The largest database of trusted experimental protocols

6 protocols using pcdna3 myc dnmt1

1

Plasmid Construction and Validation

Check if the same lab product or an alternative is used in the 5 most similar protocols
Kaiso-GFP, BTB-HA, pX459-Kaiso constructs were used the same as in [19 (link)]. Full-length Kaiso (1–692) was cloned in pGex-2T. pcDNA3/Myc-DNMT3B1 (Addgene plasmid # 35522), pcDNA3/Myc-DNMT3A (Addgene plasmid # 35521), pcDNA3/Myc-DNMT1 (Addgene plasmid # 36939) were a gifts from Arthur Riggs [42 (link),43 (link)]. For lentivirus purification, we used the pCDF system (System Bioscience): pVSV-G pFiv-34N plasmids. Kaiso was subcloned into pCDF1lentivirus-MCS2-EF1-Puro vector.
Plasmid for KLF4 editing was obtained as follows: ligation of BbsI-digested pSPCas9(BB)-2A-Puro (PX459) (Addgene # 48139) plasmid with annealed sgRNA oligo insert: Crisp_KLF4_for 5′-CACCGGAGCCGGTGCGGCTTGCGG, Crisp_KLF4_rev 5′-AAACCCGCAAGCCGCACCGGCTCC.All plasmids were verified by Sanger sequence analysis.
+ Open protocol
+ Expand
2

Engineered CRISPR Epigenetic Modifiers

Check if the same lab product or an alternative is used in the 5 most similar protocols
The dCas9 coding sequence was derived from pHR-SFFV-dCas9-BFP-KRAB (Addgene ID 46911) (a gift from Stanley Qi and Jonathan Weissman). The catalytic domains of DNMT1, DNMT3A, and DNMT3B were polymerase chain reaction (PCR)–amplified from pcDNA3/Myc-DNMT1 (Addgene ID 36939), pcDNA3/Myc-DNMT3A (Addgene ID 35521), and pcDNA3/Myc-DNMT3B1 (Addgene ID 35522) (a gift from Arthur Riggs), respectively. The DNMT3A (E752A) and DNMT3B (E697A) catalytically inactivating mutations were introduced by site-directed mutagenesis. All plasmids described in this study have been validated by Sanger sequencing and will be publically available through Addgene [17 ] (Supplementary Table S1).
+ Open protocol
+ Expand
3

Plasmid Transfection and Overexpression

Check if the same lab product or an alternative is used in the 5 most similar protocols
The following constructs were obtained from Addgene: pcDNA3/Myc-DNMT1 (plasmid 36939, from A. Riggs), pRK5-HA-Ubiquitin-WT (plasmid 17608, from T. Dawson), pCDNA3 Flag MKK3b(Glu) (plasmid 50449, from R. Davis), and pcDNA3 Flag HA (plasmid 10792, from W. Sellers). We obtained pCMV6-AC-GFP-NOS2 (NOS2-GFP) from OriGene (RG211819), and pcDNA3.1-HA-KAT5 (isoform 3) and pcDNA3.1-HA-KAT5 (isoform 3; T191A) were synthesized by GenScript. Cells (0.25 × 106 in 3 mL of medium) were seeded into 6-well plates and cultured overnight. Plasmids were diluted in Opti-MEM medium (125 µL/well) and supplemented with P3000 (5 µL/well) and added to Lipofectamine 3000 (5 µL/well) diluted in Opti-MEM medium (125 µL/well). DNA complexes were incubated for 15 min at room temperature and added dropwise to cells. Mock-transfected cells were treated with Lipofectamine and P3000 diluted in Opti-MEM as described. Cells were then incubated for the times indicated before analysis.
+ Open protocol
+ Expand
4

Recombinant Expression of PHF6 and SUV4-20H2

Check if the same lab product or an alternative is used in the 5 most similar protocols
The PHF6 and SUV4-20H2 genes were amplified with specific primers using the cDNA of 293T as the template. The amplicons were ligated into pCMV-3× HA and pEGFP-C1, respectively, to generate recombinant expression constructs. pcDNA3/Myc-DNMT1 (Addgene plasmid # 36939) and pcDNA3/Myc-DNMT3A (Addgene plasmid # 35521) were kind gifts from Arthur Riggs.
The anti-DNMT3A (sc-20703), anti-RPA194 (sc-28714), anti-UBF (sc-9131 X), and anti-c Myc (sc-40 X) antibodies were purchased from Santa Cruz. The anti-α-tubulin (T6199), anti-HA (H9658), and anti-bromodeoxyuridine (BrdU) (B2531) antibodies were bought from Sigma. The anti-5-methylcytosine (BI-MECY-0100) antibody was purchased from Eurogentec, and the anti-PHF6 (Bethyl-451A) was purchased from Bethyl Laboratories. The anti-H4K20me3 (ab9053), anti-DNMT1 (ab13537), anti-GFP (ab290), and anti-H3 (ab1791) antibodies were bought from Abcam. The secondary antibodies, IRDye800CW goat anti-mouse IgG (926-32210) and IRDye800CW goat anti-rabbit IgG (926-32211) were purchased from LI-COR.
+ Open protocol
+ Expand
5

Recombinant DNMT Expression and Mutagenesis

Check if the same lab product or an alternative is used in the 5 most similar protocols
Human DNMT1 and human DNMT3A cloned into pCAG-EGFP were kindly provided by Dr. Isao Suetake45 (link),46 (link). Human DNMT3B1 cloned into p3 × FLAG-CMV10 was kindly provided by Drs. Motoka Unoki and Hiroyuki Sasaki47 (link). Mutants of DNMT3B were generated by substituting serine for cysteine using the QuickChange Site-Directed Mutagenesis Kit (Agilent Technologies) according to the manufacturer’s instructions using the following primers: C651S mutant 5′-GAT TGG CGG AAG CCC AAG CAA CGA TCT CTC AAA TG-3′ and 5′-CAT TTG AGA GAT CGT TGC TTG GGC TTC CGC CAA TC-3′, C716S mutant 5′-CAT CTC ACG GTT CCT GGA GAG TAA TCC AGT GAT TG-3′ and 5′-CAA TCA CTG GAT TAC TCT CCA GGA ACC GTG AGA TG-3′. A DNMT3B Q772A/F809A double mutant was generated by the megaprimer method using PrimerStar MAX Premix (Takara). F809A mutant 5′-CTC GAA AGG ATC GCT GGC TTT CCT GTG-3′ and 5′-GGG AGA TCT CTA TTC ACA TGC AAA G-3′, Q772A mutant 5′-CCC CTC GAG CTG CAG GAC TGC TTG GAA TAC AAT AGG ATA GCC AAG TTA AAG AAA GTA GAG ACA ATA ACC AAG-3′. All constructs were verified by sequencing. pcDNA3/Myc-DNMT1 (Addgene plasmid # 36939) and pcDNA3/Myc-DNMT3B1 (Addgene plasmid # 35522) were a gift from Arthur Riggs48 . Each plasmid was transiently introduced into cells with polyethylene imine (PEI)-max (Polysciences) or Lipofectamine 2000 (Thermo Fisher Scientific), and the S-nitrosylation of proteins was analyzed after 24 h.
+ Open protocol
+ Expand
6

DNMT Isoform Selectivity Assay

Check if the same lab product or an alternative is used in the 5 most similar protocols
Compounds 1, 22 and 24 were tested to evaluate their selectivity on the different DNMT isoforms. To work selectively on DNMT1, DNMT3A, and DNMT3B, HEK293T cells were transfected with the plasmids containing the three different DNMTs' sequences and mock control. Cells were transfected with 2.5 μg of expression plasmid using Lipofectamine 3000 reagent (Invitrogen, Carlsbad, CA, USA) according the manufacturer's instruction. Plasmids pcDNA3/Myc-DNMT1 (Addgene plasmid # 36939), pcDNA3/Myc-DNMT3A (Addgene plasmid # 35521), and pcDNA3/Myc-DNMT3B1 (Addgene plasmid # 35522) were a gift from Arthur Riggs. [39, 40] The presence of exogenous DNMTs was checked by Western blot (not shown), and afterward, the transfected cells were freshly lysed in RIPA buffer as above. Cellular extract of 35 μg were incubated with selected compounds at different concentration in the 1-150 μm range (1% DMSO final conc.) or with vehicle alone (1% DMSO) at 37 °C for 2 h. RG108 (Cayman) was used as positive controls, while as negative control, lysates were denatured at 100 °C for 30 min. DNMT activity was detected by DNMT activity/inhibitor assay kit (Epigentek). Data are presented as means ± SD; each compound was tested at least three times.
+ 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!