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1x evagreen  (Jena Bioscience)


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    Structured Review

    Jena Bioscience 1x evagreen
    1x Evagreen, supplied by Jena Bioscience, used in various techniques. Bioz Stars score: 94/100, based on 14 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/evagreen+fluorescent+dna+stain/InfiniteGreen+Fluorescent+DNA+Stain/bio_rxiv__64898__2026__05__06__723196-362-21-23
    Average 94 stars, based on 14 article reviews
    1x evagreen - by Bioz Stars, 2026-10
    94/100 stars

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    Related Articles

    Gene Expression:

    Article Title: Deazaflavin metabolite produced by endosymbiotic bacteria controls fungal host reproduction
    Article Snippet: .. All primer pairs have an efficiency of 93% to 96% and were used in subsequent gene expression experiments ( ) using My Taq HS Mix (Bioline, London, UK) and EvaGreen® Fluorescent DNA Stain (Jena Bioscience, Jena, Germany). .. All primer pairs have an efficiency of 93% to 96% and were used in subsequent gene expression experiments ( ) using My Taq HS Mix (Bioline, London, UK) and EvaGreen Fluorescent DNA Stain (Jena Bioscience, Jena, Germany).

    Staining:

    Article Title: Deazaflavin metabolite produced by endosymbiotic bacteria controls fungal host reproduction
    Article Snippet: .. All primer pairs have an efficiency of 93% to 96% and were used in subsequent gene expression experiments ( ) using My Taq HS Mix (Bioline, London, UK) and EvaGreen® Fluorescent DNA Stain (Jena Bioscience, Jena, Germany). .. All primer pairs have an efficiency of 93% to 96% and were used in subsequent gene expression experiments ( ) using My Taq HS Mix (Bioline, London, UK) and EvaGreen Fluorescent DNA Stain (Jena Bioscience, Jena, Germany).

    Article Title: Microcapsule for detecting and/or quantitating an analyte in a sample
    Article Snippet: Components Per mL Polymerisation Mix Reaction mix 20% (w/v) N-Isopropylacrylamide (NIPAM) 250 μl 2.5% (w/v) N,N′-Methylenebisacrylamide 20 μl 2.5% Biotin-modified monomer 10 μl 5% (w/v) Ammonium persulfate 150 μl Deionised water 570 μl Component 2 (Reagent Phase): A (2-Hydroxypropyl)-y-cyclodextrine stock solution (100%) was also prepared in nuclease-free water using Cavasol W7 or W8 (Sigma) and stored at room temperature. .. The final mixture for PCR accommodating all reagents to be encapsulated contained the following: 1.25 U/μl Hot Start Taq DNA Polymerase (biotechrabbit GmbH) 4.0 mM dNTPs (biotechrabbit GmbH) 8.0 μM sense primer (5′-GCAGTGGCGCCCGAACAGG-3′) (Metabion International AG) 8.0 μM antisense primer (5′-ACTGACGCTCTCGCACCCATCT-3′) (Metabion International AG) 8.0 μM Taq-Man probe (5′-CF647-CTCCGACGCAACGGGCTCG-BHQ3-3′) (Metabion International AG) or 10× EvaGreen® Fluorescent DNA Stain (Jena Bioscience GmbH) Sodiumpolyphosphate (Merck) 9% (w/v) (2-Hydroxypropyl)-y-cyclodextrine (Sigma) The reagent mix was spray-dried using the Nano Spray Dryer B-90 (Büchi Labortechnik GmbH) to obtain nanoparticle-sized reagent. .. Nanoparticles were subsequently dried under vacuum just before dispersing them in the tristearin Softenol 3118 (IOI Oleo GmbH) at a maximum concentration of 10% (w/v) by ultrasonic treatment at elevated temperature (80-90° C.) using the S-450D Digital Sonifier (Branson).

    Article Title: Stimulus-responsive nanocarrier from star-shaped polyethyleneimine-β-cyclodextrin coated mesoporous silica for targeted combination cancer therapy
    Article Snippet: In this study, a stimulus-responsive organic/inorganic supramolecular nanostructure (SRN) was designed to develop a multifunctional nano-drug delivery system for combined chemo/gene/magnetic hyperthermia therapy targeting multidrug-resistant cancer.. SRNs have been successfully fabricated based on host/guest interactions between folate-appended-polyethyleneimine-β-cyclodextrin (FPC) and benzimidazole-modified magnetic-hollow mesoporous silica nanoparticles (BM-MHMSNs).. A typical antitumor drug, Doxorubicin (DOX), was successfully loaded in the pore of BM-MHMSNs and capped by FPC.

    Article Title: Dynamics of the milk microbial community during subacute ruminal acidosis with or without intramammary lipopolysaccharide challenge in dairy cows
    Article Snippet: .. The DNA samples were assayed in duplicate in a 23 μL reaction mixture, which contained 12.7 μL DEPC-treated water, 2.5 μL 10 × buffer, 1.0 μL 2 mM MgCl 2 (stock concentration 50 mM), 2.5 μL of each primer (stock concentration 2.5 μM), 0.5 μL of EvaGreen fluorescent DNA stain (JenaBioscience, Jena, Germany), 1.0 μL of dNTP Mix (stock concentration 20 mM, 5 mM of each dNTP; Thermofisher, Vienna, Austria), 0.3 μL of Platinum Taq DNA polymerase (5 U/μl; Thermo Fisher Scientific, Vienna, Austria), and 2 μL of the diluted template (gDNA). .. The quantification of DNA was performed in an Mx3000P qPCR instrument (v.4.10; Stratagene, La Jolla, CA, United States) with an initial denaturation at 95 °C for 3 min, followed by 45 cycles of 95 °C for 5 s, 60 °C for 20 s. To determine the specificity of the amplifications, dissociation curves after each reaction were recorded and carried out at 95 °C for 1 min, followed by complete annealing at 50 °C for 30 s, and a gradually increasing temperature up to 95 °C.

    Article Title: Microcapsule for detecting and/or quantitating an analyte in a sample
    Article Snippet: A (2-Hydroxypropyl)-y-cyclodextrine stock solution (100%) was also prepared in nuclease-free water using Cavasol W7 or W8 (Sigma) and stored at room temperature. .. The final mixture for PCR accommodating all reagents to be encapsulated contained the following: Component 2: 1.25 U/μl Hot Start Taq DNA Polymerase (biotechrabbit GmbH) 4.0 mM dNTPs (biotechrabbit GmbH) 8.0 μM sense primer (5′-GCAGTGGCGCCCGAACAGG-3′) (Metabion International AG) 8.0 μM antisense primer (5′-ACTGACGCTCTCGCACCCATCT-3′) (Metabion International AG) 8.0 μM Taq-Man probe (5′-Cy5-CTCCGACGCAACGGGCTCG-BHQ3-3′) (Metabion International AG) or 10× EvaGreen® Fluorescent DNA Stain (Jena Bioscience GmbH) Sodiumpolyphosphate (Merck) 9% (w/v) (2-Hydroxypropyl)-y-cyclodextrine (Sigma) The reagent mix was spray-dried using the Nano Spray Dryer B-90 (Büchi Labortechnik GmbH) to obtain nanoparticle-sized reagent. .. Preparation of Microcapsule Solutions Ultra-low gelling temperature agarose A2576 (Sigma) with a gel point 20° C. and a melting point of ≤62° C. is labeled with reactive biotin monochlorotriazinyl dye (INNOVENT).

    Article Title: Mouse nuclear RNAi-defective 2 promotes splicing of weak 5' splice sites.
    Article Snippet: The reaction was slowly cooled down to room temperature with a Δ −1°C/sec gradient, and 0.5 μL each of 5 U/μL RNase H (NEB), 1000U/μLRNase T1 (ThermoFisher Scientific), and 20U/μLExonuclease I (NEB)were added todegrade the excess TSOandRTprimer for 20minat37°C, followedbya15-minheat inactivationat 80°C. .. To amplify the cDNA library, the eluates from the previous step were transferred to a 0.2-mL low-profile PCR tube (Bio-Rad) and mixed with a master mix consisting of 20 μL of 2× NEBNext Ultra II Q5 Master Mix (NEB), 1 μL of 40 μM P5∗ primer, 1 μL of 40 μM PE∗ primer, and 0.8 μL of 100 μM EvaGreen Fluorescent DNA Stain (Jena Bioscience). .. To amplify the cDNA library, the eluates from the previous step were transferred to a 0.2-mL low-profile PCR tube (Bio-Rad) and mixed with a master mix consisting of 20 μL of 2× NEBNext Ultra II Q5 Master Mix (NEB), 1 μL of 40 μM P5∗ primer, 1 μL of 40 μM PE∗ primer, and 0.8 μL of 100 μM EvaGreen Fluorescent DNA Stain (Jena Bioscience).

    Article Title: Dynamics of the milk microbial community during subacute ruminal acidosis with or without intramammary lipopolysaccharide challenge in dairy cows.
    Article Snippet: The resulting DNA was purified using the innuPREP PCRpure Kit (ist Innuscreen GmbH, Berlin, Germany) and quantified with the Qubit ds BR Assay Kit (Thermo Fisher Scientific, Austria). .. The DNA samples were assayed in duplicate in a 23 μL reaction mixture, which contained 12.7 μL DEPC-treated water, 2.5 μL 10 × buffer, 1.0 μL 2 mM MgCl2 (stock concentration 50 mM), 2.5 μL of each primer (stock concentration 2.5 μM), 0.5 μL of EvaGreen fluorescent DNA stain (JenaBioscience, Jena, Germany), 1.0 μL of dNTP Mix (stock concentration 20 mM, 5 mM of each dNTP; Thermofisher, Vienna, Austria), 0.3 μL of Platinum Taq DNA polymerase (5 U/μl; Thermo Fisher Scientific, Vienna, Austria), and 2 μL of the diluted template (gDNA). .. The DNA samples were assayed in duplicate in a 23 μL reaction mixture, which contained 12.7 μL DEPC-treated water, 2.5 μL 10 × buffer, 1.0 μL 2 mM MgCl2 (stock concentration 50 mM), 2.5 μL of each primer (stock concentration 2.5 μM), 0.5 μL of EvaGreen fluorescent DNA stain (JenaBioscience, Jena, Germany), 1.0 μL of dNTP Mix (stock concentration 20 mM, 5 mM of each dNTP; Thermofisher, Vienna, Austria), 0.3 μL of Platinum Taq DNA polymerase (5 U/μl; Thermo Fisher Scientific, Vienna, Austria), and 2 μL of the diluted template (gDNA).

    Polymerase Chain Reaction:

    Article Title: Microcapsule for detecting and/or quantitating an analyte in a sample
    Article Snippet: Components Per mL Polymerisation Mix Reaction mix 20% (w/v) N-Isopropylacrylamide (NIPAM) 250 μl 2.5% (w/v) N,N′-Methylenebisacrylamide 20 μl 2.5% Biotin-modified monomer 10 μl 5% (w/v) Ammonium persulfate 150 μl Deionised water 570 μl Component 2 (Reagent Phase): A (2-Hydroxypropyl)-y-cyclodextrine stock solution (100%) was also prepared in nuclease-free water using Cavasol W7 or W8 (Sigma) and stored at room temperature. .. The final mixture for PCR accommodating all reagents to be encapsulated contained the following: 1.25 U/μl Hot Start Taq DNA Polymerase (biotechrabbit GmbH) 4.0 mM dNTPs (biotechrabbit GmbH) 8.0 μM sense primer (5′-GCAGTGGCGCCCGAACAGG-3′) (Metabion International AG) 8.0 μM antisense primer (5′-ACTGACGCTCTCGCACCCATCT-3′) (Metabion International AG) 8.0 μM Taq-Man probe (5′-CF647-CTCCGACGCAACGGGCTCG-BHQ3-3′) (Metabion International AG) or 10× EvaGreen® Fluorescent DNA Stain (Jena Bioscience GmbH) Sodiumpolyphosphate (Merck) 9% (w/v) (2-Hydroxypropyl)-y-cyclodextrine (Sigma) The reagent mix was spray-dried using the Nano Spray Dryer B-90 (Büchi Labortechnik GmbH) to obtain nanoparticle-sized reagent. .. Nanoparticles were subsequently dried under vacuum just before dispersing them in the tristearin Softenol 3118 (IOI Oleo GmbH) at a maximum concentration of 10% (w/v) by ultrasonic treatment at elevated temperature (80-90° C.) using the S-450D Digital Sonifier (Branson).

    Article Title: Microcapsule for detecting and/or quantitating an analyte in a sample
    Article Snippet: A (2-Hydroxypropyl)-y-cyclodextrine stock solution (100%) was also prepared in nuclease-free water using Cavasol W7 or W8 (Sigma) and stored at room temperature. .. The final mixture for PCR accommodating all reagents to be encapsulated contained the following: Component 2: 1.25 U/μl Hot Start Taq DNA Polymerase (biotechrabbit GmbH) 4.0 mM dNTPs (biotechrabbit GmbH) 8.0 μM sense primer (5′-GCAGTGGCGCCCGAACAGG-3′) (Metabion International AG) 8.0 μM antisense primer (5′-ACTGACGCTCTCGCACCCATCT-3′) (Metabion International AG) 8.0 μM Taq-Man probe (5′-Cy5-CTCCGACGCAACGGGCTCG-BHQ3-3′) (Metabion International AG) or 10× EvaGreen® Fluorescent DNA Stain (Jena Bioscience GmbH) Sodiumpolyphosphate (Merck) 9% (w/v) (2-Hydroxypropyl)-y-cyclodextrine (Sigma) The reagent mix was spray-dried using the Nano Spray Dryer B-90 (Büchi Labortechnik GmbH) to obtain nanoparticle-sized reagent. .. Preparation of Microcapsule Solutions Ultra-low gelling temperature agarose A2576 (Sigma) with a gel point 20° C. and a melting point of ≤62° C. is labeled with reactive biotin monochlorotriazinyl dye (INNOVENT).

    Article Title: Mouse nuclear RNAi-defective 2 promotes splicing of weak 5' splice sites.
    Article Snippet: The reaction was slowly cooled down to room temperature with a Δ −1°C/sec gradient, and 0.5 μL each of 5 U/μL RNase H (NEB), 1000U/μLRNase T1 (ThermoFisher Scientific), and 20U/μLExonuclease I (NEB)were added todegrade the excess TSOandRTprimer for 20minat37°C, followedbya15-minheat inactivationat 80°C. .. To amplify the cDNA library, the eluates from the previous step were transferred to a 0.2-mL low-profile PCR tube (Bio-Rad) and mixed with a master mix consisting of 20 μL of 2× NEBNext Ultra II Q5 Master Mix (NEB), 1 μL of 40 μM P5∗ primer, 1 μL of 40 μM PE∗ primer, and 0.8 μL of 100 μM EvaGreen Fluorescent DNA Stain (Jena Bioscience). .. To amplify the cDNA library, the eluates from the previous step were transferred to a 0.2-mL low-profile PCR tube (Bio-Rad) and mixed with a master mix consisting of 20 μL of 2× NEBNext Ultra II Q5 Master Mix (NEB), 1 μL of 40 μM P5∗ primer, 1 μL of 40 μM PE∗ primer, and 0.8 μL of 100 μM EvaGreen Fluorescent DNA Stain (Jena Bioscience).

    Real-time Polymerase Chain Reaction:

    Article Title: Stimulus-responsive nanocarrier from star-shaped polyethyleneimine-β-cyclodextrin coated mesoporous silica for targeted combination cancer therapy
    Article Snippet: In this study, a stimulus-responsive organic/inorganic supramolecular nanostructure (SRN) was designed to develop a multifunctional nano-drug delivery system for combined chemo/gene/magnetic hyperthermia therapy targeting multidrug-resistant cancer.. SRNs have been successfully fabricated based on host/guest interactions between folate-appended-polyethyleneimine-β-cyclodextrin (FPC) and benzimidazole-modified magnetic-hollow mesoporous silica nanoparticles (BM-MHMSNs).. A typical antitumor drug, Doxorubicin (DOX), was successfully loaded in the pore of BM-MHMSNs and capped by FPC.

    other:

    Article Title: Microbial dynamics in the ripening process of Vorarlberger Alpkäse: farm-specific variations at two Austrian alpine farms
    Article Snippet: The resulting DNA was purified using the innuPREP PCRpure Kit (IST Innuscreen GmbH, Germany) and quantified with the Qubit dsDNA BR Assay Kit (Invitrogen).

    Concentration Assay:

    Article Title: Dynamics of the milk microbial community during subacute ruminal acidosis with or without intramammary lipopolysaccharide challenge in dairy cows
    Article Snippet: .. The DNA samples were assayed in duplicate in a 23 μL reaction mixture, which contained 12.7 μL DEPC-treated water, 2.5 μL 10 × buffer, 1.0 μL 2 mM MgCl 2 (stock concentration 50 mM), 2.5 μL of each primer (stock concentration 2.5 μM), 0.5 μL of EvaGreen fluorescent DNA stain (JenaBioscience, Jena, Germany), 1.0 μL of dNTP Mix (stock concentration 20 mM, 5 mM of each dNTP; Thermofisher, Vienna, Austria), 0.3 μL of Platinum Taq DNA polymerase (5 U/μl; Thermo Fisher Scientific, Vienna, Austria), and 2 μL of the diluted template (gDNA). .. The quantification of DNA was performed in an Mx3000P qPCR instrument (v.4.10; Stratagene, La Jolla, CA, United States) with an initial denaturation at 95 °C for 3 min, followed by 45 cycles of 95 °C for 5 s, 60 °C for 20 s. To determine the specificity of the amplifications, dissociation curves after each reaction were recorded and carried out at 95 °C for 1 min, followed by complete annealing at 50 °C for 30 s, and a gradually increasing temperature up to 95 °C.

    Article Title: Dynamics of the milk microbial community during subacute ruminal acidosis with or without intramammary lipopolysaccharide challenge in dairy cows.
    Article Snippet: The resulting DNA was purified using the innuPREP PCRpure Kit (ist Innuscreen GmbH, Berlin, Germany) and quantified with the Qubit ds BR Assay Kit (Thermo Fisher Scientific, Austria). .. The DNA samples were assayed in duplicate in a 23 μL reaction mixture, which contained 12.7 μL DEPC-treated water, 2.5 μL 10 × buffer, 1.0 μL 2 mM MgCl2 (stock concentration 50 mM), 2.5 μL of each primer (stock concentration 2.5 μM), 0.5 μL of EvaGreen fluorescent DNA stain (JenaBioscience, Jena, Germany), 1.0 μL of dNTP Mix (stock concentration 20 mM, 5 mM of each dNTP; Thermofisher, Vienna, Austria), 0.3 μL of Platinum Taq DNA polymerase (5 U/μl; Thermo Fisher Scientific, Vienna, Austria), and 2 μL of the diluted template (gDNA). .. The DNA samples were assayed in duplicate in a 23 μL reaction mixture, which contained 12.7 μL DEPC-treated water, 2.5 μL 10 × buffer, 1.0 μL 2 mM MgCl2 (stock concentration 50 mM), 2.5 μL of each primer (stock concentration 2.5 μM), 0.5 μL of EvaGreen fluorescent DNA stain (JenaBioscience, Jena, Germany), 1.0 μL of dNTP Mix (stock concentration 20 mM, 5 mM of each dNTP; Thermofisher, Vienna, Austria), 0.3 μL of Platinum Taq DNA polymerase (5 U/μl; Thermo Fisher Scientific, Vienna, Austria), and 2 μL of the diluted template (gDNA).

    Platinum:

    Article Title: Dynamics of the milk microbial community during subacute ruminal acidosis with or without intramammary lipopolysaccharide challenge in dairy cows
    Article Snippet: .. The DNA samples were assayed in duplicate in a 23 μL reaction mixture, which contained 12.7 μL DEPC-treated water, 2.5 μL 10 × buffer, 1.0 μL 2 mM MgCl 2 (stock concentration 50 mM), 2.5 μL of each primer (stock concentration 2.5 μM), 0.5 μL of EvaGreen fluorescent DNA stain (JenaBioscience, Jena, Germany), 1.0 μL of dNTP Mix (stock concentration 20 mM, 5 mM of each dNTP; Thermofisher, Vienna, Austria), 0.3 μL of Platinum Taq DNA polymerase (5 U/μl; Thermo Fisher Scientific, Vienna, Austria), and 2 μL of the diluted template (gDNA). .. The quantification of DNA was performed in an Mx3000P qPCR instrument (v.4.10; Stratagene, La Jolla, CA, United States) with an initial denaturation at 95 °C for 3 min, followed by 45 cycles of 95 °C for 5 s, 60 °C for 20 s. To determine the specificity of the amplifications, dissociation curves after each reaction were recorded and carried out at 95 °C for 1 min, followed by complete annealing at 50 °C for 30 s, and a gradually increasing temperature up to 95 °C.

    cDNA Library Assay:

    Article Title: Mouse nuclear RNAi-defective 2 promotes splicing of weak 5' splice sites.
    Article Snippet: The reaction was slowly cooled down to room temperature with a Δ −1°C/sec gradient, and 0.5 μL each of 5 U/μL RNase H (NEB), 1000U/μLRNase T1 (ThermoFisher Scientific), and 20U/μLExonuclease I (NEB)were added todegrade the excess TSOandRTprimer for 20minat37°C, followedbya15-minheat inactivationat 80°C. .. To amplify the cDNA library, the eluates from the previous step were transferred to a 0.2-mL low-profile PCR tube (Bio-Rad) and mixed with a master mix consisting of 20 μL of 2× NEBNext Ultra II Q5 Master Mix (NEB), 1 μL of 40 μM P5∗ primer, 1 μL of 40 μM PE∗ primer, and 0.8 μL of 100 μM EvaGreen Fluorescent DNA Stain (Jena Bioscience). .. To amplify the cDNA library, the eluates from the previous step were transferred to a 0.2-mL low-profile PCR tube (Bio-Rad) and mixed with a master mix consisting of 20 μL of 2× NEBNext Ultra II Q5 Master Mix (NEB), 1 μL of 40 μM P5∗ primer, 1 μL of 40 μM PE∗ primer, and 0.8 μL of 100 μM EvaGreen Fluorescent DNA Stain (Jena Bioscience).



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    Amplicon production of E. coli 16S rRNA gene variable regions was monitored using qPCR. Non-degenerate and degenerate primer pairs were compared for each amplified region (four replicates each). These reactions used the EMP cycling protocol and Platinum II Taq polymerase (supplemented with EvaGreen reporter dye, 97.5 pg/ μ L genomic DNA, 0.5 μ M each primer). Primer pairs: V3-V4 (ND_F1 & ND_R1; Pro_341F & Pro_805R), V4-V5 (ND_V4_F & ND_V5_R; 515F-Y & 926R), V4 (ND_V4_F & ND_V4_R; 515F-Y & 806RB). Schematics of the degenerate primers and the positions of variations are indicated on the left of each panel. Each reaction’s data were globally fit to obtain seed , max , and K D values and then a max / K D ratio was calculated. Insets show averages with standard deviations in parentheses. The poorer performance of the degenerate primers was associated with higher max / K D ratios.

    Journal: PeerJ

    Article Title: Thermal-bias PCR: generation of amplicon libraries without degenerate primer interference

    doi: 10.7717/peerj.20241

    Figure Lengend Snippet: Amplicon production of E. coli 16S rRNA gene variable regions was monitored using qPCR. Non-degenerate and degenerate primer pairs were compared for each amplified region (four replicates each). These reactions used the EMP cycling protocol and Platinum II Taq polymerase (supplemented with EvaGreen reporter dye, 97.5 pg/ μ L genomic DNA, 0.5 μ M each primer). Primer pairs: V3-V4 (ND_F1 & ND_R1; Pro_341F & Pro_805R), V4-V5 (ND_V4_F & ND_V5_R; 515F-Y & 926R), V4 (ND_V4_F & ND_V4_R; 515F-Y & 806RB). Schematics of the degenerate primers and the positions of variations are indicated on the left of each panel. Each reaction’s data were globally fit to obtain seed , max , and K D values and then a max / K D ratio was calculated. Insets show averages with standard deviations in parentheses. The poorer performance of the degenerate primers was associated with higher max / K D ratios.

    Article Snippet: Platinum II Taq and Ultra II Q5 reactions were supplemented with EvaGreen dye (Jena Bioscience, cat. # PCR-379); iTaq Universal SYBR Green (Bio-Rad, cat. # 1725120) and SsoFast EvaGreen (Bio-Rad, cat.172-5201) were used without modification.

    Techniques: Amplification, Platinum, Polymerase Chain Reaction, Real-time Polymerase Chain Reaction

    Reporter templates were constructed to evaluate the relative performance of primer pairs and the impact of sequence variations in primer binding sites. (A) Schematic of the templates. The match template contained consensus primer-binding sites and the mismatch template contained two sequence changes in the forward and reverse primer-binding sites (G to C at −4 and −8 in the forward binding site; T to G at −14 and G to C at −15 in the reverse binding site). Each template contained a unique restriction site (BamHI in the match, SpeI in the mismatch). (B) qPCR reactions comparing the amplification performance of non-degenerate or degenerate (Pro_341F & Pro_805R) primers using each template independently or an equal mixture of the two (each having the same final template concentration, four replicates each). These reactions used Platinum II Taq polymerase supplemented with EvaGreen and used the EMP protocol. The non-degenerate primers performed better in each case, even on the mismatch template. Poorer performance was associated with higher max / K D ratios. (C) DNA from each qPCR reaction set was pooled, purified, and subsequently digested using either BamHI or SpeI. There was no detectable mismatch amplicon (SpeI digested) in the amplicon pools derived from either of the mixed-template reactions.

    Journal: PeerJ

    Article Title: Thermal-bias PCR: generation of amplicon libraries without degenerate primer interference

    doi: 10.7717/peerj.20241

    Figure Lengend Snippet: Reporter templates were constructed to evaluate the relative performance of primer pairs and the impact of sequence variations in primer binding sites. (A) Schematic of the templates. The match template contained consensus primer-binding sites and the mismatch template contained two sequence changes in the forward and reverse primer-binding sites (G to C at −4 and −8 in the forward binding site; T to G at −14 and G to C at −15 in the reverse binding site). Each template contained a unique restriction site (BamHI in the match, SpeI in the mismatch). (B) qPCR reactions comparing the amplification performance of non-degenerate or degenerate (Pro_341F & Pro_805R) primers using each template independently or an equal mixture of the two (each having the same final template concentration, four replicates each). These reactions used Platinum II Taq polymerase supplemented with EvaGreen and used the EMP protocol. The non-degenerate primers performed better in each case, even on the mismatch template. Poorer performance was associated with higher max / K D ratios. (C) DNA from each qPCR reaction set was pooled, purified, and subsequently digested using either BamHI or SpeI. There was no detectable mismatch amplicon (SpeI digested) in the amplicon pools derived from either of the mixed-template reactions.

    Article Snippet: Platinum II Taq and Ultra II Q5 reactions were supplemented with EvaGreen dye (Jena Bioscience, cat. # PCR-379); iTaq Universal SYBR Green (Bio-Rad, cat. # 1725120) and SsoFast EvaGreen (Bio-Rad, cat.172-5201) were used without modification.

    Techniques: Construct, Sequencing, Binding Assay, Amplification, Concentration Assay, Platinum, Purification, Derivative Assay, Real-time Polymerase Chain Reaction, Restriction Assay