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DNA Polymerase III

DNA Polymerase III is a key enzyme involved in the replicaton of DNA in prokaryotic organisms.
It is responsible for the high-fidelity synthesis of DNA during cell division, ensuring accurate duplication of genetic material.
This enzyme is composed of multiple subunits and utilizes a sliding clamp mechanism to maintain processivity during DNA replication.
Researchers studying DNA Polymerase III can optimize their experriments and achieve more reliable results by using the PubCompare.ai platform, which provides easy access to relevant protocols from literature, preprints, and patents, while using AI-powered comparisons to identify the best methods and products for their specific research needs.
PubCompare.ai helps streamline DNA Polymerase III experiments and enhances reproducibility and accuracy, enabling researchers to push the boundaries of their work in this important area of molecular biology.

Most cited protocols related to «DNA Polymerase III»

(i) The pCasper-Gateway(W)-LexA::GAD vector was created by excision of the Repo promotor fragment with NotI and AccI (Roche) from pCasper-Repo-LexA::GAD.8 (link) Blunt ends were created with the Klenow fragment of DNA Polymerase III (Promega), then the Gateway Reading Frame B (Invitrogen) was ligated into the vector using T4 DNA Ligase (Promega). The plasmid was transformed into DB3.1 cells (Invitrogen) and selected for Kanamycin resistance. DNA was extracted and verified by sequencing. The sequence of the vector is available as a supplementary data file (Suppl. 1).
(ii) The pLOT-Gateway vector was created by opening the pLexOp-vector8 (link) with EcoRI (Roche). Ends were blunted, the Gateway Reading Frame B (Invitrogen) was ligated in and the vector was introduced into DB3.1 cells as outlined above. The sequence of the vector is available as a supplementary data file (Suppl. 2).
(iii) Sensory LexA::GAD driver line: A 3.3 kb fragment from the Cha promotor was amplified by Polymerase Chain Reaction (PCR) using the following Gateway primers: attB1-GAA TTC TTA ATT GAA AAT AAA CAT TAA GG and attB2-GGA TCC GGT TGG TTT GGC CCC TTT TTC TTT GTC GCT. The PCR product was introduced into pDONRTM221 (Invitrogen) via Gateway cloning to create the pEntry-vector. In the subsequent Gateway cloning reaction this vector was combined with the newly developed pCasper-Gateway-LexA::GAD (above) to recombine the Cha promotor fragment with the LexA::GAD. DNA was purified using a Qiagen Midi Kit and transgenic lines were generated by BestGene Inc., (Chino Hills, CA, USA).
(iv) lexAop-myr-mCherry was created using the Multisite Gateway technique. One pEntry vector for the myristoylation site was created using the primers: attB1-ATG GGC AAC AAA TGC TCC AG and attB5r-TGG TCT GAT GAT GTC AAC CCC. Another, pEntry-mCherry entry vector was generated using the primers attB5-AAGAGCTCCGCCACCATGG and attB2-GGT TTA CGT CAC GTG GAC CGG TG. Both pEntry-vectors were combined into the new pLOT-Gateway vector using the MultiSite Gateway Kit from Invitrogen. Clones were selected on Ampicillin plates and DNA isolated and sequenced. Purified DNA was sent for embryo injection services to BestGene Inc., (Chino Hills, CA, USA).
Publication 2008
Ampicillin Animals, Transgenic Cells Clone Cells Cloning Vectors Deoxyribonuclease EcoRI DNA Polymerase I DNA Polymerase III Embryo Kanamycin Resistance Oligonucleotide Primers Plasmids Polymerase Chain Reaction Promega Reading Frames T4 DNA Ligase

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Publication 2017
Amino Acids Anabolism Cambodians Catalytic RNA Cloning Vectors Cytomegalovirus Digestion DNA, Complementary DNA Polymerase III DNA Restriction Enzymes Escherichia coli Genes Genome Hemagglutinin Hepatitis Delta Virus Influenza Mammals Mutation Oligonucleotide Primers Parent Plasmids Platinum Polyproteins Protein C Reading Frames Reverse Transcriptase Polymerase Chain Reaction RNA, Viral Strains Tissue, Membrane Transcription, Genetic Vero Cells Virus Zika Virus Zika Virus Infection

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Publication 2017
Cell Lines DNA Polymerase III Formalin GAPDH protein, human Gene Fusion Homo sapiens Needles Neoplasms Nested Polymerase Chain Reaction Oligonucleotide Primers Paraffin Embedding Platinum Reverse Transcriptase Polymerase Chain Reaction
A total of 40 positive nasopharyngeal and/or throat swab samples (except the first specimens from the Chinese traveller from Wuhan) were confirmed to be SARS-CoV-2-positive via two separate multiplex real-time reverse transcription polymerase chain reaction (RT-PCR) assays. In the first multiplex assay the Allplex 2019-nCoV (Seegene, Seoul, Republic of Korea) incorporating primers and probes specifically targeting RdRp, N and E genes was used. The second assay used the LightMix Modular SARS and Wuhan CoV (TIB-Molbiol, Berlin, Germany) incorporating primers and probes corresponding to the RdRp and E genes. Viral RNA was extracted from 200 µL of sample using a magLEAD 12gC instrument (Precision System Science, Chiba, Japan) with a magLEAD Consumable Kit (Precision System Science, Chiba, Japan) in accordance with the manufacturer’s instructions. All RNA specimens were transferred to the Center of Excellence in Clinical Virology at Chulalongkorn University for conventional PCR and sequencing, and SARS-CoV-2 RdRp, S, N and E genes were amplified via a primer set specific for SARS-CoV-2 (Table S1).
The one-step RT-PCR reactions were conducted using the SuperScript III Platinum One-Step RT-PCR System with Platinum Taq DNA Polymerase (Invitrogen, Carlsbad, CA). Briefly, the PCR reaction mixture contained 2–3 μL of RNA, 0.5 μM of each primer, 12.5 μL of 2X Reaction Mix (Invitrogen) and 1 μL of SSIII RT/Platinum Taq Mix, and was adjusted to a final volume of 25 μL with nuclease-free water. Amplification was conducted in a thermal cycler (Eppendorf, Hamburg, Germany) via a protocol including reverse transcription at 45 °C for 30 min, initial denaturation at 94 °C for 3 min, 40 cycles of 30 s of denaturation at 94 °C, 30 s of primer annealing at 53 °C, 90 s of extension at 68 °C, and further extension for 7 min at 68 °C. PCR products were separated on a 2% agarose gel with a 100-base pair DNA ladder and visualized on an ultraviolet trans-illuminator. PCR products were gel-purified using the HiYield Gel/PCR DNA Fragment Extraction kit (RBC Bioscience Co, Taipei, Taiwan). DNA sequencing was performed by First BASE Laboratories Sdn Bhd, Selangor, Malaysia.
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Publication 2020
Base Pairing Biological Assay Chinese DNA Polymerase III Genes Nasopharynx Oligonucleotide Primers Pharynx Platinum Real-Time Polymerase Chain Reaction Reverse Transcriptase Polymerase Chain Reaction Reverse Transcription RNA, Viral SARS-CoV-2 Sepharose Severe Acute Respiratory Syndrome
ALK positivity was ascertained by FISH using ALK break-apart probes (Vysis LSI ALK (2p23) Dual Color, Break Apart Rearrangement Probe; Abbott Molecular). The FISH assays and analyses were performed as described previously with minor modifications (14 (link)). Using the ALK beak-apart probe, 3’ (red) and 5’ (green) signals physically separated by ≥2 signal diameters were considered split. Specimens were considered positive for ALK rearrangement if <15% of tumor cells showed split signals or single red signals. Copy number of ALK rearrangement was based upon determination of the mean of split and isolated red signals per tumor cell (15 ). At least 100 tumor cells were analyzed per specimen.
RNA from either FFPE or Frozen tissue was processed using the RecoverAll™ Total Nucleic Acid Isolation Kit from Ambion (Austin, TX). RT-PCR was carried out using the SuperScript III One-Step RT-PCR System with Platinum Taq DNA Polymerase from Invitrogen (Carlsbad, CA) with primers to EML4-ALK. PCR products were either resolved on an agarose gel or analyzed with a Bioanalyzer from Agilent Technology (Santa Clara, CA), excised, and purified using Wizard SV Gel and PCR Clean Up Kit from Promega (Madison, WI) then sequenced as described below. Primers used for RT-PCR or multiplexed RT-PCR of the EML4-ALK gene fusion transcript are listed in Supplementary Table 1 or have been previously described (16 (link), 17 (link)).
Publication 2012
austin Beak Biological Assay Cells DNA Polymerase III Fishes Freezing Gene Fusion isolation Neoplasms Nucleic Acids Oligonucleotide Primers Platinum Promega Reverse Transcriptase Polymerase Chain Reaction Sepharose Signal Transduction Tissues

Most recents protocols related to «DNA Polymerase III»

Initially, three multiplex HRM assays, each containing three different primer pairs were developed and evaluated in this study. These assays identified combinations of variant-defining mutations for SARS-CoV-2 VOCs, with a focus on differentiation of Alpha from 19A, and later Delta from Alpha, to understand the epidemiology of these variants at the time in the UK.
Each assay was performed using 2.5 μL of RNA template and in 12.5 μl final reaction volumes, using the SuperScript™ III One-Step RT-PCR System with Platinum™ Taq DNA Polymerase kit (ThermoFisher, USA), with final reagent quantities as follows: 1X reaction mix, 0.25 μL of SuperScript™ III RT/Platinum™ Taq Mix, 1X EvaGreen® dye (Biotium, USA), and primers added to their optimised concentration (Table 2).

Optimised final reaction primer concentrations for primer set in each multiplex assay, A-D. Primer set names as described in Table 1.

Primer setFinal forward primer concentration (nM)Final reverse primer concentration (nM)
Multiplex A
 S_del.156–157100150
 S_K417N150225
 N_D3L600900
Multiplex B
S_E484K300450
S_del.242–244150225
S_P681H/R150225
Multiplex C
Orf1ab_del.3675–3677200300
S_del.242–244200300
N_D3L175262.5
Multiplex D
S_del.156–157100100
S_K417N150150
N_D3L600600
S_EPE250250
Reactions were performed using the RGQ 6000 5-plex HRM platform (Qiagen, Germany) with the following thermal cycle profile: reverse transcription at 50 °C for 15 min, initial denaturation at 95 °C for 5 min, followed by 40 cycles of 95 °C for 10 s, 56 °C for 30 s and 72 °C for 20 s. HRM was then performed, melting from 73 °C to 85 °C, acquiring data to the HRM channel in 0.1 °C increments, with a 2 s stabilisation between each step. For each assay a reference control of 19A strain SARS-CoV-2 RNA, confirmed by WGS to be negative for all mutations of interest, and a no template negative control were included.
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Publication 2023
Biological Assay DNA Polymerase III Mutation Oligonucleotide Primers Platinum Reverse Transcriptase Polymerase Chain Reaction Reverse Transcription SARS-CoV-2 Strains
The partial genome consensus sequence generated from initial metagenomic sequence analysis was used to design primers to generate three PCR amplicons (UTR-Amp1 [Forward: GAA TGC TCA CAG AGT CTG C, Reverse: TCG GCG TCT TCT CCA]; UTR-Amp2 [Forward: AAG CGA AGG AGA CAT CC, Reverse: TCG GCG TCT TCT CCA]; UTR-Amp3 [Forward: AAG CGA AGG AGA CAT CC, Reverse: AGA ACC TTG CCC AGC]) covering the unsequenced region of the UTR. PCR amplification of the extracted lung and liver-derived nucleic acid was conducted using the SuperScript™ III One-Step RT-PCR System with Platinum™ Taq DNA Polymerase kit (ThermoFisher) according to manufacturer’s recommendations. The PCR mixture consisted of 2 µL of extracted nucleic acid, 0.3 µM of each primer, and 2 µL of SuperScript™ III RT/Platinum™ Taq Mix in 1 × reaction buffer in a final volume of 50 µL with UltraPure Distilled Water (Sigma-Aldrich). Amplification conditions were denaturation at 94 °C for 2 min followed by 40 PCR cycles with denaturation at 94 °C for 15 s., annealing at 55 °C for 30 s. and extension at 68 °C for 1 min. with a final extension step of 68 °C for 5 min. PCR product was visualized using a QIAxcel instrument (QIAGEN) and prepared for sequencing using the Nextera XT Library Prep Kit (Illumina), and sequenced on the Illumina MiSeq with a V2 flow cell using a 300 cycle kit (Illumina).
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Publication 2023
Buffers Cells Consensus Sequence DNA Library DNA Polymerase III Genome Liver Lung Metagenome Nucleic Acids Oligonucleotide Primers Platinum Reverse Transcriptase Polymerase Chain Reaction
To measure viral load in SARS-CoV-2-infected patients, we performed quantitative reverse transcription-PCR (RT-qPCR) in the midturbinate swabs. Total RNA was extracted from the swabs using a phenol-chloroform-based method. The swabs were placed in red 1.5-mL RINO screw-cap tubes (NextAdvance) prefilled with RNase-free zirconium oxide beads, and QIAzol lysis reagent (Qiagen) was added. Samples were then homogenized in a Bullet Blender 24 Gold (NextAdvance) system for 3 min at maximum speed. Following homogenization, genomic DNA was eliminated with genomic DNA (gDNA) eliminator columns (Qiagen), and RNA was purified using the RNeasy mini plus kit (Qiagen) following the manufacturer’s protocol. The RNA quality was measured using a 2100 bioanalyzer (Agilent Technologies). The United States Centers for Disease Control and Prevention primers and probes designed for the detection of SARS-CoV-2 (2019-nCoV) were purchased from Integrated DNA Technologies (IDT) (48 ). Both the SARS-CoV-2 nucleocapsid gene region 1 (N1) and nucleocapsid gene region 2 (N2) were targeted to detect SARS-CoV-2. RNase P was also examined as a measure of RNA quality and quantity. RT-qPCR was performed using the SuperScript III one-step RT-PCR system with Platinum Taq DNA polymerase (Invitrogen) as per manufacturer’s instructions on a CFX96 touch real-time PCR detection system (Bio-Rad). Plasmid controls for 2 SARS-CoV-2 nucleocapsids and RNase P were also ordered from IDT at a concentration of 66,666 copies/reaction. No-template controls and an extraction negative were used as negative controls. Reactions were prepared using 12.5 μL of SuperScript III master mix (ThermoFisher), 1 μL each of 400-nm forward and reverse primer, 1 μL of 400 nM FAM-labeled probe, 1 μL of Platinum Taq polymerase, 3 μL of template RNA, and 7.25 μL of PCR-certified water (Teknova). RNA was reverse transcribed at 50°C for 15 min, and PCR conditions were run on a 95°C denaturation step for 2 min, followed by 40 cycles of 95°C for 15 s and 55°C for 30 s. The cycle threshold (CT) values were captured and calculated by the CFX Maestro (Bio-Rad) software and used as a measure of viral load.
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Publication 2023
A(2)C Chloroform DNA Polymerase III Endoribonucleases Genes Genome Gold Nucleocapsid Oligonucleotide Primers Patients Phenol Plasmids Platinum Reverse Transcriptase Polymerase Chain Reaction Reverse Transcription RNase P SARS-CoV-2 Taq Polymerase Touch TRAF3 protein, human zirconium oxide
We attempted to sequence all retrieved specimens (ie, screening by viral quantitation was not performed). RNA was harvested from residual clinical respiratory samples using Applied Biosystems MagMAX Viral/Pathogen Nucleic Acid Isolation Kit (#A48383). After RNA extraction, RNA samples were reverse-transcribed into complementary DNA and amplified using primers and probes developed by the Centers for Disease Control and Prevention Influenza Division on the SuperScript III One-Step RT-PCR system with Platinum Taq High Fidelity DNA Polymerase (ThermoFisher #12574-035). DNA cleanup was done using Ampure beads (Beckman #A63881).
Barcoded next-generation sequencing (NGS) sequencing libraries were prepared using Nextera DNA Prep Kit (Illumina #20018705). Samples were pooled (up to 96), 5 μL of each, into libraries and concentration was measured using Qubit 1 × double-stranded DNA HA Assay kit (Q33231) before Illumina sequencing.
Publication 2023
Biological Assay DNA, Complementary DNA, Double-Stranded DNA Polymerase III Influenza isolation Nucleic Acids Oligonucleotide Primers Pathogenicity Platinum Respiratory Rate Reverse Transcriptase Polymerase Chain Reaction
During the 2018–2019 and 2019–2020 influenza seasons, 105 and 218 A(H1N1)pdm09 viruses, respectively, were isolated from respiratory specimens by using the hCK cells incubated at 33 °C. Viral RNA was extracted from the isolated viruses by using ISOGEN-LS (Nippon gene). The HA, NA, and PA genes were amplified by using the SuperScript III One-Step RT–PCR System with Platinum Taq DNA polymerase (Invitrogen) and the following primers: HA-U12+16F (5′-AGCAAAAGCAGGGGAAAATAAAAGCAAC-3′) and HA-U13+16R (5′-AGTAGAAACAAAGGGTGTTTTTTCTCATG-3′) for HA; NA-U12+15F (5′-AGCAAAAGCAGGAGTTCAAAATGAATC-3′) and NA-U13+17R (5′-TTATATGGTCTCGTATTAGTAGAAACAAGG-3′) for NA; and PA-U12+15F (5′-AGCAAAAGCAGGTACTGATCCAAAATG-3′) and PA-U13+20R (5′-AGTAGAAACAAGGTACTTTTTCGGACAGTATGG-3′) for PA. If no PCR products were detected, RT-PCR was repeated using the following primers: HA-U12+16F, HA-420R (5′-TTTCAAATGATGACACTGAGCTCA-3′), HA-301F (5′-CAAGCTCATGGTCCTACATTGTGG-3′), and HA-U13+16R for HA; NA-U12+15F, NA-480R (5′-GGCTCCTGTCTTTAATGGTTCCATTGG-3′), NA-301F (5′-TTAGTGGATGGGCTATATACAG-3′), and NA-U13+17R for NA; and PA-U12+15F, PA-1440R (5′-TGCATTGAGCAAGGCCGTATTTATG-3′), PA-1201F (5′-TATGACAGTGATGAGCCAGAGCCC-3′), and PA-U13+20R for PA. The PCR products were purified using the Gel Extraction Kit (Qiagen) and were Sanger sequenced using the following primers: for HA, we used primers HA-12+16F, HA-301F, HA-601F (5′-TCCTCGTGCTATGGGGCATTCACC-3′), HA-1201F (5′-CTAACAAAGTAAATTCTGTTATTG-3′), and HA-420R; for NA, we used NA-U12+15F, NA-301F, NA-601F (5′-GAATTTCTGGCCCAGACAATGGGGC-3′), NA-1081F (5′-GCAATGGTGTTTGGATAGGGAGAAC-3′), and NA-480R; and for PA, we used PA-U12+15F, PA-301F (5′-AGTATATGTAACACAACAGGGGTAG-3′), PA-601F (5′-CAGTCCGAAAGAGGCGAAGAGAC-3′), PA-901F (5′-GAAGACCCGAGTCACGAGGGGGAGGG-3′), PA-1201F, PA-1801F (5′-GAGAGCATGATTGAGGCCGAGTCTTCTG-3′), and PA-540R (5′-TTTGATTCTTGCCCTGCTCTCTTCG-3′).
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Publication 2023
Cells DNA Polymerase III Genes Influenza Influenza A Virus, H1N1 Subtype Oligonucleotide Primers Platinum Respiratory Rate Reverse Transcriptase Polymerase Chain Reaction RNA, Viral Virus

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More about "DNA Polymerase III"

DNA Polymerase III is a crucial enzyme involved in the replication of DNA in prokaryotic organisms.
It is responsible for the high-fidelity synthesis of DNA during cell division, ensuring accurate duplication of genetic material.
This enzyme, composed of multiple subunits, utilizes a sliding clamp mechanism to maintain processivity during DNA replication.
Researchers studying DNA Polymerase III can optimize their experiments and achieve more reliable results by utilizing the PubCompare.ai platform.
This AI-driven platform provides easy access to relevant protocols from literature, preprints, and patents, while using AI-powered comparisons to identify the best methods and products for their specific research needs.
PubCompare.ai helps streamline DNA Polymerase III experiments and enhances reproducibility and accuracy, enabling researchers to push the boundaries of their work in this important area of molecular biology.
In addition to DNA Polymerase III, researchers may also find the Platinum Taq DNA Polymerase, SuperScript III One-Step RT-PCR System, and QIAamp Viral RNA Mini Kit useful for their studies.
The Platinum Taq DNA Polymerase is a high-fidelity enzyme that can be used for a variety of PCR applications, while the SuperScript III One-Step RT-PCR System and QIAamp Viral RNA Mini Kit are useful for RNA extraction and RT-PCR experiments.
The SuperScript III One-Step RT-PCR System with Platinum Taq DNA Polymerase combines the benefits of both the SuperScript III and Platinum Taq DNA Polymerase, providing a streamlined solution for RT-PCR experiments.
Researchers can also consider the use of the RNeasy Mini Kit for RNA purification and the QIAquick PCR Purification Kit for the purification of PCR products.
The TRIzol reagent is another useful tool for RNA extraction, while the SuperScript™ III One-Step RT-PCR System with Platinum™ Taq High Fidelity DNA Polymerase offers a high-fidelity solution for RT-PCR experiments.
By leveraging the insights and tools provided by PubCompare.ai, as well as the various enzymes and kits mentioned, researchers can streamline their DNA Polymerase III experiments, enhance reproducibility, and achieve more reliable results in their molecular biology research.