Kod buffer

Manufactured by Toyobo

Sourced in Japan

KOD buffer is a specialized buffer solution used in molecular biology and biochemistry applications. It is designed to maintain the optimal pH and ionic conditions for the KOD DNA polymerase enzyme, which is commonly used for high-fidelity DNA amplification. The buffer composition ensures the efficient and accurate performance of the KOD polymerase during PCR and other DNA-based experiments.

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Lab products found in correlation

T100 thermal cycler, by Bio-Rad (2 mentions) Superscript 3 reverse transcriptase, by Thermo Fisher Scientific (1 mentions) Kod plus neo, by Toyobo (1 mentions) First strand buffer, by Thermo Fisher Scientific (1 mentions) Droplet generator, by Bio-Rad (1 mentions) Kod plus, by Toyobo (1 mentions) Evagreen, by Biotium (1 mentions) Kod fx polymerase, by Toyobo (1 mentions) M mlv reverse transcriptase, by Takara Bio (1 mentions) Cfx96 real time pcr detection system, by Bio-Rad (1 mentions) Dntps, by Toyobo (1 mentions) E z n a stool dna kit, by Omega Bio-Tek (1 mentions) Kod polymerase, by Toyobo (1 mentions)

Spelling variants of this product

KOD-Plus-Neo buffer (5 citations) KOD FX neo buffer (3 citations) 2x PCR Buffer for KOD FX Neo (2 citations)

5 protocols using kod buffer

Reverse Transcription and RT-PCR Protocol

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Primer annealing to RNA was conducted in the presence of 0.5 mM
dNTPs, 0.5 μM RT primer (5′-dTAACCGGTACGCGTAGAATCTTTTTTTTTTTTTTTTTTTT-3′),
and 2 ng/μL base-converted RNA for 5 min at 65 °C and kept
on ice. After annealing, 1× First Strand Buffer (Thermo SCIENTIFIC),
5 mM DTT, and 10 U/μL SuperScript III reverse transcriptase
(Thermo SCIENTIFIC) were added. Reverse transcription was performed
for 45 min at 50 °C, and reverse transcriptase was inactivated
by heating for 15 min at 70 °C. Then, 1:20 volume of the reverse-transcribed
sample was transferred to a PCR tube. 0.5 μM each forward (5′-dCATGGACTACAAGGACGACGAC-3′
for targeting 696 bp DNA or 5′-dGCCTGATCAACCCCGACGGC-3′
for targeting 175 bp DNA) and reverse primer (5′-dTAACCGGTACGCGTAGAATC-3′),
1× KOD buffer (TOYOBO), 1.5 mM MgSO₄, 0.2 mM dNTPs,
and 0.02 U/μL KOD plus neo (TOYOBO) were added, and the thermal
cycle (95 °C for 2 min, (98 °C for 10 s, 68 °C for
30 s) × 25 cycles) was performed using a T100 thermal cycler
(Bio-Rad). The PCR products were analyzed by using 1.2% agarose gel
electrophoresis (100 V, 20 min).

Ohashi S., Nakamura M., Acharyya S., Inagaki M., Abe N., Kimura Y., Hashiya F, & Abe H. (2024). Development and Comparison of 4-Thiouridine to Cytidine Base Conversion Reaction. ACS Omega, 9(8), 9300-9308.

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Characterization of TaPpm1 and TaPpb1 in Wheat

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The promoter and genomic fragments of TaPpm1 and TaPpb1 in the 12 selected varieties (two purple-, two blue-, and eight white-grained lines) were amplified and sequenced. cDNAs designated TaPpm1a, TaPpm1b, TaPpm1c, and TaPpm1d were amplified from the varieties H76, Hedongwumai, Bobwhite, and A14, respectively. The cDNA of TaPpm2 and TaPpm3 were amplified from H76. The cDNA of TaPpb1a and TaPpb1b were amplified from H76 and A14, respectively. The promoters of TaPpb1a and TaPpb1b were amplified from H76 and A14, respectively. The PCR mixture (20 μl) contained 1 μl of genomic DNA or cDNA, 2× KOD buffer, 2 mM dNTP, 0.5 μM primers, 3 μl ddH₂O, and 0.4 μl of KOD (TOYOBO, Japan). A total of 35 PCR cycles were performed, with each cycle involving 20 s at 98 °C, 15 s at 56–59 °C (according to the different T_m of primers), and 1–3.5 min at 68 °C. All primers are listed in Supplementary Table S1. Multiple sequence alignments were performed using ClustalX 1.83 (http://www.ebi.ac.uk). Cis-acting elements were predicted using the PlantCARE program (http://bioinformatics.psb.ugent.be/webtools/plantcare/html/).

Jiang W., Liu T., Nan W., Jeewani D.C., Niu Y., Li C., Wang Y., Shi X., Wang C., Wang J., Li Y., Gao X, & Wang Z. (2018). Two transcription factors TaPpm1 and TaPpb1 co-regulate anthocyanin biosynthesis in purple pericarps of wheat. Journal of Experimental Botany, 69(10), 2555-2567.

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Droplet Digital PCR for PIK3CA H1047R

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A 107 bp fragment of PIK3CA containing the codon for amino acid residue 1047 was amplified from cfDNA by ddPCR. cfDNA (2.5 ng) from patients was amplified in a 20-μl reaction solution containing 10x KOD buffer (Toyobo), 0.2U KOD plus (Toyobo), 2x Droplet supermix (Bio-Rad) and 10 μM primers (nested primers: Fw 5’-ACTGAGCAAGAGGCTTTGGA-3’ and Rv 5’-GCATGCTGTTTAATTGTGTGG-3’). The entire reaction mixture was loaded into a droplet generator (Bio-Rad). PCR pre-amplification was carried out on a T100 thermal cycler (Bio-Rad) using a thermal profile beginning with 95°C for 10 min, followed by 9 cycles of 95°C for 30 sec and 60°C for 60 sec, and finally 1 cycle of 98°C for 10 min. Droplets of PCR products were disrupted, 200 μl chloroform and 80 μl TE Buffer were added, and the sample was vortexed for 1 min, then centrifuged at 10,000 × g for 10 min. The supernatants were removed and purified using MinElute (Qiagen) following the manufacturer's instructions. One microliter of the first PCR product was re-amplified by ddPCR using the LNA probe and the primer for PIK3CA-H1047R and was detected as described above.

Morikawa A., Hayashi T., Shimizu N., Kobayashi M., Taniue K., Takahashi A., Tachibana K., Saito M., Kawabata A., Iida Y., Ueda K., Saito M., Yanaihara N., Tanabe H., Yamada K., Takano H., Nureki O., Okamoto A, & Akiyama T. (2018). PIK3CA and KRAS mutations in cell free circulating DNA are useful markers for monitoring ovarian clear cell carcinoma. Oncotarget, 9(20), 15266-15274.

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Quantification of SSTR2 Gene Expression

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For reverse transcription, 2 μg of total RNA and 0.5 μg of oligodeoxythymide were mixed in a total volume of 5 μL, incubated at 70 °C for 10 min and cooled at 42 °C for 2 min. Then, the first-strand buffer, 0.5 mM each deoxynucleotide triphosphate (dNTP), and 100 U Moloney murine leukemia virus (MMLV) reverse transcriptase (Takara, Japanese) were added into the reaction mix in a total volume of 10 μL. Reverse transcription (RT) was performed at 42 °C for 90 min.
According to our previously established method [29 (link)], quantitative real-time PCR was performed to examine the expression of SSTR2 mRNA among chicken tissues. The qPCR primers of chicken SSTR2 (Sense: 5′-AGCGCGGAGCCGATCGGAACG-3′; Antisense: 5′-CTGGGCCGTCTCCACTTGGCAG-3′) were designed based on the sequence in the GenBank (NM_001030345.3). The primers (20 μM), dNTP (10 mM), KOD Buffer, KOD FX polymerase (TOYOBO, Japanese), Eva Green (Biotium, CA, USA), MilliQ-H₂O and templates were mixed in a total volume of 20 μL. Amplification of SSTR2 fragments was performed on the CFX96 Real-time PCR Detection System (Bio-Rad, Hercules, CA, USA). The amplification conditions included an initial denaturation for 10 min at 94 °C followed by 20 s denaturation at 94 °C, 15 s annealing at 60 °C, and 30 s extension at 72 °C for 40 cycles.

Zhang X., Zhang J., Huang T., Wang X., Su J., He J., Shi N., Wang Y, & Li J. (2024). SSTR2 Mediates the Inhibitory Effect of SST/CST on Lipolysis in Chicken Adipose Tissue. Animals : an Open Access Journal from MDPI, 14(7), 1034.

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Microbial Diversity Analysis of Koumiss

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Microbial DNA was extracted from koumiss using an EZNA stool DNA kit (Omega Bio-tek, Norcross, GA) according to the manufacturer's protocols. The V3-V4 region of the 16S rRNA gene was amplified by PCR using primers 341F 5′-CCTACGGGNGGCWGCAG-3′ and 806R 5′-GGACTACHVGGGTATCTAAT-3′, where the barcode was an 8-base sequence to each sample. The internal transcribed spacer (ITS) region of the rRNA gene was amplified by PCR using primers ITS3-KYO2F 5′-GATGAAGAACGYAGYRAA-3′ and ITS4R 5′-TCCTCCGCTTATTGATATGC-3′, where the barcode was an 8-base sequence to each sample. The PCR reaction was performed in a mixture containing 5 μL of 10× KOD buffer (Toyobo, Osaka, Japan), 5 μL of 2.5 mM dNTPs (Toyobo), 1.5 μL of each primer (5 μM), 1 μL of KOD polymerase (Toyobo), and 100 ng of template DNA extracted from koumiss and was executed under the following program: 95°C for 2 min; 27 cycles of 98°C for 10 s, 62°C for 30 s, and 68°C for 30 s; and a final extension at 68°C for 10 min.

Guo L., Ya M., Guo Y.S., Xu W.L., Li C.D., Sun J.P., Zhu J.J, & Qian J.P. (2019). Study of bacterial and fungal community structures in traditional koumiss from Inner Mongolia. Journal of dairy science, 102(3).

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