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  • 98
    Promega polymerase chain reaction pcr clean up system
    The H2A variant H2A.Z is not involved in INO80 related effects at stress genes. H2A.Z is not involved in delayed promoter <t>nucleosome</t> repopulation in arp8 Δ. ( A and B ) Nucleosome scanning assay of the CTT1 locus (−600 to +350 bp). Wild-type and htz1 Δ cells were treated with 0.4M NaCl for 10, 30 and 60 min or left untreated. NuSA are shown in (A) and quantification of NuSA of the CTT1 −1 and +1 nucleosomes in wild-type and htz1 Δ are shown in (B). Graphs in (B) are normalized to the untreated wild-type sample. ( C ) The stress induced transient recruitment of INO80 to the 5΄ end of the CTT1 locus is similar in wild-type and htz1 Δ mutant. Recruitment to the CTT1 5΄ region (+275) including the +1 nucleosome during osmotic stress (for indicated time points) was measured by ChIP of Ino80-TAP. ( D ) Expression of the CTT1 locus during osmotic stress is not influenced by absence of H2A.Z. Wild-type cells (BY4741), arp8 Δ, htz1 Δ and htz1 Δ arp8 Δ mutants were treated with 0.4M NaCl for indicated time points. CTT1 expression levels were quantified relative to VCX1 by <t>qRT-PCR.</t> Expression levels were normalized to the maximum expression levels in wild-type (10 min).
    Polymerase Chain Reaction Pcr Clean Up System, supplied by Promega, used in various techniques. Bioz Stars score: 98/100, based on 26 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Promega pcr clean up system kit promega
    Comparison of the sensitivities for bla L1 gene detection by LAMP and conventional <t>PCR</t> methods. Pure genomic <t>DNA</t> extracted from S. maltophilia- K279a was diluted tenfold (379.0 ng/μl to 0.00379 pg/μl) and the DNA assayed by LAMP (A,B) and PCR (C) . (A) Turbidity was monitored using the Loopamp real-time turbidimeter and the OD recorded at 650 nm, at 6 s intervals. (B) Visual inspection of the color change, post-LAMP assay, and in the presence of calcein/Mn 2+ complex. (C) PCR products were analyzed by 2% agarose gel electrophoresis and stained with ethidium bromide. The DNA marker is D2000 DNA Marker (Tiangen Biotech Co., Ltd.) The size is about 179 bp.
    Pcr Clean Up System Kit Promega, supplied by Promega, used in various techniques. Bioz Stars score: 90/100, based on 3471 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Promega wizard pcr clean up system
    <t>PCR</t> and <t>DNA</t> sequencing
    Wizard Pcr Clean Up System, supplied by Promega, used in various techniques. Bioz Stars score: 99/100, based on 218 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Promega wizard sv pcr clean up system
    Diagrammatic representation of the RNA silencing constructs (not drawn to scale). (A) A 21 nucleotide artificial microRNA (ami-BEIIb)-based osa -miR528 was synthesized by fusion <t>PCR</t> and cloned into Vec8, a Ti binary vector with a wheat high molecular weight glutenin promoter (wHMGPro) and nopaline synthase terminator (NOS). (B) The secondary structure of the osa -miR528 backbone as predicted by RNAfold, including information on ami-BEIIb (reverse complement). The predicted target cleavage site (arrow with sequence bold and highlighted) is located between positions 10 and 11 of the <t>amiRNA,</t> while the two mismatches (grey highlight) are located at positions 1 and 21. (C) The hairpin RNA (hp-BEIIb) was cloned in Vec8 by inserting a 397 bp BEIIb fragment in the sense (BEIIb→) and antisense (BEIIb←) orientations. The two fragments are flanked by two rice introns, Rint4 and Rint9, which form a hairpin loop. The amiRNA and hp-RNA fragments were directionally cloned using several restriction sites (H, Hin dIII; B, Bam HI; K, Kpn I; N, Not I; E Eco RI; S, Spe I).
    Wizard Sv Pcr Clean Up System, supplied by Promega, used in various techniques. Bioz Stars score: 96/100, based on 247 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Promega wizard pcr clean up system kit
    Diagrammatic representation of the RNA silencing constructs (not drawn to scale). (A) A 21 nucleotide artificial microRNA (ami-BEIIb)-based osa -miR528 was synthesized by fusion <t>PCR</t> and cloned into Vec8, a Ti binary vector with a wheat high molecular weight glutenin promoter (wHMGPro) and nopaline synthase terminator (NOS). (B) The secondary structure of the osa -miR528 backbone as predicted by RNAfold, including information on ami-BEIIb (reverse complement). The predicted target cleavage site (arrow with sequence bold and highlighted) is located between positions 10 and 11 of the <t>amiRNA,</t> while the two mismatches (grey highlight) are located at positions 1 and 21. (C) The hairpin RNA (hp-BEIIb) was cloned in Vec8 by inserting a 397 bp BEIIb fragment in the sense (BEIIb→) and antisense (BEIIb←) orientations. The two fragments are flanked by two rice introns, Rint4 and Rint9, which form a hairpin loop. The amiRNA and hp-RNA fragments were directionally cloned using several restriction sites (H, Hin dIII; B, Bam HI; K, Kpn I; N, Not I; E Eco RI; S, Spe I).
    Wizard Pcr Clean Up System Kit, supplied by Promega, used in various techniques. Bioz Stars score: 86/100, based on 48 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Promega pcr clean up system purification kit
    Diagrammatic representation of the RNA silencing constructs (not drawn to scale). (A) A 21 nucleotide artificial microRNA (ami-BEIIb)-based osa -miR528 was synthesized by fusion <t>PCR</t> and cloned into Vec8, a Ti binary vector with a wheat high molecular weight glutenin promoter (wHMGPro) and nopaline synthase terminator (NOS). (B) The secondary structure of the osa -miR528 backbone as predicted by RNAfold, including information on ami-BEIIb (reverse complement). The predicted target cleavage site (arrow with sequence bold and highlighted) is located between positions 10 and 11 of the <t>amiRNA,</t> while the two mismatches (grey highlight) are located at positions 1 and 21. (C) The hairpin RNA (hp-BEIIb) was cloned in Vec8 by inserting a 397 bp BEIIb fragment in the sense (BEIIb→) and antisense (BEIIb←) orientations. The two fragments are flanked by two rice introns, Rint4 and Rint9, which form a hairpin loop. The amiRNA and hp-RNA fragments were directionally cloned using several restriction sites (H, Hin dIII; B, Bam HI; K, Kpn I; N, Not I; E Eco RI; S, Spe I).
    Pcr Clean Up System Purification Kit, supplied by Promega, used in various techniques. Bioz Stars score: 85/100, based on 34 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    The H2A variant H2A.Z is not involved in INO80 related effects at stress genes. H2A.Z is not involved in delayed promoter nucleosome repopulation in arp8 Δ. ( A and B ) Nucleosome scanning assay of the CTT1 locus (−600 to +350 bp). Wild-type and htz1 Δ cells were treated with 0.4M NaCl for 10, 30 and 60 min or left untreated. NuSA are shown in (A) and quantification of NuSA of the CTT1 −1 and +1 nucleosomes in wild-type and htz1 Δ are shown in (B). Graphs in (B) are normalized to the untreated wild-type sample. ( C ) The stress induced transient recruitment of INO80 to the 5΄ end of the CTT1 locus is similar in wild-type and htz1 Δ mutant. Recruitment to the CTT1 5΄ region (+275) including the +1 nucleosome during osmotic stress (for indicated time points) was measured by ChIP of Ino80-TAP. ( D ) Expression of the CTT1 locus during osmotic stress is not influenced by absence of H2A.Z. Wild-type cells (BY4741), arp8 Δ, htz1 Δ and htz1 Δ arp8 Δ mutants were treated with 0.4M NaCl for indicated time points. CTT1 expression levels were quantified relative to VCX1 by qRT-PCR. Expression levels were normalized to the maximum expression levels in wild-type (10 min).

    Journal: Nucleic Acids Research

    Article Title: INO80 represses osmostress induced gene expression by resetting promoter proximal nucleosomes

    doi: 10.1093/nar/gkw1292

    Figure Lengend Snippet: The H2A variant H2A.Z is not involved in INO80 related effects at stress genes. H2A.Z is not involved in delayed promoter nucleosome repopulation in arp8 Δ. ( A and B ) Nucleosome scanning assay of the CTT1 locus (−600 to +350 bp). Wild-type and htz1 Δ cells were treated with 0.4M NaCl for 10, 30 and 60 min or left untreated. NuSA are shown in (A) and quantification of NuSA of the CTT1 −1 and +1 nucleosomes in wild-type and htz1 Δ are shown in (B). Graphs in (B) are normalized to the untreated wild-type sample. ( C ) The stress induced transient recruitment of INO80 to the 5΄ end of the CTT1 locus is similar in wild-type and htz1 Δ mutant. Recruitment to the CTT1 5΄ region (+275) including the +1 nucleosome during osmotic stress (for indicated time points) was measured by ChIP of Ino80-TAP. ( D ) Expression of the CTT1 locus during osmotic stress is not influenced by absence of H2A.Z. Wild-type cells (BY4741), arp8 Δ, htz1 Δ and htz1 Δ arp8 Δ mutants were treated with 0.4M NaCl for indicated time points. CTT1 expression levels were quantified relative to VCX1 by qRT-PCR. Expression levels were normalized to the maximum expression levels in wild-type (10 min).

    Article Snippet: Mono nucleosome DNA bands were purified (Wizard® SV Gel and polymerase chain reaction (PCR) Clean-Up System, Promega).

    Techniques: Variant Assay, Mutagenesis, Chromatin Immunoprecipitation, Expressing, Quantitative RT-PCR

    Comparison of the sensitivities for bla L1 gene detection by LAMP and conventional PCR methods. Pure genomic DNA extracted from S. maltophilia- K279a was diluted tenfold (379.0 ng/μl to 0.00379 pg/μl) and the DNA assayed by LAMP (A,B) and PCR (C) . (A) Turbidity was monitored using the Loopamp real-time turbidimeter and the OD recorded at 650 nm, at 6 s intervals. (B) Visual inspection of the color change, post-LAMP assay, and in the presence of calcein/Mn 2+ complex. (C) PCR products were analyzed by 2% agarose gel electrophoresis and stained with ethidium bromide. The DNA marker is D2000 DNA Marker (Tiangen Biotech Co., Ltd.) The size is about 179 bp.

    Journal: Frontiers in Microbiology

    Article Title: Prevalence and detection of Stenotrophomonas maltophilia carrying metallo-β-lactamase blaL1 in Beijing, China

    doi: 10.3389/fmicb.2014.00692

    Figure Lengend Snippet: Comparison of the sensitivities for bla L1 gene detection by LAMP and conventional PCR methods. Pure genomic DNA extracted from S. maltophilia- K279a was diluted tenfold (379.0 ng/μl to 0.00379 pg/μl) and the DNA assayed by LAMP (A,B) and PCR (C) . (A) Turbidity was monitored using the Loopamp real-time turbidimeter and the OD recorded at 650 nm, at 6 s intervals. (B) Visual inspection of the color change, post-LAMP assay, and in the presence of calcein/Mn 2+ complex. (C) PCR products were analyzed by 2% agarose gel electrophoresis and stained with ethidium bromide. The DNA marker is D2000 DNA Marker (Tiangen Biotech Co., Ltd.) The size is about 179 bp.

    Article Snippet: The DNA was purified with the SV GEL and PCR Clean-Up System (Promega Co., USA).

    Techniques: Polymerase Chain Reaction, Lamp Assay, Agarose Gel Electrophoresis, Staining, Marker

    Illustrative representation of HSP 70 (234) amplification for Leishmania sp. before and after re-amplification of the PCR products. (A) PCR products of first amplification of HSP 70 (234) targeting analyzed by electrophoresis polyacrylamide gel stained with silver. Lanes: bp. molecular-weight marker (50 bp DNA ladder); 1. Infected Thrichomys laurentius from São Raimundo Nonato/PI; 2. Negative control of PCR reaction. (B) PCR products of re-amplification of the product obtained in the first PCR reaction. Lanes: bp. molecular-weight marker (50 bp DNA ladder); 1. Negative Thrichomys fosteri from Corumbá/MS (Positive only in kDNA); 2–5. Infected T. laurentius from São Raimundo Nonato/PI; 6. Infected T. fosteri from Corumbá/MS; 7. Negative control of PCR after re-amplification.

    Journal: PLoS Neglected Tropical Diseases

    Article Title: Distinct Leishmania Species Infecting Wild Caviomorph Rodents (Rodentia: Hystricognathi) from Brazil

    doi: 10.1371/journal.pntd.0003389

    Figure Lengend Snippet: Illustrative representation of HSP 70 (234) amplification for Leishmania sp. before and after re-amplification of the PCR products. (A) PCR products of first amplification of HSP 70 (234) targeting analyzed by electrophoresis polyacrylamide gel stained with silver. Lanes: bp. molecular-weight marker (50 bp DNA ladder); 1. Infected Thrichomys laurentius from São Raimundo Nonato/PI; 2. Negative control of PCR reaction. (B) PCR products of re-amplification of the product obtained in the first PCR reaction. Lanes: bp. molecular-weight marker (50 bp DNA ladder); 1. Negative Thrichomys fosteri from Corumbá/MS (Positive only in kDNA); 2–5. Infected T. laurentius from São Raimundo Nonato/PI; 6. Infected T. fosteri from Corumbá/MS; 7. Negative control of PCR after re-amplification.

    Article Snippet: The PCR products obtained for HSP70 (234) targeting and the products positive only in kDNA targeting were purified using the Wizard SV Gel kit and PCR Clean-up System kit (Promega).

    Techniques: Amplification, Polymerase Chain Reaction, Electrophoresis, Staining, Molecular Weight, Marker, Infection, Negative Control, Mass Spectrometry

    Identification of osKaR insertion site Arbitrary-primed PCR (AP-PCR) is a quick method to precisely identify the genomic region where a transposon has inserted. The following is specific for osKaR insertions: genomic DNA of the osKaR mutant is extracted (see Basic Protocol 1) and used for a semi-random PCR using the osKaR -specific primer oPCR1 and the random primer Deg3. The Deg3 primer consists of an 11-nucleotide random primer (in blue) with a 25-nucleotide specific tail (in red). The resulting PCR product is purified and used for a 2 nd PCR using the osKaR -specific primer Anchor1 and the Deg3-tail specific primer Deg4. The resulting PCR product is purified and DNA sequencing is performed using the osKaR -specific primer Anchor2.

    Journal: Current protocols in microbiology

    Article Title: Genetic Manipulation of Streptococcus pyogenes (The Group A Streptococcus, GAS)

    doi: 10.1002/9780471729259.mc09d03s30

    Figure Lengend Snippet: Identification of osKaR insertion site Arbitrary-primed PCR (AP-PCR) is a quick method to precisely identify the genomic region where a transposon has inserted. The following is specific for osKaR insertions: genomic DNA of the osKaR mutant is extracted (see Basic Protocol 1) and used for a semi-random PCR using the osKaR -specific primer oPCR1 and the random primer Deg3. The Deg3 primer consists of an 11-nucleotide random primer (in blue) with a 25-nucleotide specific tail (in red). The resulting PCR product is purified and used for a 2 nd PCR using the osKaR -specific primer Anchor1 and the Deg3-tail specific primer Deg4. The resulting PCR product is purified and DNA sequencing is performed using the osKaR -specific primer Anchor2.

    Article Snippet: Genomic DNA of GAS osKaR mutant (see Basic Protocol 1) Primers oPCR1, Deg3, Anchor1, Deg4 and Anchor2 (see recipe) Reagents and equipment for PCR Gel and PCR Clean-Up System kit (Wizard SV, Promega Cat. No. A9282)

    Techniques: Polymerase Chain Reaction, Mutagenesis, Purification, DNA Sequencing

    PCR verification of mt minichromosomes of Haematopinus suis and H. apri . ( A ) Lanes 1 and 14: low mass ladder (LML). Lanes 2 and 13: molecular weight marker VII (MWM). Lanes 3–10: amplicons from eight minichromosomes of H. suis (B2311), rrnS -trnC , trnL 1 - rrnL , nad2-trnI- cox1 -trnL 2 , trnR- nad4L -nad6-trnM , trnK-nad4-atp8 - atp6 -trnN , trnE - cob- trnV , trnQ - nad1 -trnT-trnG-nad3-trnW , and trnD-trnY-cox2-trnS1-trnS2-trnP- cox3 -trnA . Lanes 11–12: PCR amplicons from two minichromosomes of H. apri (B2418), rrnS -trnC , and trnQ - nad1 -trnT-trnG-nad3-trnW . Genes where PCR primers were designed are in bold. ( B ) Lane 1: amplicon from trnH- nad5 -trnF minichromosome of H. suis (B2311). Lanes 2, 9, and 15: 1-kb ladder. Lanes 3–8 and 10–14: PCR amplicons from seven minichromosomes of H. apri (B2418), trnK-nad4-atp8 - atp6 -trnN , trnK- nad4 -atp8-atp6-trnN , nad2-trnI- cox1 -trnL 2 , nad2 -trnI-cox1-trnL 2 , trnD-trnY- cox2 -trnS1-trnS2-trnP-cox3-trnA , trnD-trnY-cox2-trnS1-trnS2-trnP- cox3 -trnA , trnE- cob- trnV , trnH- nad5 -trnF , trnR- nad4L -nad6-trnM , trnR-nad4L- nad6 -trnM , and trnL 1 - rrnL . ( C ) Amplicons by pig-lice-specific primers, PGC1F-PGC1R and PG12SF-PG12SR, from the entire nad2-trnI-cox1-trnL 2 minichromosome (4.5 kb, Lane 1) and the entire rrnS-trnC minichromosome (3.5 kb, Lane 4) of H. suis . Lane 2: LML. Lane 3: 1-kb Ladder. ( D ) Amplicons from the coding regions of mt minichromosomes of H. suis and H. apri . Lanes 1 and 11: LML. Lanes 2 and 10: MWM. Lanes 3–4: H. suis from Australia (B2311). Lanes 5–6: H. suis from Poland (B2419). Lanes 7–8: H. apri from Japan (B4218). Lane 9: H. suis from China (B2572).

    Journal: Genome Biology and Evolution

    Article Title: Substantial Variation in the Extent of Mitochondrial Genome Fragmentation among Blood-Sucking Lice of Mammals

    doi: 10.1093/gbe/evt094

    Figure Lengend Snippet: PCR verification of mt minichromosomes of Haematopinus suis and H. apri . ( A ) Lanes 1 and 14: low mass ladder (LML). Lanes 2 and 13: molecular weight marker VII (MWM). Lanes 3–10: amplicons from eight minichromosomes of H. suis (B2311), rrnS -trnC , trnL 1 - rrnL , nad2-trnI- cox1 -trnL 2 , trnR- nad4L -nad6-trnM , trnK-nad4-atp8 - atp6 -trnN , trnE - cob- trnV , trnQ - nad1 -trnT-trnG-nad3-trnW , and trnD-trnY-cox2-trnS1-trnS2-trnP- cox3 -trnA . Lanes 11–12: PCR amplicons from two minichromosomes of H. apri (B2418), rrnS -trnC , and trnQ - nad1 -trnT-trnG-nad3-trnW . Genes where PCR primers were designed are in bold. ( B ) Lane 1: amplicon from trnH- nad5 -trnF minichromosome of H. suis (B2311). Lanes 2, 9, and 15: 1-kb ladder. Lanes 3–8 and 10–14: PCR amplicons from seven minichromosomes of H. apri (B2418), trnK-nad4-atp8 - atp6 -trnN , trnK- nad4 -atp8-atp6-trnN , nad2-trnI- cox1 -trnL 2 , nad2 -trnI-cox1-trnL 2 , trnD-trnY- cox2 -trnS1-trnS2-trnP-cox3-trnA , trnD-trnY-cox2-trnS1-trnS2-trnP- cox3 -trnA , trnE- cob- trnV , trnH- nad5 -trnF , trnR- nad4L -nad6-trnM , trnR-nad4L- nad6 -trnM , and trnL 1 - rrnL . ( C ) Amplicons by pig-lice-specific primers, PGC1F-PGC1R and PG12SF-PG12SR, from the entire nad2-trnI-cox1-trnL 2 minichromosome (4.5 kb, Lane 1) and the entire rrnS-trnC minichromosome (3.5 kb, Lane 4) of H. suis . Lane 2: LML. Lane 3: 1-kb Ladder. ( D ) Amplicons from the coding regions of mt minichromosomes of H. suis and H. apri . Lanes 1 and 11: LML. Lanes 2 and 10: MWM. Lanes 3–4: H. suis from Australia (B2311). Lanes 5–6: H. suis from Poland (B2419). Lanes 7–8: H. apri from Japan (B4218). Lane 9: H. suis from China (B2572).

    Article Snippet: PCR amplicons used for sequencing were purified with Wizard SV Gel/PCR Clean-up System (Promega).

    Techniques: Polymerase Chain Reaction, Molecular Weight, Marker, Amplification

    PCR and DNA sequencing

    Journal:

    Article Title: Production of a unique pneumococcal capsule serotype belonging to serogroup 6

    doi: 10.1099/mic.0.024521-0

    Figure Lengend Snippet: PCR and DNA sequencing

    Article Snippet: PCR products were purified using Wizard PCR Clean-up System (Promega), and the DNA sequencing was performed by the genomics core facility at the University of Alabama at Birmingham (UAB).

    Techniques: Polymerase Chain Reaction, DNA Sequencing

    Diagrammatic representation of the RNA silencing constructs (not drawn to scale). (A) A 21 nucleotide artificial microRNA (ami-BEIIb)-based osa -miR528 was synthesized by fusion PCR and cloned into Vec8, a Ti binary vector with a wheat high molecular weight glutenin promoter (wHMGPro) and nopaline synthase terminator (NOS). (B) The secondary structure of the osa -miR528 backbone as predicted by RNAfold, including information on ami-BEIIb (reverse complement). The predicted target cleavage site (arrow with sequence bold and highlighted) is located between positions 10 and 11 of the amiRNA, while the two mismatches (grey highlight) are located at positions 1 and 21. (C) The hairpin RNA (hp-BEIIb) was cloned in Vec8 by inserting a 397 bp BEIIb fragment in the sense (BEIIb→) and antisense (BEIIb←) orientations. The two fragments are flanked by two rice introns, Rint4 and Rint9, which form a hairpin loop. The amiRNA and hp-RNA fragments were directionally cloned using several restriction sites (H, Hin dIII; B, Bam HI; K, Kpn I; N, Not I; E Eco RI; S, Spe I).

    Journal: Journal of Experimental Botany

    Article Title: Impact of down-regulation of starch branching enzyme IIb in rice by artificial microRNA- and hairpin RNA-mediated RNA silencing

    doi: 10.1093/jxb/err188

    Figure Lengend Snippet: Diagrammatic representation of the RNA silencing constructs (not drawn to scale). (A) A 21 nucleotide artificial microRNA (ami-BEIIb)-based osa -miR528 was synthesized by fusion PCR and cloned into Vec8, a Ti binary vector with a wheat high molecular weight glutenin promoter (wHMGPro) and nopaline synthase terminator (NOS). (B) The secondary structure of the osa -miR528 backbone as predicted by RNAfold, including information on ami-BEIIb (reverse complement). The predicted target cleavage site (arrow with sequence bold and highlighted) is located between positions 10 and 11 of the amiRNA, while the two mismatches (grey highlight) are located at positions 1 and 21. (C) The hairpin RNA (hp-BEIIb) was cloned in Vec8 by inserting a 397 bp BEIIb fragment in the sense (BEIIb→) and antisense (BEIIb←) orientations. The two fragments are flanked by two rice introns, Rint4 and Rint9, which form a hairpin loop. The amiRNA and hp-RNA fragments were directionally cloned using several restriction sites (H, Hin dIII; B, Bam HI; K, Kpn I; N, Not I; E Eco RI; S, Spe I).

    Article Snippet: After PCR purification using Wizard SV PCR Clean-up System (Promega), the amiRNA precursor (254 bp) was cloned into pGEM-T Easy (Promega) using E. coli DH5α.

    Techniques: Construct, Synthesized, Polymerase Chain Reaction, Clone Assay, Plasmid Preparation, Molecular Weight, Sequencing