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Promega bamhi restriction enzymes
Determination of copy number by Southern blot. A: EgDEF1 gene; B: gypsy retroelement. One L2T-related genotype (left: LMC343 or LMC51) is compared to one non-L2T-related genotype (right: FC2317 or FC2318). Lowercase letters signal the hybridizing bands that are predicted by the in silico digestion of the Eg133H20 BAC sequence with the appropriate restriction enzyme (a: 4,069 bp <t>EcoRI</t> fragment; b: 4,841 bp HindIII fragment; c: 6,251 <t>BamHI</t> fragment; d: 6,138 bp HindIII fragment; e: 13,132 bp BamHI fragment), asterisks indicate supernumerary bands.
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Article Title: DNA Methylation and Expression of the EgDEF1 Gene and Neighboring Retrotransposons in mantled Somaclonal Variants of Oil Palm

Journal: PLoS ONE

doi: 10.1371/journal.pone.0091896

Determination of copy number by Southern blot. A: EgDEF1 gene; B: gypsy retroelement. One L2T-related genotype (left: LMC343 or LMC51) is compared to one non-L2T-related genotype (right: FC2317 or FC2318). Lowercase letters signal the hybridizing bands that are predicted by the in silico digestion of the Eg133H20 BAC sequence with the appropriate restriction enzyme (a: 4,069 bp EcoRI fragment; b: 4,841 bp HindIII fragment; c: 6,251 BamHI fragment; d: 6,138 bp HindIII fragment; e: 13,132 bp BamHI fragment), asterisks indicate supernumerary bands.
Figure Legend Snippet: Determination of copy number by Southern blot. A: EgDEF1 gene; B: gypsy retroelement. One L2T-related genotype (left: LMC343 or LMC51) is compared to one non-L2T-related genotype (right: FC2317 or FC2318). Lowercase letters signal the hybridizing bands that are predicted by the in silico digestion of the Eg133H20 BAC sequence with the appropriate restriction enzyme (a: 4,069 bp EcoRI fragment; b: 4,841 bp HindIII fragment; c: 6,251 BamHI fragment; d: 6,138 bp HindIII fragment; e: 13,132 bp BamHI fragment), asterisks indicate supernumerary bands.

Techniques Used: Southern Blot, In Silico, BAC Assay, Sequencing

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Clone Assay:

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Article Snippet: Diap2 coding sequence was subcloned from the donor plasmid pCMV6-Ac-GFP-diap2 (Origene) into the receiver plasmid pEGFP-C3 (Takara), using In-Fusion HD Cloning Kit (Takara; National Center for Biotechnology Information Reference Sequence for diap2 , NM_172493.2). .. The receiver plasmid was digested with XhoI and BamHI restriction enzymes (Promega).

Article Title: Nostophycin Biosynthesis Is Directed by a Hybrid Polyketide Synthase-Nonribosomal Peptide Synthetase in the Toxic Cyanobacterium Nostoc sp. Strain 152
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Article Title: Role of RcsF in Signaling to the Rcs Phosphorelay Pathway in Escherichia coli
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Centrifugation:

Article Title: Structural Analysis of the DNA-binding Domain of the Helicobacter pylori Response Regulator ArsR
Article Snippet: Purified PCR products were digested with KpnI and BamHI restriction enzymes (Promega, Madison, WI) and ligated into linearized pET-BNK, a modified pET vector (Novagen, Madison, WI) developed specifically for expressing NMR protein targets. .. When the culture reached an A 600 of 1.0, protein expression was induced for 4 h with 0.8 m m isopropyl-β- d -thiogalactopyranoside.

Amplification:

Article Title: DNA Methylation and Expression of the EgDEF1 Gene and Neighboring Retrotransposons in mantled Somaclonal Variants of Oil Palm
Article Snippet: Seven micrograms of oil palm genomic DNA extracts were digested in parallel by either EcoRI, HindIII or BamHI restriction enzymes (Promega) according to the manufacturer's instructions. .. Seven micrograms of oil palm genomic DNA extracts were digested in parallel by either EcoRI, HindIII or BamHI restriction enzymes (Promega) according to the manufacturer's instructions.

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Article Title: Remodeling of the Inner Hair Cell Microtubule Meshwork in a Mouse Model of Auditory Neuropathy AUNA1
Article Snippet: Diap2 coding sequence was amplified from the donor plasmid using the primers diap2-PEGFP-3-F (5′-GTACTCAGATCTCGAGATGGAGGAGCTCGGGG-3′) and diap2-PEGFP-2-R (5′-TAGATCCGGTGGATCCTTGGATGACATGGCTCCATTG-3′; Eurogentec). .. The receiver plasmid was digested with XhoI and BamHI restriction enzymes (Promega).

Article Title: Nostophycin Biosynthesis Is Directed by a Hybrid Polyketide Synthase-Nonribosomal Peptide Synthetase in the Toxic Cyanobacterium Nostoc sp. Strain 152
Article Snippet: Adenylation (A) domains were amplified using degenerate PCR primers based on the A2 (KAGGAY) and A10 (NGKID) A domain conserved motifs ( ). .. The resulting PCR products were purified with the PCR purification kit (Edge Bio Systems), digested with XhoI and BamHI restriction enzymes (Promega), and ligated to pBluescript SK+ vector opened with the same enzymes.

Article Title: Structural Analysis of the DNA-binding Domain of the Helicobacter pylori Response Regulator ArsR
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Article Title: Role of RcsF in Signaling to the Rcs Phosphorelay Pathway in Escherichia coli
Article Snippet: Amplification of rcsF from the chromosome of E. coli was done using forward primer 5′-GGAATTCCTCGAGATGCGTGCTTTACCG and reverse primer 5′-CGCGGATCCGGAAACTGCTCATTTCGCCGT (IDT, Coralville, IA). .. Plasmids containing rcsF were digested and subcloned into pTrc99a from Amersham Pharmacia (Piscataway, NJ) using EcoRI and BamHI restriction enzymes (Promega, Madison, WI).

In Vitro:

Article Title: Evidence for redox sensing by a human cardiac calcium channel
Article Snippet: Mutants were confirmed by automated DNA sequencing and restriction digests using XbaI and BamHI restriction enzymes (Promega). .. Mutants were confirmed by automated DNA sequencing and restriction digests using XbaI and BamHI restriction enzymes (Promega).

Southern Blot:

Article Title: DNA Methylation and Expression of the EgDEF1 Gene and Neighboring Retrotransposons in mantled Somaclonal Variants of Oil Palm
Article Snippet: Paragraph title: Southern blot ... Seven micrograms of oil palm genomic DNA extracts were digested in parallel by either EcoRI, HindIII or BamHI restriction enzymes (Promega) according to the manufacturer's instructions.

Polymerase Chain Reaction:

Article Title: DNA Methylation and Expression of the EgDEF1 Gene and Neighboring Retrotransposons in mantled Somaclonal Variants of Oil Palm
Article Snippet: Seven micrograms of oil palm genomic DNA extracts were digested in parallel by either EcoRI, HindIII or BamHI restriction enzymes (Promega) according to the manufacturer's instructions. .. Seven micrograms of oil palm genomic DNA extracts were digested in parallel by either EcoRI, HindIII or BamHI restriction enzymes (Promega) according to the manufacturer's instructions.

Article Title: Evidence for redox sensing by a human cardiac calcium channel
Article Snippet: A standard amplification protocol was performed (MJ Research PTC-200 Thermal Cycler PCR). .. Mutants were confirmed by automated DNA sequencing and restriction digests using XbaI and BamHI restriction enzymes (Promega).

Article Title: Nostophycin Biosynthesis Is Directed by a Hybrid Polyketide Synthase-Nonribosomal Peptide Synthetase in the Toxic Cyanobacterium Nostoc sp. Strain 152
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Article Title: Structural Analysis of the DNA-binding Domain of the Helicobacter pylori Response Regulator ArsR
Article Snippet: The full-length arsR gene and a fragment encoding the DNA-binding domain were amplified by PCR from H. pylori strain J99 (gene JHP0152 ) using genomic DNA as template and pairs of primers including 5′ BamHI and 3′ KpnI restriction endonuclease sites (5′-CGGGATCCATGATAGAAGTTTTAATGATAGAAGATGATATAG and 5′-CGGGTACCTCAGTATTCTAATTTATAACCAATCCCTCT for full-length ArsR and 5′-GCGGGATCCGAAGAGGTGAGTGAGCCAGGC and 5′-GCGGGTACCTCAGTATTCTAATTTATAACCAATCCCTCT for ArsR-DBD). .. Purified PCR products were digested with KpnI and BamHI restriction enzymes (Promega, Madison, WI) and ligated into linearized pET-BNK, a modified pET vector (Novagen, Madison, WI) developed specifically for expressing NMR protein targets. .. The vector contains a 5′-coding sequence for an N-terminal purification tag MRGSHHHHHHGS in-frame with the insert coding for the desired proteins.

Article Title: Role of RcsF in Signaling to the Rcs Phosphorelay Pathway in Escherichia coli
Article Snippet: The PCR product was cloned into Invitrogen's TOPO2.1 plasmid (Carlsbad, CA) according to the manufacturer's specifications. .. Plasmids containing rcsF were digested and subcloned into pTrc99a from Amersham Pharmacia (Piscataway, NJ) using EcoRI and BamHI restriction enzymes (Promega, Madison, WI).

Mutagenesis:

Article Title: Evidence for redox sensing by a human cardiac calcium channel
Article Snippet: Paragraph title: Preparation of mutant constructs ... Mutants were confirmed by automated DNA sequencing and restriction digests using XbaI and BamHI restriction enzymes (Promega).

Construct:

Article Title: Evidence for redox sensing by a human cardiac calcium channel
Article Snippet: Paragraph title: Preparation of mutant constructs ... Mutants were confirmed by automated DNA sequencing and restriction digests using XbaI and BamHI restriction enzymes (Promega).

Purification:

Article Title: DNA Methylation and Expression of the EgDEF1 Gene and Neighboring Retrotransposons in mantled Somaclonal Variants of Oil Palm
Article Snippet: Seven micrograms of oil palm genomic DNA extracts were digested in parallel by either EcoRI, HindIII or BamHI restriction enzymes (Promega) according to the manufacturer's instructions. .. Seven micrograms of oil palm genomic DNA extracts were digested in parallel by either EcoRI, HindIII or BamHI restriction enzymes (Promega) according to the manufacturer's instructions.

Article Title: Nostophycin Biosynthesis Is Directed by a Hybrid Polyketide Synthase-Nonribosomal Peptide Synthetase in the Toxic Cyanobacterium Nostoc sp. Strain 152
Article Snippet: Reaction conditions for PCR were as follows: one cycle of 95°C for 2 min, 55°C for 40 s, and 72°C for 1 min; 25 cycles of 95°C for 30 s, 57°C for 30 s, and 72°C for 1 min; followed with the final extension step at 72°C for 5 min. DyNAzyme II polymerase (Finnzymes), 0.2 U, was used in the reaction volume in 20 μl with the buffer (10 mM Tris-HCl [pH = 8.8], 1.5 mM MgCl2 , 50 mM KCl, and 0.1% Triton X-100), 0.2 mM each nucleotide, 0.5 mM primers, and 10 to 50 ng of DNA. .. The resulting PCR products were purified with the PCR purification kit (Edge Bio Systems), digested with XhoI and BamHI restriction enzymes (Promega), and ligated to pBluescript SK+ vector opened with the same enzymes. .. The resulting PCR products were purified with the PCR purification kit (Edge Bio Systems), digested with XhoI and BamHI restriction enzymes (Promega), and ligated to pBluescript SK+ vector opened with the same enzymes.

Article Title: Structural Analysis of the DNA-binding Domain of the Helicobacter pylori Response Regulator ArsR
Article Snippet: The full-length arsR gene and a fragment encoding the DNA-binding domain were amplified by PCR from H. pylori strain J99 (gene JHP0152 ) using genomic DNA as template and pairs of primers including 5′ BamHI and 3′ KpnI restriction endonuclease sites (5′-CGGGATCCATGATAGAAGTTTTAATGATAGAAGATGATATAG and 5′-CGGGTACCTCAGTATTCTAATTTATAACCAATCCCTCT for full-length ArsR and 5′-GCGGGATCCGAAGAGGTGAGTGAGCCAGGC and 5′-GCGGGTACCTCAGTATTCTAATTTATAACCAATCCCTCT for ArsR-DBD). .. Purified PCR products were digested with KpnI and BamHI restriction enzymes (Promega, Madison, WI) and ligated into linearized pET-BNK, a modified pET vector (Novagen, Madison, WI) developed specifically for expressing NMR protein targets. .. The vector contains a 5′-coding sequence for an N-terminal purification tag MRGSHHHHHHGS in-frame with the insert coding for the desired proteins.

Produced:

Article Title: Nostophycin Biosynthesis Is Directed by a Hybrid Polyketide Synthase-Nonribosomal Peptide Synthetase in the Toxic Cyanobacterium Nostoc sp. Strain 152
Article Snippet: The resulting PCR products were purified with the PCR purification kit (Edge Bio Systems), digested with XhoI and BamHI restriction enzymes (Promega), and ligated to pBluescript SK+ vector opened with the same enzymes. .. The resulting PCR products were purified with the PCR purification kit (Edge Bio Systems), digested with XhoI and BamHI restriction enzymes (Promega), and ligated to pBluescript SK+ vector opened with the same enzymes.

Sequencing:

Article Title: DNA Methylation and Expression of the EgDEF1 Gene and Neighboring Retrotransposons in mantled Somaclonal Variants of Oil Palm
Article Snippet: Seven micrograms of oil palm genomic DNA extracts were digested in parallel by either EcoRI, HindIII or BamHI restriction enzymes (Promega) according to the manufacturer's instructions. .. Seven micrograms of oil palm genomic DNA extracts were digested in parallel by either EcoRI, HindIII or BamHI restriction enzymes (Promega) according to the manufacturer's instructions.

Article Title: Remodeling of the Inner Hair Cell Microtubule Meshwork in a Mouse Model of Auditory Neuropathy AUNA1
Article Snippet: Diap2 coding sequence was amplified from the donor plasmid using the primers diap2-PEGFP-3-F (5′-GTACTCAGATCTCGAGATGGAGGAGCTCGGGG-3′) and diap2-PEGFP-2-R (5′-TAGATCCGGTGGATCCTTGGATGACATGGCTCCATTG-3′; Eurogentec). .. The receiver plasmid was digested with XhoI and BamHI restriction enzymes (Promega).

Article Title: Nostophycin Biosynthesis Is Directed by a Hybrid Polyketide Synthase-Nonribosomal Peptide Synthetase in the Toxic Cyanobacterium Nostoc sp. Strain 152
Article Snippet: The resulting PCR products were purified with the PCR purification kit (Edge Bio Systems), digested with XhoI and BamHI restriction enzymes (Promega), and ligated to pBluescript SK+ vector opened with the same enzymes. .. The resulting PCR products were purified with the PCR purification kit (Edge Bio Systems), digested with XhoI and BamHI restriction enzymes (Promega), and ligated to pBluescript SK+ vector opened with the same enzymes.

Nuclear Magnetic Resonance:

Article Title: Structural Analysis of the DNA-binding Domain of the Helicobacter pylori Response Regulator ArsR
Article Snippet: The full-length arsR gene and a fragment encoding the DNA-binding domain were amplified by PCR from H. pylori strain J99 (gene JHP0152 ) using genomic DNA as template and pairs of primers including 5′ BamHI and 3′ KpnI restriction endonuclease sites (5′-CGGGATCCATGATAGAAGTTTTAATGATAGAAGATGATATAG and 5′-CGGGTACCTCAGTATTCTAATTTATAACCAATCCCTCT for full-length ArsR and 5′-GCGGGATCCGAAGAGGTGAGTGAGCCAGGC and 5′-GCGGGTACCTCAGTATTCTAATTTATAACCAATCCCTCT for ArsR-DBD). .. Purified PCR products were digested with KpnI and BamHI restriction enzymes (Promega, Madison, WI) and ligated into linearized pET-BNK, a modified pET vector (Novagen, Madison, WI) developed specifically for expressing NMR protein targets. .. The vector contains a 5′-coding sequence for an N-terminal purification tag MRGSHHHHHHGS in-frame with the insert coding for the desired proteins.

Random Primer DNA Labeling:

Article Title: DNA Methylation and Expression of the EgDEF1 Gene and Neighboring Retrotransposons in mantled Somaclonal Variants of Oil Palm
Article Snippet: Seven micrograms of oil palm genomic DNA extracts were digested in parallel by either EcoRI, HindIII or BamHI restriction enzymes (Promega) according to the manufacturer's instructions. .. Seven micrograms of oil palm genomic DNA extracts were digested in parallel by either EcoRI, HindIII or BamHI restriction enzymes (Promega) according to the manufacturer's instructions.

DNA Sequencing:

Article Title: Evidence for redox sensing by a human cardiac calcium channel
Article Snippet: A standard amplification protocol was performed (MJ Research PTC-200 Thermal Cycler PCR). .. Mutants were confirmed by automated DNA sequencing and restriction digests using XbaI and BamHI restriction enzymes (Promega). .. Correct mutant DNA was then purified from an overnight culture using low copy plasmid purification protocol (Nucleobond Xtra Midi plus) kit.

Expressing:

Article Title: Remodeling of the Inner Hair Cell Microtubule Meshwork in a Mouse Model of Auditory Neuropathy AUNA1
Article Snippet: Plasmids used for diap1-GFP and diap3-GFP expression in HEK293 cells were pReceiver-M03-Diap1 (GeneCopoeia) and pEFmEGFP-mDia2 (Addgene), respectively (GenBank accession numbers: diap1, BC070412.1; diap3, AF094519.1). .. The receiver plasmid was digested with XhoI and BamHI restriction enzymes (Promega).

Article Title: Structural Analysis of the DNA-binding Domain of the Helicobacter pylori Response Regulator ArsR
Article Snippet: The full-length arsR gene and a fragment encoding the DNA-binding domain were amplified by PCR from H. pylori strain J99 (gene JHP0152 ) using genomic DNA as template and pairs of primers including 5′ BamHI and 3′ KpnI restriction endonuclease sites (5′-CGGGATCCATGATAGAAGTTTTAATGATAGAAGATGATATAG and 5′-CGGGTACCTCAGTATTCTAATTTATAACCAATCCCTCT for full-length ArsR and 5′-GCGGGATCCGAAGAGGTGAGTGAGCCAGGC and 5′-GCGGGTACCTCAGTATTCTAATTTATAACCAATCCCTCT for ArsR-DBD). .. Purified PCR products were digested with KpnI and BamHI restriction enzymes (Promega, Madison, WI) and ligated into linearized pET-BNK, a modified pET vector (Novagen, Madison, WI) developed specifically for expressing NMR protein targets. .. The vector contains a 5′-coding sequence for an N-terminal purification tag MRGSHHHHHHGS in-frame with the insert coding for the desired proteins.

Modification:

Article Title: Structural Analysis of the DNA-binding Domain of the Helicobacter pylori Response Regulator ArsR
Article Snippet: The full-length arsR gene and a fragment encoding the DNA-binding domain were amplified by PCR from H. pylori strain J99 (gene JHP0152 ) using genomic DNA as template and pairs of primers including 5′ BamHI and 3′ KpnI restriction endonuclease sites (5′-CGGGATCCATGATAGAAGTTTTAATGATAGAAGATGATATAG and 5′-CGGGTACCTCAGTATTCTAATTTATAACCAATCCCTCT for full-length ArsR and 5′-GCGGGATCCGAAGAGGTGAGTGAGCCAGGC and 5′-GCGGGTACCTCAGTATTCTAATTTATAACCAATCCCTCT for ArsR-DBD). .. Purified PCR products were digested with KpnI and BamHI restriction enzymes (Promega, Madison, WI) and ligated into linearized pET-BNK, a modified pET vector (Novagen, Madison, WI) developed specifically for expressing NMR protein targets. .. The vector contains a 5′-coding sequence for an N-terminal purification tag MRGSHHHHHHGS in-frame with the insert coding for the desired proteins.

IA:

Article Title: Role of RcsF in Signaling to the Rcs Phosphorelay Pathway in Escherichia coli
Article Snippet: Amplification of rcsF from the chromosome of E. coli was done using forward primer 5′-GGAATTCCTCGAGATGCGTGCTTTACCG and reverse primer 5′-CGCGGATCCGGAAACTGCTCATTTCGCCGT (IDT, Coralville, IA). .. Plasmids containing rcsF were digested and subcloned into pTrc99a from Amersham Pharmacia (Piscataway, NJ) using EcoRI and BamHI restriction enzymes (Promega, Madison, WI).

Sonication:

Article Title: Structural Analysis of the DNA-binding Domain of the Helicobacter pylori Response Regulator ArsR
Article Snippet: Purified PCR products were digested with KpnI and BamHI restriction enzymes (Promega, Madison, WI) and ligated into linearized pET-BNK, a modified pET vector (Novagen, Madison, WI) developed specifically for expressing NMR protein targets. .. When the culture reached an A 600 of 1.0, protein expression was induced for 4 h with 0.8 m m isopropyl-β- d -thiogalactopyranoside.

Transformation Assay:

Article Title: Structural Analysis of the DNA-binding Domain of the Helicobacter pylori Response Regulator ArsR
Article Snippet: Purified PCR products were digested with KpnI and BamHI restriction enzymes (Promega, Madison, WI) and ligated into linearized pET-BNK, a modified pET vector (Novagen, Madison, WI) developed specifically for expressing NMR protein targets. .. The vector contains a 5′-coding sequence for an N-terminal purification tag MRGSHHHHHHGS in-frame with the insert coding for the desired proteins.

Positron Emission Tomography:

Article Title: Structural Analysis of the DNA-binding Domain of the Helicobacter pylori Response Regulator ArsR
Article Snippet: The full-length arsR gene and a fragment encoding the DNA-binding domain were amplified by PCR from H. pylori strain J99 (gene JHP0152 ) using genomic DNA as template and pairs of primers including 5′ BamHI and 3′ KpnI restriction endonuclease sites (5′-CGGGATCCATGATAGAAGTTTTAATGATAGAAGATGATATAG and 5′-CGGGTACCTCAGTATTCTAATTTATAACCAATCCCTCT for full-length ArsR and 5′-GCGGGATCCGAAGAGGTGAGTGAGCCAGGC and 5′-GCGGGTACCTCAGTATTCTAATTTATAACCAATCCCTCT for ArsR-DBD). .. Purified PCR products were digested with KpnI and BamHI restriction enzymes (Promega, Madison, WI) and ligated into linearized pET-BNK, a modified pET vector (Novagen, Madison, WI) developed specifically for expressing NMR protein targets. .. The vector contains a 5′-coding sequence for an N-terminal purification tag MRGSHHHHHHGS in-frame with the insert coding for the desired proteins.

Plasmid Preparation:

Article Title: Remodeling of the Inner Hair Cell Microtubule Meshwork in a Mouse Model of Auditory Neuropathy AUNA1
Article Snippet: Diap2 coding sequence was amplified from the donor plasmid using the primers diap2-PEGFP-3-F (5′-GTACTCAGATCTCGAGATGGAGGAGCTCGGGG-3′) and diap2-PEGFP-2-R (5′-TAGATCCGGTGGATCCTTGGATGACATGGCTCCATTG-3′; Eurogentec). .. The receiver plasmid was digested with XhoI and BamHI restriction enzymes (Promega). .. Subcloning was performed following the instructions from the manufacturer (Takara).

Article Title: Nostophycin Biosynthesis Is Directed by a Hybrid Polyketide Synthase-Nonribosomal Peptide Synthetase in the Toxic Cyanobacterium Nostoc sp. Strain 152
Article Snippet: Reaction conditions for PCR were as follows: one cycle of 95°C for 2 min, 55°C for 40 s, and 72°C for 1 min; 25 cycles of 95°C for 30 s, 57°C for 30 s, and 72°C for 1 min; followed with the final extension step at 72°C for 5 min. DyNAzyme II polymerase (Finnzymes), 0.2 U, was used in the reaction volume in 20 μl with the buffer (10 mM Tris-HCl [pH = 8.8], 1.5 mM MgCl2 , 50 mM KCl, and 0.1% Triton X-100), 0.2 mM each nucleotide, 0.5 mM primers, and 10 to 50 ng of DNA. .. The resulting PCR products were purified with the PCR purification kit (Edge Bio Systems), digested with XhoI and BamHI restriction enzymes (Promega), and ligated to pBluescript SK+ vector opened with the same enzymes. .. The resulting PCR products were purified with the PCR purification kit (Edge Bio Systems), digested with XhoI and BamHI restriction enzymes (Promega), and ligated to pBluescript SK+ vector opened with the same enzymes.

Article Title: Structural Analysis of the DNA-binding Domain of the Helicobacter pylori Response Regulator ArsR
Article Snippet: The full-length arsR gene and a fragment encoding the DNA-binding domain were amplified by PCR from H. pylori strain J99 (gene JHP0152 ) using genomic DNA as template and pairs of primers including 5′ BamHI and 3′ KpnI restriction endonuclease sites (5′-CGGGATCCATGATAGAAGTTTTAATGATAGAAGATGATATAG and 5′-CGGGTACCTCAGTATTCTAATTTATAACCAATCCCTCT for full-length ArsR and 5′-GCGGGATCCGAAGAGGTGAGTGAGCCAGGC and 5′-GCGGGTACCTCAGTATTCTAATTTATAACCAATCCCTCT for ArsR-DBD). .. Purified PCR products were digested with KpnI and BamHI restriction enzymes (Promega, Madison, WI) and ligated into linearized pET-BNK, a modified pET vector (Novagen, Madison, WI) developed specifically for expressing NMR protein targets. .. The vector contains a 5′-coding sequence for an N-terminal purification tag MRGSHHHHHHGS in-frame with the insert coding for the desired proteins.

Article Title: Role of RcsF in Signaling to the Rcs Phosphorelay Pathway in Escherichia coli
Article Snippet: The PCR product was cloned into Invitrogen's TOPO2.1 plasmid (Carlsbad, CA) according to the manufacturer's specifications. .. Plasmids containing rcsF were digested and subcloned into pTrc99a from Amersham Pharmacia (Piscataway, NJ) using EcoRI and BamHI restriction enzymes (Promega, Madison, WI).

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    Promega restriction endonuclease bamhi
    Restriction enzyme analysis of genomic Arg827/04 <t>DNA</t> in comparison with HAdV-3p strain GB and HAdV-16p strain Ch79. <t>BamHI</t> profiles for HAdV-16p and the 3-16 intertypic recombinant Arg827/04 exhibited identical band patterns, which are illustrated in a single lane. HindIII profiles for HAdV-3p and the 3-16 intertypic recombinant Arg827/04 exhibited identical band patterns that were also illustrated in a single lane. M, 1-kbp plus 100-bp molecular markers.
    Restriction Endonuclease Bamhi, supplied by Promega, used in various techniques. Bioz Stars score: 77/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    PCR ( A ), Southern blot ( B ) and sequence analysis ( C ) of the selected zeocin-resistant clones. (A). Aliquots from three different clones obtained from cells that expressed wt IN (wt 1–3 ), D116A IN (D116A 1–3 ), or no IN (-IN) were subjected to total genomic DNA extraction and PCR using 5′-U3-Zeo and 3′-U5-Zeo primers (B). Total genomic DNA was digested by BamH1 restriction enzyme and submitted to Southern blot analysis with (5′- 32 P) 5′-U3-Zeo as a probe. M: DNA size marker (bp). (C) Total genomic DNA was cut by BamH1 restriction enzyme, ligated, amplified using 5′-U3-junction and 3′-U5-junction primers and sequenced using the same primers. The name of the disrupted ORF is mentioned as well as the integration site inside the gene. The 5 bp repeats are underlined, dotted lines indicate base deletions at the integration site. ( D ) The sequences of the integrated products obtained either in an in vitro concerted integration assay [data obtained from Ref. ( 17 )] or from the in vivo yeast integration system were compared. The number of duplications and deletions in both systems are reported. 'Other duplications' indicate the number of cases that exhibited duplications comprising sizes from 3 to 6 bp.

    Journal: Nucleic Acids Research

    Article Title: Chromosomal integration of LTR-flanked DNA in yeast expressing HIV-1 integrase: down regulation by RAD51

    doi: 10.1093/nar/gkl843

    Figure Lengend Snippet: PCR ( A ), Southern blot ( B ) and sequence analysis ( C ) of the selected zeocin-resistant clones. (A). Aliquots from three different clones obtained from cells that expressed wt IN (wt 1–3 ), D116A IN (D116A 1–3 ), or no IN (-IN) were subjected to total genomic DNA extraction and PCR using 5′-U3-Zeo and 3′-U5-Zeo primers (B). Total genomic DNA was digested by BamH1 restriction enzyme and submitted to Southern blot analysis with (5′- 32 P) 5′-U3-Zeo as a probe. M: DNA size marker (bp). (C) Total genomic DNA was cut by BamH1 restriction enzyme, ligated, amplified using 5′-U3-junction and 3′-U5-junction primers and sequenced using the same primers. The name of the disrupted ORF is mentioned as well as the integration site inside the gene. The 5 bp repeats are underlined, dotted lines indicate base deletions at the integration site. ( D ) The sequences of the integrated products obtained either in an in vitro concerted integration assay [data obtained from Ref. ( 17 )] or from the in vivo yeast integration system were compared. The number of duplications and deletions in both systems are reported. 'Other duplications' indicate the number of cases that exhibited duplications comprising sizes from 3 to 6 bp.

    Article Snippet: Southern blot analysis was performed on genomic DNA according to a previously described protocol ( ) and using BamH1 restriction enzyme (PROMEGA) and the 32 P-labeled ODN, 5′-32 P-U3-Zeo described above as probe.

    Techniques: Polymerase Chain Reaction, Southern Blot, Sequencing, Clone Assay, DNA Extraction, Marker, Amplification, In Vitro, In Vivo

    Restriction enzyme analysis of genomic Arg827/04 DNA in comparison with HAdV-3p strain GB and HAdV-16p strain Ch79. BamHI profiles for HAdV-16p and the 3-16 intertypic recombinant Arg827/04 exhibited identical band patterns, which are illustrated in a single lane. HindIII profiles for HAdV-3p and the 3-16 intertypic recombinant Arg827/04 exhibited identical band patterns that were also illustrated in a single lane. M, 1-kbp plus 100-bp molecular markers.

    Journal:

    Article Title: Molecular Characterization of an Adenovirus 3-16 Intertypic Recombinant Isolated in Argentina from an Infant Hospitalized with Acute Respiratory Infection

    doi: 10.1128/JCM.02289-09

    Figure Lengend Snippet: Restriction enzyme analysis of genomic Arg827/04 DNA in comparison with HAdV-3p strain GB and HAdV-16p strain Ch79. BamHI profiles for HAdV-16p and the 3-16 intertypic recombinant Arg827/04 exhibited identical band patterns, which are illustrated in a single lane. HindIII profiles for HAdV-3p and the 3-16 intertypic recombinant Arg827/04 exhibited identical band patterns that were also illustrated in a single lane. M, 1-kbp plus 100-bp molecular markers.

    Article Snippet: For genomic characterization and genome type identification by REA, 1 μg of viral DNA was initially digested with restriction endonuclease BamHI according to the manufacturer's recommendations (Promega, Madison, WI) and further characterized by digestion with BglII, HindIII, SmaI, and XhoI.

    Techniques: Recombinant

    Determination of copy number by Southern blot. A: EgDEF1 gene; B: gypsy retroelement. One L2T-related genotype (left: LMC343 or LMC51) is compared to one non-L2T-related genotype (right: FC2317 or FC2318). Lowercase letters signal the hybridizing bands that are predicted by the in silico digestion of the Eg133H20 BAC sequence with the appropriate restriction enzyme (a: 4,069 bp EcoRI fragment; b: 4,841 bp HindIII fragment; c: 6,251 BamHI fragment; d: 6,138 bp HindIII fragment; e: 13,132 bp BamHI fragment), asterisks indicate supernumerary bands.

    Journal: PLoS ONE

    Article Title: DNA Methylation and Expression of the EgDEF1 Gene and Neighboring Retrotransposons in mantled Somaclonal Variants of Oil Palm

    doi: 10.1371/journal.pone.0091896

    Figure Lengend Snippet: Determination of copy number by Southern blot. A: EgDEF1 gene; B: gypsy retroelement. One L2T-related genotype (left: LMC343 or LMC51) is compared to one non-L2T-related genotype (right: FC2317 or FC2318). Lowercase letters signal the hybridizing bands that are predicted by the in silico digestion of the Eg133H20 BAC sequence with the appropriate restriction enzyme (a: 4,069 bp EcoRI fragment; b: 4,841 bp HindIII fragment; c: 6,251 BamHI fragment; d: 6,138 bp HindIII fragment; e: 13,132 bp BamHI fragment), asterisks indicate supernumerary bands.

    Article Snippet: Seven micrograms of oil palm genomic DNA extracts were digested in parallel by either EcoRI, HindIII or BamHI restriction enzymes (Promega) according to the manufacturer's instructions.

    Techniques: Southern Blot, In Silico, BAC Assay, Sequencing