Sybr safe dna dye

Manufactured by Thermo Fisher Scientific

Sourced in United Kingdom, United States

SYBR-safe DNA dye is a fluorescent dye used to stain DNA in various molecular biology applications. It binds to double-stranded DNA and emits a green fluorescent signal when excited by a suitable light source, allowing the visualization and quantification of DNA samples.

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Lab products found in correlation

Novex tbe gel, by Thermo Fisher Scientific (1 mentions) Dneasy blood and tissue kit, by Qiagen (1 mentions) Chemidoc imaging system, by Bio-Rad (1 mentions) Tri reagent, by Merck Group (1 mentions) Agarose, by Thermo Fisher Scientific (1 mentions) Camptothecin, by Thermo Fisher Scientific (1 mentions) Rhodamine 123 rh123, by Merck Group (1 mentions) Annexin 5 fitc, by Thermo Fisher Scientific (1 mentions) Bradford s reagent, by Bio-Rad (1 mentions) Rnase free dnase, by Thermo Fisher Scientific (1 mentions) Fetal bovine serum sfb, by Thermo Fisher Scientific (1 mentions) Mouse anti β actin, by Santa Cruz Biotechnology (1 mentions) Dulbecco s modified eagle medium dmem, by Thermo Fisher Scientific (1 mentions) Bovine serum albumin (bsa), by Merck Group (1 mentions) Celltiter glo, by Promega (1 mentions)

Spelling variants of this product

SYBR Safe (589 citations) SYBR Safe dye (34 citations) SYBR® Safe DNA (19 citations) SYBR safe DNA Gel stain dye (4 citations) SYBR™ Safe DNA Gel Dye (2 citations)

6 protocols using sybr safe dna dye

Tissue Preservation and Genotyping in Mice

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Liver, lung, kidney and bone marrow were quickly removed and frozen in liquid nitrogen following mouse cervical dislocation. Tissues were stored at −80 °C prior to cryogenic grinding (Cryotec) and subsequent DNA extraction. Genotyping was performed on genomic DNA extracted from WT, NeoR/PLA2R1 and Tg-hPLA2R1 mice. Sequences of the genotyping primers are indicated in Fig. 1C. PCR products were run on 2% agarose gels and stained using SYBR-safe DNA dye (Thermofisher).

Jaber S., Goehrig D., Bertolino P., Massemin A., Bihl F., Chabry J., Lambeau G., Vindrieux D, & Bernard D. (2020). Generation of a conditional transgenic mouse model expressing human Phospholipase A2 Receptor 1. Scientific Reports, 10, 8190.

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DNA Fragmentation Analysis via Gel Electrophoresis

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DNA fragmentation test was performed as previously described [19 ]. Genomic DNA was isolated from cells using DNeasy Blood and Tissue Kit (QIAGEN) according to the manufacturer’s manual. Five hundred nanograms of DNA was resolved on 4–20% Novex TBE gel (Thermo Fisher). The gel was stained with SYBR Safe DNA dye (Thermo Fisher) and visualized using a Bio-Rad ChemiDoc Imaging System.

Cao X., Lu Y., Liu Y., Zhou Y., Song H., Zhang W., Davis D., Cui J., Hao S., Jung J., Wu Q., Park D.M, & Yang C. (2019). Combination of PARP inhibitor and temozolomide to suppress chordoma progression. Journal of molecular medicine (Berlin, Germany), 97(8), 1183-1193.

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Electrophoretic Mobility Shift Assay

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EMSA was performed in 20 mM HEPES (pH 7.6), 250 mM NaCl, 1 mM DTT, 12% glycerol in a 10 μl volume. The final concentration of DNA was kept at 10 μM. The final concentration of MEF2 Chim WT (residues 1–95) and MEF2B (residues 1–93) was kept at 10 μM. The final NKX2-5 (residues 138–197) concentration was kept at 10 μM (DNA: MEF2: NKX2-5 molar ratio 1:1:1) or 20 μM (DNA: MEF2: NKX2-5 molar ratio 1:1:2). The binding reactions were analyzed on a 4%–20% (w/v) acrylamide gradient native gel in TBE and stained with Sybr Safe DNA Dye (Thermo Fisher Scientific).

Lei X., Zhao J., Sagendorf J.M., Rajashekar N., Xu J., Machado A.C., Sen C., Rohs R., Feng P, & Chen L. (2020). Crystal Structures of Ternary Complexes of MEF2 and NKX2-5 Bound to DNA Reveal a Disease Related Protein-Protein Interaction Interface. Journal of molecular biology, 432(19), 5499-5508.

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Total RNA Extraction and PCR Amplification

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Total RNA extraction from cells was performed using Tri reagent (Sigma-Aldrich). Following reverse transcription, PCR was carried out using GoTaq DNA olymerase (Promega, Southampton, UK). Reactions were carried out with the following process: 94°C for 5 min, 30 cycles of 94°C for 30 sec, 55°C for 30 sec and 72°C for 30 sec, followed by a final extension of 7 min at 72°C. PCR products were separated on a 1.5% agarose gel and photographed after staining with SYBR Safe DNA dye (Invitrogen, Paisley, UK).

Sun P.H., Chen G., Mason M., Jiang W.G, & Ye L. (2017). Dual roles of protein tyrosine phosphatase kappa in coordinating angiogenesis induced by pro-angiogenic factors. International Journal of Oncology, 50(4), 1127-1135.

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Mitochondrial and Nuclear DNA Analysis

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Mitochondrial and nuclear fractionation was followed as previously reported using bovine retina [7 (link)]. Isolated bovine retina cells were washed in PBS buffer three times and homogenized in a prechilled Dounce homogenizer using protease inhibitors and centrifuged (800 × g, 15 minutes). The pellet was saved for the nuclear fraction and the supernatant was centrifuged (6,000 × g, 15 minutes) and the pellet from the supernatant was used for the mitochondrial fraction. Mitochondrial and nuclear fractions were applied to Zymo DNA isolation Kit (Quick-gDNA™ MiniPrep) to purify mitochondrial and nuclear DNA. DNA samples were loaded on 0.5% agarose gel. Formation of DNA-prohibitin complexes was followed as reported [26 (link)]. Ten μg of total mitochondrial proteins and nuclear proteins were incubated (room temperature, 40 minutes) using 5 μg of mitochondrial DNA or nuclear DNA. Protein-DNA mixtures were centrifuged (16,000 × g, 30 minutes) and supernatant/pellet were separated using SDS-PAGE (8 16%). Prohibitin and DNA were analyzed using Western blotting and SYBR® Safe DNA dye (Invitrogen).

Sripathi S.R., Sylvester O., He W., Moser T., Um J.Y., Lamoke F., Ramakrishna W., Bernstein P.S., Bartoli M, & Jahng W.J. (2016). Prohibitin as the Molecular Binding Switch in the Retinal Pigment Epithelium. The protein journal, 35(1), 1-16.

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Apoptosis and Oxidative Stress Assays

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Secondary mouse IgGκ BP-HRP antibody (sc-516102), mouse anti-Bax (sc-20067), mouse anti-Bcl2 (sc-7382), mouse anti-caspase 9 (sc-56076), mouse anti-caspase 3 (sc-56053), mouse anti-matrix metalloproteinase-9 (MMP-9) (sc-93859), mouse anti-cytochrome C (sc-13561), and mouse anti-β-actin (sc-69879) were purchased from Santa Cruz Biotechnology (SCBT) (Santa Cruz, CA, USA). Bradford’s reagent was obtained from Bio-Rad. CellTiter-Glo was acquired from Promega. Annexin V fit-C, Agarose, Camptothecin (CPT), DNase-free RNase, dichlorodihydrofluorescein diacetate (H₂DCFDA), Hoechst-33342 (2’-[4-ethoxyphenyl]-5-[4-methyl-1-piperazinyl]-2,5’-bi-1H-benzimidazole trihydrate), 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), diphenyl-1-pyrenylphosphine (DPPP), Proteinase K, and SYBR^® Safe DNA dye were purchased from Invitrogen (Eugene, Oregon, USA). Dulbecco’s Modified Eagle Medium (DMEM) and Fetal Bovine Serum (SFB) were purchased from Gibco (Grand Island, NE, USA). Bovine serum albumin (BSA), Carbonylcyanide m-chlorophenylhydrazone (CCCP), Dimethylsulfoxide (DMSO), glycine, glutathione reduced (GSH), acridine orange (AO), tetramethylrhodamine ethyl ester (TMRE), digitonin, propidium iodide (IP), o- phthalaldehyde (OPA), hydrogen peroxide (H₂O₂), potassium cyanide (KCN), and Rhodamine 123 (Rh123) were purchased from Sigma Aldrich (St Louis, MO, USA).

Zani A.P., Zani C.P., Din Z.U., Rodrigues-Filho E., Ueda-Nakamura T., Garcia F.P., de Oliveira Silva S, & Nakamura C.V. (2023). Dibenzylideneacetone Induces Apoptosis in Cervical Cancer Cells through Ros-Mediated Mitochondrial Damage. Antioxidants, 12(2), 317.

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