones displaying homology with nucleotides 372–472. After analyzing a multiple sequence alignment of the identified TcT-E clones, a 280-bp consensus sequence with 3′ and 5′ polypyrimidine tracts (bold) and a variable number of TAA repeats (bold underlined) was obtained, and defined as TcT-Eelement (TcT-E elem ). (B) Analysis of TcT-E elem copy number. T. cruzi genomic DNA (CL-Brener strain) was digested with restriction enzymes having no internal site within the TcT-E elem , electrophoresed on TAE-agarose gel and transferred by standard procedures. A probe specific for the TcT-E elem was synthesized and labelled by PCR with 32 P. (C) The mRNA of the CDSs located upstream of the TcT-E are preferentially expressed in trypomastigotes. Northern blots probed with the complete ORF Tcruzi_1863-4-1211-93 ( http://TriTrypDB.org ). (D) The TcT-E elem is present 30–70 bp downstream of a stop codon in many coding sequences in T.cruzi . The consensus sequence of TcT-E elem was used as bait to search the T. cruzi database; WGSs with more than 80% identity to TcT-E elem and longer than 1000 bp were retrieved and analyzed. The schematic map of the relative position of TcT-E elem in relation to coding sequences in T. cruzi genome is shown. (E) Mature mRNA transcripts contain both the TcT-E elem and different CDSs. Total RNA from trypomastigotes (T) and epimastigotes (E) was purified and treated with RQ1 DNase. First strand cDNA was synthesized by RT using an oligo dT primer. PCR was performed using a 5′ primer specific for the T. cruzi miniexon (ME) and a 3′ antisense primer corresponding to the 3′ region of the TcT-E elem . Alternatively, PCR was performed with primers corresponding to the 5′ and 3′ conserved regions of most CDSs (CDS-L and CDS-R) or with a 5′primer specific for the CDS and a 3′ primer specific for the TcT-E elem . The relative position of the primers is indicated in Fig. 2D . PCR- and RT- denote the negative controls for each reaction.
Figure Legend Snippet: The TcT-E element (TcT-E elem ) is present in multiple copies in the T. cruzi genome and is associated with different coding regions. (A) Identification of an enriched 280-bp element in the TcT-E library. In silico screening of the TcT-E library using the FL-160-2 3′ UTR as bait depicted a large number of clones displaying homology with nucleotides 372–472. After analyzing a multiple sequence alignment of the identified TcT-E clones, a 280-bp consensus sequence with 3′ and 5′ polypyrimidine tracts (bold) and a variable number of TAA repeats (bold underlined) was obtained, and defined as TcT-Eelement (TcT-E elem ). (B) Analysis of TcT-E elem copy number. T. cruzi genomic DNA (CL-Brener strain) was digested with restriction enzymes having no internal site within the TcT-E elem , electrophoresed on TAE-agarose gel and transferred by standard procedures. A probe specific for the TcT-E elem was synthesized and labelled by PCR with 32 P. (C) The mRNA of the CDSs located upstream of the TcT-E are preferentially expressed in trypomastigotes. Northern blots probed with the complete ORF Tcruzi_1863-4-1211-93 ( http://TriTrypDB.org ). (D) The TcT-E elem is present 30–70 bp downstream of a stop codon in many coding sequences in T.cruzi . The consensus sequence of TcT-E elem was used as bait to search the T. cruzi database; WGSs with more than 80% identity to TcT-E elem and longer than 1000 bp were retrieved and analyzed. The schematic map of the relative position of TcT-E elem in relation to coding sequences in T. cruzi genome is shown. (E) Mature mRNA transcripts contain both the TcT-E elem and different CDSs. Total RNA from trypomastigotes (T) and epimastigotes (E) was purified and treated with RQ1 DNase. First strand cDNA was synthesized by RT using an oligo dT primer. PCR was performed using a 5′ primer specific for the T. cruzi miniexon (ME) and a 3′ antisense primer corresponding to the 3′ region of the TcT-E elem . Alternatively, PCR was performed with primers corresponding to the 5′ and 3′ conserved regions of most CDSs (CDS-L and CDS-R) or with a 5′primer specific for the CDS and a 3′ primer specific for the TcT-E elem . The relative position of the primers is indicated in Fig. 2D . PCR- and RT- denote the negative controls for each reaction.

Techniques Used: In Silico, Clone Assay, Sequencing, Agarose Gel Electrophoresis, Synthesized, Polymerase Chain Reaction, Northern Blot, Purification

6) Product Images from "A DNase from a Fungal Phytopathogen Is a Virulence Factor Likely Deployed as Counter Defense against Host-Secreted Extracellular DNA"

Article Title: A DNase from a Fungal Phytopathogen Is a Virulence Factor Likely Deployed as Counter Defense against Host-Secreted Extracellular DNA

Journal: mBio

doi: 10.1128/mBio.02805-18

C. heterostrophus secretes DNases, and secretion is induced by plant tissue. WT, nuc1 mutant, nuc2 mutant, and nuc1 nuc2 double-mutant filtrates degrade intact λ DNA in the presence of plant material. The nuc1 single mutant and nuc1 nuc2 double mutant degrade lambda DNA less well than the WT or the nuc2 single mutant. This indicates that DNase(s) are secreted by the fungus, that the nuc1 mutant secretes a DNase that is important in DNA degradation, and that secretion is induced by host material. Left, size markers in kilobases. +, addition of corn leaf (CL) fragments, lambda DNA, or purified RQ1 RNase-free DNase. Culture filtrates examined were from WT strain C4, nuc1 mutant strains 144206-3-1 and 8-1, nuc2 mutant strains 149183-2-1 and 3-1, and nuc1 nuc2 double-mutant strains 144206/149183-4-1 and 8-1. The negative-control reaction with λ DNA did not degrade the DNA, while the positive-control reaction with λ DNA plus DNase did. Also note that λ DNA was not degraded by the CL material.
Figure Legend Snippet: C. heterostrophus secretes DNases, and secretion is induced by plant tissue. WT, nuc1 mutant, nuc2 mutant, and nuc1 nuc2 double-mutant filtrates degrade intact λ DNA in the presence of plant material. The nuc1 single mutant and nuc1 nuc2 double mutant degrade lambda DNA less well than the WT or the nuc2 single mutant. This indicates that DNase(s) are secreted by the fungus, that the nuc1 mutant secretes a DNase that is important in DNA degradation, and that secretion is induced by host material. Left, size markers in kilobases. +, addition of corn leaf (CL) fragments, lambda DNA, or purified RQ1 RNase-free DNase. Culture filtrates examined were from WT strain C4, nuc1 mutant strains 144206-3-1 and 8-1, nuc2 mutant strains 149183-2-1 and 3-1, and nuc1 nuc2 double-mutant strains 144206/149183-4-1 and 8-1. The negative-control reaction with λ DNA did not degrade the DNA, while the positive-control reaction with λ DNA plus DNase did. Also note that λ DNA was not degraded by the CL material.

Techniques Used: Mutagenesis, Lambda DNA Preparation, Purification, Negative Control, Positive Control

7) Product Images from "Salmonella enterica Serovar Typhimurium NiFe Uptake-Type Hydrogenases Are Differentially Expressed In Vivo ▿"

Article Title: Salmonella enterica Serovar Typhimurium NiFe Uptake-Type Hydrogenases Are Differentially Expressed In Vivo ▿

Journal:

doi: 10.1128/IAI.00741-08

STM 1788 expression in wild-type and hya mutant cells. RNAs were extracted from wild-type and hya mutant cell cultures grown aerobically overnight in LB broth, using an Aurum Total RNA Mini kit (Bio-Rad). RNAs were digested with RQ1 DNase (Promega) to
Figure Legend Snippet: STM 1788 expression in wild-type and hya mutant cells. RNAs were extracted from wild-type and hya mutant cell cultures grown aerobically overnight in LB broth, using an Aurum Total RNA Mini kit (Bio-Rad). RNAs were digested with RQ1 DNase (Promega) to

Techniques Used: Expressing, Mutagenesis

8) Product Images from "Salmonella enterica Serovar Typhimurium NiFe Uptake-Type Hydrogenases Are Differentially Expressed In Vivo ▿"

Article Title: Salmonella enterica Serovar Typhimurium NiFe Uptake-Type Hydrogenases Are Differentially Expressed In Vivo ▿

Journal:

doi: 10.1128/IAI.00741-08

STM 1788 expression in wild-type and hya mutant cells. RNAs were extracted from wild-type and hya mutant cell cultures grown aerobically overnight in LB broth, using an Aurum Total RNA Mini kit (Bio-Rad). RNAs were digested with RQ1 DNase (Promega) to
Figure Legend Snippet: STM 1788 expression in wild-type and hya mutant cells. RNAs were extracted from wild-type and hya mutant cell cultures grown aerobically overnight in LB broth, using an Aurum Total RNA Mini kit (Bio-Rad). RNAs were digested with RQ1 DNase (Promega) to

Techniques Used: Expressing, Mutagenesis

9) Product Images from "miR482 Regulation of NBS-LRR Defense Genes during Fungal Pathogen Infection in Cotton"

Article Title: miR482 Regulation of NBS-LRR Defense Genes during Fungal Pathogen Infection in Cotton

Journal: PLoS ONE

doi: 10.1371/journal.pone.0084390

Expression analysis of ghr-miR482/miR482.2. A) Northern blot detection of ghr-miR482/482.2 in leaves collected from V. dahliae -infected and mock-treated cotton plants at one day-post-inoculation (1 dpi). Oligos antisense to ghr-miR482a and ghr-miR482e.2 were used together as probes. The values underneath the image are the relative signal intensity of ghr-miR482a/482e.2, which were determined using the MultiGauge V2.0 (Fuji Film) and normalized based on U6. V.d: V. dahliae -infected. B to H) Stem-loop qRT-PCR analysis of the expression level of individual members of the ghr-miR482 family. RQ1 DNase treated total RNA isolated from leaves and roots of 1-dpi plants was analysed using ghr-miR482/miR482.2 member specific stem-loop RT and PCR primers. Expression level was normalized to reference gene Histone 3. Error bars represent standard deviation of the expression ratio. * and ** denote significant relative to the corresponding mock-infected control at p
Figure Legend Snippet: Expression analysis of ghr-miR482/miR482.2. A) Northern blot detection of ghr-miR482/482.2 in leaves collected from V. dahliae -infected and mock-treated cotton plants at one day-post-inoculation (1 dpi). Oligos antisense to ghr-miR482a and ghr-miR482e.2 were used together as probes. The values underneath the image are the relative signal intensity of ghr-miR482a/482e.2, which were determined using the MultiGauge V2.0 (Fuji Film) and normalized based on U6. V.d: V. dahliae -infected. B to H) Stem-loop qRT-PCR analysis of the expression level of individual members of the ghr-miR482 family. RQ1 DNase treated total RNA isolated from leaves and roots of 1-dpi plants was analysed using ghr-miR482/miR482.2 member specific stem-loop RT and PCR primers. Expression level was normalized to reference gene Histone 3. Error bars represent standard deviation of the expression ratio. * and ** denote significant relative to the corresponding mock-infected control at p

Techniques Used: Expressing, Northern Blot, Infection, Quantitative RT-PCR, Isolation, Polymerase Chain Reaction, Standard Deviation

10) Product Images from "snRNA-specific role of SMN in trypanosome snRNP biogenesis in vivo"

Article Title: snRNA-specific role of SMN in trypanosome snRNP biogenesis in vivo

Journal: RNA Biology

doi: 10.4161/rna.8.1.13985

Nuclear accumulation of SL RNA and Sm proteins during SMN knockdown. (A) T. brucei cells without (t0) and after one, two and three days of RNAi-mediated SMN knockdown (t1–t3) were fixed, treated with RQ1-DNase (brightfield) and stained with DAPI
Figure Legend Snippet: Nuclear accumulation of SL RNA and Sm proteins during SMN knockdown. (A) T. brucei cells without (t0) and after one, two and three days of RNAi-mediated SMN knockdown (t1–t3) were fixed, treated with RQ1-DNase (brightfield) and stained with DAPI

Techniques Used: Staining

SMN protein largely colocalizes with the SL RNA transcripts in the nucleus. (A and B) T. brucei cells stably expressing SMN-PTP were fixed, permeabilized and treated with RQ1-DNase to degrade cellular DNA (brightfield); for control, see DAPI staining
Figure Legend Snippet: SMN protein largely colocalizes with the SL RNA transcripts in the nucleus. (A and B) T. brucei cells stably expressing SMN-PTP were fixed, permeabilized and treated with RQ1-DNase to degrade cellular DNA (brightfield); for control, see DAPI staining

Techniques Used: Stable Transfection, Expressing, Staining

11) Product Images from "Characterization of Hydrogen Peroxide-Induced DNA Release by Streptococcus sanguinis and Streptococcus gordonii "

Article Title: Characterization of Hydrogen Peroxide-Induced DNA Release by Streptococcus sanguinis and Streptococcus gordonii

Journal: Journal of Bacteriology

doi: 10.1128/JB.00906-09

Characterization of eRNA. (A) Agarose gel electrophoresis (1%) of RNA stained with ethidium bromide (1 μg/ml) as described in Materials and Methods. The photograph is representative of three independent experiments with similar results. Lanes: 1, S. gordonii ; 2, S. sanguinis ; 3, S. gordonii Pox − ; 4, S. sanguinis Pox − . (B) Precipitated nucleic acids from S. gordonii were digested with DNase RQ1 and RNase A, resolved by agarose gel electrophoresis (1%), and stained with ethidium bromide (1 μg/ml). (C) Quantification of eRNA by use of an RNA-specific fluorescent dye with the Quant-iT RNA assay. Sg, S. gordonii ; Ss, S. sanguinis . (D) Relative amounts of RNA normalized to cell density measured at A 600 . Data presented are the means ± SD of results from three independent experiments done on different days. (E) eRNA degradation. Total RNA from S. mutans ). Shown are means ± SD of results from at least two independent experiments with BHI, with the 0-min arbitrary level set to 100%.
Figure Legend Snippet: Characterization of eRNA. (A) Agarose gel electrophoresis (1%) of RNA stained with ethidium bromide (1 μg/ml) as described in Materials and Methods. The photograph is representative of three independent experiments with similar results. Lanes: 1, S. gordonii ; 2, S. sanguinis ; 3, S. gordonii Pox − ; 4, S. sanguinis Pox − . (B) Precipitated nucleic acids from S. gordonii were digested with DNase RQ1 and RNase A, resolved by agarose gel electrophoresis (1%), and stained with ethidium bromide (1 μg/ml). (C) Quantification of eRNA by use of an RNA-specific fluorescent dye with the Quant-iT RNA assay. Sg, S. gordonii ; Ss, S. sanguinis . (D) Relative amounts of RNA normalized to cell density measured at A 600 . Data presented are the means ± SD of results from three independent experiments done on different days. (E) eRNA degradation. Total RNA from S. mutans ). Shown are means ± SD of results from at least two independent experiments with BHI, with the 0-min arbitrary level set to 100%.

Techniques Used: Agarose Gel Electrophoresis, Staining

12) Product Images from "Detection of Viable Listeria monocytogenes with a 5? Nuclease PCR Assay"

Article Title: Detection of Viable Listeria monocytogenes with a 5? Nuclease PCR Assay

Journal: Applied and Environmental Microbiology

doi:

RT-5′ nuclease assay readout as a function of L. monocytogenes CFU in a background of nonviable cells. Results for a 10-fold dilution of RQ1 DNase-treated templates subjected to an RT-5′-nuclease assay with primers HLYP1 and HLYP2 (○) or primers HLYP8 and HLYP9 (□) are shown. All assays were carried out with HLYAP15 probe under the conditions described in Materials and Methods.
Figure Legend Snippet: RT-5′ nuclease assay readout as a function of L. monocytogenes CFU in a background of nonviable cells. Results for a 10-fold dilution of RQ1 DNase-treated templates subjected to an RT-5′-nuclease assay with primers HLYP1 and HLYP2 (○) or primers HLYP8 and HLYP9 (□) are shown. All assays were carried out with HLYAP15 probe under the conditions described in Materials and Methods.

Techniques Used: Nuclease Assay

13) Product Images from "miR482 Regulation of NBS-LRR Defense Genes during Fungal Pathogen Infection in Cotton"

Article Title: miR482 Regulation of NBS-LRR Defense Genes during Fungal Pathogen Infection in Cotton

Journal: PLoS ONE

doi: 10.1371/journal.pone.0084390

Expression analysis of ghr-miR482/miR482.2. A) Northern blot detection of ghr-miR482/482.2 in leaves collected from V. dahliae -infected and mock-treated cotton plants at one day-post-inoculation (1 dpi). Oligos antisense to ghr-miR482a and ghr-miR482e.2 were used together as probes. The values underneath the image are the relative signal intensity of ghr-miR482a/482e.2, which were determined using the MultiGauge V2.0 (Fuji Film) and normalized based on U6. V.d: V. dahliae -infected. B to H) Stem-loop qRT-PCR analysis of the expression level of individual members of the ghr-miR482 family. RQ1 DNase treated total RNA isolated from leaves and roots of 1-dpi plants was analysed using ghr-miR482/miR482.2 member specific stem-loop RT and PCR primers. Expression level was normalized to reference gene Histone 3. Error bars represent standard deviation of the expression ratio. * and ** denote significant relative to the corresponding mock-infected control at p
Figure Legend Snippet: Expression analysis of ghr-miR482/miR482.2. A) Northern blot detection of ghr-miR482/482.2 in leaves collected from V. dahliae -infected and mock-treated cotton plants at one day-post-inoculation (1 dpi). Oligos antisense to ghr-miR482a and ghr-miR482e.2 were used together as probes. The values underneath the image are the relative signal intensity of ghr-miR482a/482e.2, which were determined using the MultiGauge V2.0 (Fuji Film) and normalized based on U6. V.d: V. dahliae -infected. B to H) Stem-loop qRT-PCR analysis of the expression level of individual members of the ghr-miR482 family. RQ1 DNase treated total RNA isolated from leaves and roots of 1-dpi plants was analysed using ghr-miR482/miR482.2 member specific stem-loop RT and PCR primers. Expression level was normalized to reference gene Histone 3. Error bars represent standard deviation of the expression ratio. * and ** denote significant relative to the corresponding mock-infected control at p

Techniques Used: Expressing, Northern Blot, Infection, Quantitative RT-PCR, Isolation, Polymerase Chain Reaction, Standard Deviation

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Concentration Assay:

Article Title: In vivo and in vitro interaction between human transcription factor MOK2 and nuclear lamin A/C
Article Snippet: .. In brief, transfected HeLa cells were sequentially extracted with: 1% Triton X-100 in TMS buffer (50 mM Tris–HCl pH 7.4, 5 mM MgSO4 , 250 mM sucrose) for 5 min at RT (fraction 1); 50 U/ml RNase-free DNase RQ1 (Promega) in TMS at 37°C for 30 min and adding ammonium sulfate to a final concentration of 0.25 M (fraction 2); 2 M NaCl in TM buffer (10 mM Tris–HCl pH 7.4, 0.02 mM MgSO4 ) twice for 15 min at RT (fraction 3); 50 µg/ml RNase A in TM for 15 min at RT (fraction 4). ..

Transfection:

Article Title: Nonencapsidated 5′ Copy-Back Defective Interfering Genomes Produced by Recombinant Measles Viruses Are Recognized by RIG-I and LGP2 but Not MDA5
Article Snippet: .. Total RNAs extracted from HEK293-T7 and HEK293-T7-NP cells transfected with p2RZ vector in the presence or absence of pEMC-La (a kind gift of M. A. Billeter) were treated with RQ1 RNase-free DNase (Promega). .. Expression levels of IFN-β or ISG (Mx1 and DHX58) were quantified by one-step real-time PCR, using glyceraldehyde-3-phosphate dehydrogenase (GAPDH) mRNA expression as an internal control.

Article Title: In vivo and in vitro interaction between human transcription factor MOK2 and nuclear lamin A/C
Article Snippet: .. In brief, transfected HeLa cells were sequentially extracted with: 1% Triton X-100 in TMS buffer (50 mM Tris–HCl pH 7.4, 5 mM MgSO4 , 250 mM sucrose) for 5 min at RT (fraction 1); 50 U/ml RNase-free DNase RQ1 (Promega) in TMS at 37°C for 30 min and adding ammonium sulfate to a final concentration of 0.25 M (fraction 2); 2 M NaCl in TM buffer (10 mM Tris–HCl pH 7.4, 0.02 mM MgSO4 ) twice for 15 min at RT (fraction 3); 50 µg/ml RNase A in TM for 15 min at RT (fraction 4). ..

Plasmid Preparation:

Article Title: Nonencapsidated 5′ Copy-Back Defective Interfering Genomes Produced by Recombinant Measles Viruses Are Recognized by RIG-I and LGP2 but Not MDA5
Article Snippet: .. Total RNAs extracted from HEK293-T7 and HEK293-T7-NP cells transfected with p2RZ vector in the presence or absence of pEMC-La (a kind gift of M. A. Billeter) were treated with RQ1 RNase-free DNase (Promega). .. Expression levels of IFN-β or ISG (Mx1 and DHX58) were quantified by one-step real-time PCR, using glyceraldehyde-3-phosphate dehydrogenase (GAPDH) mRNA expression as an internal control.

Hybridization:

Article Title: snRNA-specific role of SMN in trypanosome snRNP biogenesis in vivo
Article Snippet: .. Optional RQ1-DNase treatment was done, using 6 U of RQ1 RNase-free DNase (Promega) for 1 h at 37°C to exclude the possibility of hybridization with DNA. .. The fixed and permeabilized cells were washed with PBS and the slides were prehybridized with hybridization buffer (60% deionized formamide, 50 mM sodium phosphate pH 7.2, 0.5 mg/ml salmon sperm DNA, 1 µg/µl yeast tRNA and 5x Denhardt's solution in 2x SSC) for 3–4 h at 72°C in a humid chamber.

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    Promega optional rq1 dnase treatment
    Nuclear accumulation of SL RNA and Sm proteins during SMN knockdown. (A) T. brucei cells without (t0) and after one, two and three days of RNAi-mediated SMN knockdown (t1–t3) were fixed, treated with <t>RQ1-DNase</t> (brightfield) and stained with DAPI
    Optional Rq1 Dnase Treatment, supplied by Promega, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/optional rq1 dnase treatment/product/Promega
    Average 85 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    optional rq1 dnase treatment - by Bioz Stars, 2020-05
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    99
    Promega rq1 dnase
    C. heterostrophus secretes DNases, and secretion is induced by plant tissue. WT, nuc1 mutant, nuc2 mutant, and nuc1 nuc2 double-mutant filtrates degrade intact λ DNA in the presence of plant material. The nuc1 single mutant and nuc1 nuc2 double mutant degrade lambda DNA less well than the WT or the nuc2 single mutant. This indicates that <t>DNase(s)</t> are secreted by the fungus, that the nuc1 mutant secretes a DNase that is important in DNA degradation, and that secretion is induced by host material. Left, size markers in kilobases. +, addition of corn leaf (CL) fragments, lambda DNA, or purified <t>RQ1</t> RNase-free DNase. Culture filtrates examined were from WT strain C4, nuc1 mutant strains 144206-3-1 and 8-1, nuc2 mutant strains 149183-2-1 and 3-1, and nuc1 nuc2 double-mutant strains 144206/149183-4-1 and 8-1. The negative-control reaction with λ DNA did not degrade the DNA, while the positive-control reaction with λ DNA plus DNase did. Also note that λ DNA was not degraded by the CL material.
    Rq1 Dnase, supplied by Promega, used in various techniques. Bioz Stars score: 99/100, based on 1493 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rq1 dnase/product/Promega
    Average 99 stars, based on 1493 article reviews
    Price from $9.99 to $1999.99
    rq1 dnase - by Bioz Stars, 2020-05
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    Image Search Results


    Nuclear accumulation of SL RNA and Sm proteins during SMN knockdown. (A) T. brucei cells without (t0) and after one, two and three days of RNAi-mediated SMN knockdown (t1–t3) were fixed, treated with RQ1-DNase (brightfield) and stained with DAPI

    Journal: RNA Biology

    Article Title: snRNA-specific role of SMN in trypanosome snRNP biogenesis in vivo

    doi: 10.4161/rna.8.1.13985

    Figure Lengend Snippet: Nuclear accumulation of SL RNA and Sm proteins during SMN knockdown. (A) T. brucei cells without (t0) and after one, two and three days of RNAi-mediated SMN knockdown (t1–t3) were fixed, treated with RQ1-DNase (brightfield) and stained with DAPI

    Article Snippet: Optional RQ1-DNase treatment was done, using 6 U of RQ1 RNase-free DNase (Promega) for 1 h at 37°C to exclude the possibility of hybridization with DNA.

    Techniques: Staining

    SMN protein largely colocalizes with the SL RNA transcripts in the nucleus. (A and B) T. brucei cells stably expressing SMN-PTP were fixed, permeabilized and treated with RQ1-DNase to degrade cellular DNA (brightfield); for control, see DAPI staining

    Journal: RNA Biology

    Article Title: snRNA-specific role of SMN in trypanosome snRNP biogenesis in vivo

    doi: 10.4161/rna.8.1.13985

    Figure Lengend Snippet: SMN protein largely colocalizes with the SL RNA transcripts in the nucleus. (A and B) T. brucei cells stably expressing SMN-PTP were fixed, permeabilized and treated with RQ1-DNase to degrade cellular DNA (brightfield); for control, see DAPI staining

    Article Snippet: Optional RQ1-DNase treatment was done, using 6 U of RQ1 RNase-free DNase (Promega) for 1 h at 37°C to exclude the possibility of hybridization with DNA.

    Techniques: Stable Transfection, Expressing, Staining

    C. heterostrophus secretes DNases, and secretion is induced by plant tissue. WT, nuc1 mutant, nuc2 mutant, and nuc1 nuc2 double-mutant filtrates degrade intact λ DNA in the presence of plant material. The nuc1 single mutant and nuc1 nuc2 double mutant degrade lambda DNA less well than the WT or the nuc2 single mutant. This indicates that DNase(s) are secreted by the fungus, that the nuc1 mutant secretes a DNase that is important in DNA degradation, and that secretion is induced by host material. Left, size markers in kilobases. +, addition of corn leaf (CL) fragments, lambda DNA, or purified RQ1 RNase-free DNase. Culture filtrates examined were from WT strain C4, nuc1 mutant strains 144206-3-1 and 8-1, nuc2 mutant strains 149183-2-1 and 3-1, and nuc1 nuc2 double-mutant strains 144206/149183-4-1 and 8-1. The negative-control reaction with λ DNA did not degrade the DNA, while the positive-control reaction with λ DNA plus DNase did. Also note that λ DNA was not degraded by the CL material.

    Journal: mBio

    Article Title: A DNase from a Fungal Phytopathogen Is a Virulence Factor Likely Deployed as Counter Defense against Host-Secreted Extracellular DNA

    doi: 10.1128/mBio.02805-18

    Figure Lengend Snippet: C. heterostrophus secretes DNases, and secretion is induced by plant tissue. WT, nuc1 mutant, nuc2 mutant, and nuc1 nuc2 double-mutant filtrates degrade intact λ DNA in the presence of plant material. The nuc1 single mutant and nuc1 nuc2 double mutant degrade lambda DNA less well than the WT or the nuc2 single mutant. This indicates that DNase(s) are secreted by the fungus, that the nuc1 mutant secretes a DNase that is important in DNA degradation, and that secretion is induced by host material. Left, size markers in kilobases. +, addition of corn leaf (CL) fragments, lambda DNA, or purified RQ1 RNase-free DNase. Culture filtrates examined were from WT strain C4, nuc1 mutant strains 144206-3-1 and 8-1, nuc2 mutant strains 149183-2-1 and 3-1, and nuc1 nuc2 double-mutant strains 144206/149183-4-1 and 8-1. The negative-control reaction with λ DNA did not degrade the DNA, while the positive-control reaction with λ DNA plus DNase did. Also note that λ DNA was not degraded by the CL material.

    Article Snippet: Reactions were run on 1% agarose gels at 100 V for 15 min. As a positive control for λ DNA degradation, 1 unit of RQ1 DNase (catalog no. M610A; Promega) was used.

    Techniques: Mutagenesis, Lambda DNA Preparation, Purification, Negative Control, Positive Control

    Polymerase sub-complexes lacking Rpb1 accumulate in not5Δ . A and B . Total extracts from cells expressing the indicated Tap-tagged (TT) polymerase subunits were separated on native gels (upper panels) or SDS-PAGE (lower panels) and analyzed by western blotting with anti- CBP antibodies. C . Rpb9-TT was purified by single step affinity and the purified proteins were analyzed on native gels (upper panels) or SDS-PAGE (lower panels) and western blotting with anti-CBP antibodies (left panel) or anti-Rpb1 antibodies (right panel). D . Total extracts from cells expressing Rpb11-TT were either untreated (-) or treated with DNase or RNase as indicated and separated by Native-PAGE, and analyzed by western blotting with PAP antibodies.

    Journal: PLoS Genetics

    Article Title: The Not5 Subunit of the Ccr4-Not Complex Connects Transcription and Translation

    doi: 10.1371/journal.pgen.1004569

    Figure Lengend Snippet: Polymerase sub-complexes lacking Rpb1 accumulate in not5Δ . A and B . Total extracts from cells expressing the indicated Tap-tagged (TT) polymerase subunits were separated on native gels (upper panels) or SDS-PAGE (lower panels) and analyzed by western blotting with anti- CBP antibodies. C . Rpb9-TT was purified by single step affinity and the purified proteins were analyzed on native gels (upper panels) or SDS-PAGE (lower panels) and western blotting with anti-CBP antibodies (left panel) or anti-Rpb1 antibodies (right panel). D . Total extracts from cells expressing Rpb11-TT were either untreated (-) or treated with DNase or RNase as indicated and separated by Native-PAGE, and analyzed by western blotting with PAP antibodies.

    Article Snippet: Pellets were resuspended in H2 O and were DNaseI treated (RQ1 RNase-free DNase, Promega).

    Techniques: Expressing, SDS Page, Western Blot, Purification, Clear Native PAGE

    Origin and localization of intron 18-containing CD44 transcripts in HT-29 human colon carcinoma cells. RNA preparations were subjected to DNase ( lane D ) and RNase ( lane R ) digestion before cDNA synthesis. RT-PCR was performed using primers P1 and Aex19. Products were electrophoresed and Southern blot analysis was performed using a hybridization probe specific for intron 18 (synthesized by PCR using primers I18-f2 and I18-r2). Similar analysis revealed intron 18-CD44 transcripts in both nuclear ( lane N ) and cytoplasmic ( lane C ) RNA fractions.

    Journal: The American Journal of Pathology

    Article Title: Multiple Intron Retention Occurs in Tumor Cell CD44 mRNA Processing

    doi:

    Figure Lengend Snippet: Origin and localization of intron 18-containing CD44 transcripts in HT-29 human colon carcinoma cells. RNA preparations were subjected to DNase ( lane D ) and RNase ( lane R ) digestion before cDNA synthesis. RT-PCR was performed using primers P1 and Aex19. Products were electrophoresed and Southern blot analysis was performed using a hybridization probe specific for intron 18 (synthesized by PCR using primers I18-f2 and I18-r2). Similar analysis revealed intron 18-CD44 transcripts in both nuclear ( lane N ) and cytoplasmic ( lane C ) RNA fractions.

    Article Snippet: Their 500 ng of mRNA were digested with either 1 μg of RNase (Boehringer Mannheim) or 0.1 U of RQ1 RNase-free DNase (Promega, Madison, WI) at 37°C for 20 minutes.

    Techniques: Reverse Transcription Polymerase Chain Reaction, Southern Blot, Hybridization, Synthesized, Polymerase Chain Reaction