The largest database of trusted experimental protocols

38 protocols using bglii

1

Cloning of OlyA and PFO D4 Constructs

Check if the same lab product or an alternative is used in the 5 most similar protocols
The restriction enzyme SmaI was from New England Biolabs (USA), and the FastDigest restriction enzymes BamHI, BglII, MluI, NdeI, XhoI, rapid DNA ligation kits, GeneJET PCR purification kits, GeneJET gel extraction kits, GeneJET plasmid miniprep kits, and PageRuler prestained protein ladder were all from Fermentas (Thermo Scientific, USA). The pET plasmids were from Novagen (Merck, USA), and the pmCherry plasmids from Clontech (USA). Oligonucleotide primers for the OlyA (NCBI acc. code: AGH25589) constructs were synthesised by Sigma-Aldrich (USA), while the gene coding the D4 domain of PFO was synthesised by GenScript (USA).
+ Open protocol
+ Expand
2

Linearization and Purification of Plasmids

Check if the same lab product or an alternative is used in the 5 most similar protocols
Plasmids, P2X4/ pcDNA3.1+.and pcDNA3.1+ were linearized before transfection to facilitate their stable integration in 293T cells genome. Restriction enzyme Bgl II (Fermentas) was employed to linearize pcDNA3.1+/P2X4 and pcDNA3.1+. Before using Bgl II, it had been confirmed using software NEBcutter V2.0 that this enzyme was quite safe for important sequences required for protein synthesis of the inserted gene. Bgl II cut the pcDNA3.1+ only at single site (nucleotide number 13, far away from CMV promoter. Bgl II did not cut at any nucleotide site of inserted gene P2X4 (using software NEBcutter V2.0). Plasmids were also quantified using NanoDrop® (Spectrophotometer) (ND-1000) to facilitate the optimization of linearization reaction.
Digested plasmids were run on 1% agarose gel, 80V for 90 min and analyzed under UV-light. The gel slices containing linearized/ digested products (psP2X4 and pcDNA 3.1+) were cut with sterilized blade. Plasmids were purified according to the protocol of Fermentas DNA Extraction Kit (Cat # K0513). 5μl of purified plasmid were run on 1% agarose gel with λHindIII digested marker to check concentration for transfection. Concentration was also checked on nanodrop.
+ Open protocol
+ Expand
3

Identifying Tn5 Insertion Sites via Inverse PCR

Check if the same lab product or an alternative is used in the 5 most similar protocols
The chromosomal DNA adjacent to the sites of Tn5 insertion was determined in individual mutants by inverse PCR using primers pRLSR (5′-AACAAGCCAGGGATGTAACG-3′) and pRLSF (5′- CAGCAACACCTTCTTCACGA -3′) which were designed outwardly within the transposon. The DNA of each mutant was extracted using phenol-chloroform and then digested with BglII (Fermentas) which does not cut within the transposon. Subsequently, the digested DNA was self-ligated in a 30 μl reaction with 6U of T4 DNA ligase (Promega) and transferred into E. coli strain S17-1(λpir), where circularized DNA containing flanking fragments of the site of Tn5 insertion and transposon replicate as a plasmids. Transposon junction plasmids were isolated from selected transformants and subjected to inverse PCR using primers pRLSR and pRLSF which anneal to the oriR6K and Cmr ends of the transposon, respectively. The PCR products were purified using the Gel Extraction kit (Watson Biotechnologies, China) and sequenced. Sequences were analysed using the BlastX algorithm [53 (link)] compared to the protein sequence database (GenBank).
+ Open protocol
+ Expand
4

Construction of Expression Cassette

Check if the same lab product or an alternative is used in the 5 most similar protocols

In order to construct the expression cassette, all the elements were synthesized by Generay Biotechnology Company (Shanghai, China) and sub-cloned into pGH cloning vector by NdeI and NheI restriction enzymes (Fermentas, Germany) (Figure 1). eGFP was sub-cloned into the cassette by Bglll and Notl (Figure 2). Briefly, 1 µg plasmid DNA was digested by BglII and NotI (Fermentas, Germany) and the relevant buffer was added up to the final volume of 20 µl in 37 °C for 1 h. Enzymatic reaction was inactivated by chloroform and the cloning procedure was confirmed by HindIII digestion.

Schematic view of expression cassette. Expression cassette contains CASQ2 enhancer, HRE, MLC2v promoter, IRES, and β-globin poly A sequence.

 Schematic view of eGFP cloning into the cassette. eGFP was cloned into the cassette by NotI and BglII restriction enzymes.

+ Open protocol
+ Expand
5

Construction and Storage of Genetic Vectors

Check if the same lab product or an alternative is used in the 5 most similar protocols
The expression vector pGEX-AgeI (modified pGEX-KG), and plasmids pCDNA-2, pCDNA-gs16 carrying a gs16 gene encoding the repetitive fragment of H-Chain (GS16, Figure 1A) [25 (link)], and pSL-fn (n = 1, 2, 3, 4, 8, and 12) [26 ] were constructed and stored at −80 °C in our laboratory, along with E. coli DH5α and the expression strain BL21 (DE3). The fn fragments are gene sequences encoding non-repetitive sequences of H-Chain and all multimers (F1, F4, and F8, Figure 1A). Restriction endonucleases BglII, HindIII, AgeI, and BamHI were purchased from Fermentas (vilnius, Lithuania), NgoMIV was purchased from Promega (Madison, WI, USA), and T4 DNA ligase, ScaI and DNA molecular weight standards were purchased from Takara (Kusatsu, Japan). Agarose for DNA electrophoresis was purchased from the Gene Company (Hong Kong, China).
+ Open protocol
+ Expand
6

CXCR4 Promoter Luciferase Assay

Check if the same lab product or an alternative is used in the 5 most similar protocols
MDA‐MB‐231 cells stably overexpressing FOXC1 or BT549 cells with stable knockdown of FOXC1 and their respective control transfectants were plated at a density of 1 × 105‐5 × 105 cells/mL into 24‐well plates and transfected with 0.2 μg pGL3‐CXCR4 promoter‐luciferase plasmid and 0.02 μg SV40 Renilla luciferase plasmid (Promega, Madison, WI, USA) After 48 hours, cells were lysed with lysis buffer, and cell debris were removed by centrifugation at 14 500 g for 1 minute in an Eppendorf microcentrifuge. The luciferase activity was detected with the Dual Luciferase Assay (Promega) according to the manufacturer's instructions. The relative luciferase intensity was measured by a Modulus TD20/20 Luminometer (Turner Biosystems, Sunnyvale, CA, USA). All luciferase assays were carried out in triplicate. The promoter of CXCR4 was PCR amplified from genomic DNA using the primers 5′‐GGGGTACCTTCCAGCCACCACCCTCCA‐3′ (forward), 5′‐GAAGATCTCGGCGTCACTTTGCTACCTG‐3′ (reverse), digested with KpnI (FD0524; Fermentas) and Bgl II (fd0083; Fermentas), and ligated to the corresponding sites in pGL3 Basic vector (Promega).
+ Open protocol
+ Expand
7

Cloning and Transfection of Nrn1 in Rat Cells

Check if the same lab product or an alternative is used in the 5 most similar protocols
The eukaryotic pcDNA3.1(+) vector (Clontech, Mountain View, CA, USA) carrying the constitutive cytomegalovirus (CMV) promoter was used as the transgene vector. The entire Nrn1 coding sequences with terminal NheI and XhoI restriction sites was cloned from rat RSC96 cell cDNA via PCR amplification using the primers Nrn1-NheI-F, 5'-CTA GCT AGC ATG GGA CTT AAG TTG AAC GGC-3' and Nrn1-Xho1-R, 5'-CCG CTC GAG TCA GAA GGA AAA GCC AGG TCG C-3' (the underlined letters indicate Nhe I and Xho I restriction enzyme sites, respectively). The PCR thermocycle conditions were as follows: 94° C for 5 min followed by 35 cycles of 94° C for 30 s, 58° C for 30 s, and 72° C for 30 s. The pcDNA3.1(+)-Nrn1 plasmid was constructed by inserting the Nrn1 coding sequences between the NheI and XhoI restriction sites of the pcDNA3.1(+) vector. The pcDNA3.1(+)-Nrn1 plasmid was then digested with BglII and StuI (Fermentas, MBI, USA), a linearized DNA fragment containing the CMV promoter and Nrn1 was recovered by removing macromolecular contaminants, and the purified 2.3-kb DNA fragment was used for pronuclear microinjection.
+ Open protocol
+ Expand
8

Construction of Transgenic Cassette for Dicot Expression

Check if the same lab product or an alternative is used in the 5 most similar protocols
A transgenic cassette was created for dicot expression from a combination of the promoter sequence, cp4 EPSPS, and transcriptional termination sequences. A kanamycin selectable marker (neomycin phosphotransferase II, nptII) was used for maintenance in bacteria. The cauliflower mosaic virus promoter 35S [22 (link)] was used as a promoter in the cassette. Restriction digestion of the pCambia 1301 vector was performed using the restriction enzymes NCO1 and BglII. The restriction site was created in cp4 EPSPS by amplification with primers containing the sequence of restriction enzymes. The eluted product was ligated with the pCambia 1301 vector using the Fermentas ligation kit (Cat #EL0014). To confirm the cloning, the digestion procedure was performed using the restriction enzymes listed above. Digestion reactions were performed at 37 °C overnight in a PCR machine. Each 20-µl reaction contained 4–5 µg DNA, 2 µl 10 × recommended restriction buffer, and 5 U of NCO1 and BglII (Fermentas, USA). The DNA digestion was visually inspected under the UV light after agarose gel (1.5 %) electrophoresis. Orientation of the cp4 EPSPS gene was confirmed using the vector Forward primer GATTGATGTGATATCTCCACT and the gene Reverse primer ACTCTACCCATAGGTCTCTTAG and by sequencing with gene-specific primers.
+ Open protocol
+ Expand
9

Molecular Characterization of V. cholerae O139

Check if the same lab product or an alternative is used in the 5 most similar protocols
Restriction enzymes HindIII, PstI, and BglII (Fermentas) were used for the digestion of V. cholerae O139 chromosomal DNA and immobilized on nylon membranes (Amersham International). The CT encoding gene (ctxA) probe was a 540-bp XbaI-ClaI (Fermentas) fragment cloned into the plasmid pKTN901 using EcoR1 linkers (Kaper et al., 1988 ). The 267-bp cep probe was derived from EcoR1 (Fermentas) digested pSC01 plasmid.
+ Open protocol
+ Expand
10

Plasmid Linearization Using BglII

Check if the same lab product or an alternative is used in the 5 most similar protocols
Each of the plasmids pTV-frg 1 and pTV-frg 2 was separately digested and linearized using BglII (Fermentas, Lithuania). The digestion reaction was performed on 500 ng of each plasmid with 2 units of BglII in an appropriate buffer condition. Incubation was performed at 37°C for 16 hours. Finally the products were examined on 1% agarose gel.
+ Open protocol
+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required

Sign up now

Revolutionizing how scientists
search and build protocols!