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Dna polymerase 1 large klenow fragment

Manufactured by Promega
Sourced in Italy

DNA Polymerase I Large (Klenow) Fragment is a truncated form of E. coli DNA Polymerase I that retains polymerase and 3'→5' exonuclease activities, but lacks 5'→3' exonuclease activity. It can be used for a variety of DNA synthesis and modification applications.

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6 protocols using dna polymerase 1 large klenow fragment

1

Overexpression of CDK6 using pEGFP-N1 vector

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For CDK6 overexpression, we generated a new construct starting from pHAGE-CDK6 plasmid (gift from Gordon Mills & Kenneth Scott (Ng et al., 2018 (link))) and pEGFP-N1 (Pigazzi et al., 2008 (link)). In detail, we cut pHAGE-CDK6 with NcoI and pEGFP-N1 with EcoRI, used DNA Polymerase I Large (Klenow) Fragment (Promega) to generate blunt ends, then cut both plasmids using NotI. After this second digestion, we subcloned the CDK6 fragment into pEGFP-N1 backbone, obtaining pCDK6 plasmid. Both pCDK6 and pEGFP-N1, used as control vector and indicated as pØ, were transiently transfected in SHI-1 cell line for in vitro validations.
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2

Cloning and Sequencing of ACA1_384820 from A. castellanii

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The ACA1_384820 coding sequence from A. castellanii was amplified by PCR from total cDNA with flanking NdeI and XhoI restriction sites, using the primers ACA1_384820_Fwd_NdeI and ACA1_384820_Rev_XhoI (Table 2). PCR fragments were cloned into the NdeI/XhoI sites of the expression plasmid pTBPF-eGFP [21 (link)]. For the pTBPF-empty, pTBPF-eGFP was digested by NdeI and XhoI (NEB), and the sticky 5’-overhangings ends of the vector were filled using DNA Polymerase I Large (Klenow) Fragment (Promega) and ligated (T4 DNA Ligase, Promega) following the manufacturer’s recommendations.
All plasmid constructs were transferred in chemically-competent Escherichia coli DH5α and validated by Sanger sequencing. DNA sequencing was completed with the ABI Prism BigDye™ terminator v3.1 sequencing kit (Applied Biosystems) and then analyzed using an automatic ABI Prism 3730 genetic analyzer (Applied Biosystems).
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3

SISPA-Based Sequencing Library Preparation

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Libraries were prepared as previously described by Moreno et al. [23 (link)] following the sequence independent single primer amplification (SISPA) [24 (link)]. The RNA was reverse transcribed by SuperScript IV Reverse Transcriptase (Thermo Fisher Scientific, Monza, Italy) following the manufacturer’s instructions. The second strand of cDNA was synthesized by DNA Polymerase I Large (Klenow) Fragment (Promega, Milan, Italy) and the Klenow product amplified by the PCRBIO HiFi Polymerase (PCR BIOSYSTEM, Resnova s.r.l, Roma, Italy). The purified cDNA was digested with EcoRV enzyme (New England BioLabs, Pero, MI, Italy) and the libraries prepared by NEBNext Fast DNA Library Prep Set for Ion Torrent (New England BioLabs) size selecting the 400 nt amplicons. The emulsion PCR and the sequencing run were performed using the Ion 520 & Ion 530 Kit-OT2 according to the instructions (Ion Gene Studio S5 and Ion 530 Chip).
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4

Linc-RAM Expression in Mouse Tissues

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Total RNA extracted from mouse tissues, including heart, liver, brain, lung, kidney, intestine, spleen and skeletal muscle, at 8 weeks of age were separated by PAGE (7 M urea) on 6% polyacrylamide gels and transferred to a nylon membrane (N+; Amersham). Linc-RAM probes were labelled with α-32p-cytidine triphosphate (CTP) using DNA polymerase 1 Large (Klenow) Fragment (Promega, U1100). RNA blots were hybridized in ULTRAhyb (Ambion) at 68 °C overnight, washed twice (5 min) with 2 × saline sodium citrate (SSC)/0.1% SDS wash buffer at 68 °C, followed by stringent washes (2 × 30 min) with 0.1 × SSC/0.1% SDS wash buffer at 68 °C. RNA blots were then exposed to X-ray film at −80 °C. Full scan of Northern blot were presented in Supplementary Fig. 14.
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5

Xenograft Tumor Histopathological Analysis

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The xenograft tumors harvested after sacrifice were fixed in 10% neutral buffered formalin, dehydrated, and embedded in paraffin, then serially sectioned (4 µm) thickness, and subjected to histopathological analysis. Tissue sections were stained with hematoxylin and eosin, TUNEL stain (DNA Polymerase 1 Large (Klenow) Fragment from Promega; dATP, dCTP, dGTP from Promega, Cat # M2201; Bio-11-dUTP from Cedarlane) (Wijsman et al., 1993 (link)), Ki-67 antibody (Novus Biologicals, Cat # NB110–90592, RRID:AB_1217069) and BrdU antibody (Abcam, Cat# ab6326, RRID:AB_305426) following the manufacturer’s instructions. All slides were counterstained with hematoxylin and assessed under light microscopy. For IHC analysis – TUNEL expression levels were semi-quantified using immunoreactive scores (IRS range 0–12). Score definitions: 0 (score 0–3), 1+ (score 4–6), 2+ (score 7–9), 3+ (score 10–12). For Ki-67 and BrdU percent positivity, 10 fields were randomly chosen, and the average percentage of positive cells determined. All slides were assessed by a pathologist. Slides were scanned on the Aperio Scanscope AT2 Whole Slide Scanner using a 20x objective.
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6

Northern Blot Analysis of RNA Expression

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The northern blot was performed as described [26 (link)]. In brief, total RNA extracted from mouse tissues, including muscle, brown adipose tissue (BAT), inguinal white adipose tissue (iWAT), epididymal white adipose tissue (eWAT) and spleen at 8 weeks of age were separated by PAGE (7M urea) on 6% polyacrylamide gels and transferred to a nylon membrane (N+; Amersham). AK079912 probes were labeled with α-32p-cytidine triphosphate (CTP) using DNA polymerase 1 Large (Klenow) Fragment (Promega, U1100). RNA blots were hybridized in ULTRAhyb (Ambion) at 68 °C overnight, washed twice (5min) with 2 × saline sodium citrate (SSC)/0.1% SDS wash buffer at 68 °C, followed by stringent washes (2 × 30min) with 0.1 × SSC/0.1% SDS wash buffer at 68 °C. RNA blots were then exposed to X-ray film at −80 °C.
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