pcr cleanup kit (Zymo Research)

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Zymo Research pcr cleanup kit

The site-directed mutagenesis protocol used a 27 bp mutagenic primer (12+3+12) for generating mutations in the ORF. Each mutation site required two mutagenic primers to amplify the adjacent fragments. Another set of primers were used for <t>PCR</t> of vector backbone. The three PCR fragments contained overlapping regions of 27–40 bp. The template plasmids for PCRs were linearized with appropriate restriction enzyme. For ORF PCR, ∼200 pg of template DNA was used per reaction. The PCR reactions were treated with Dpn I to eliminate the <t>original</t> <t>templates,</t> followed by HiFi assembly of the backbone and two adjacent ORF fragments.

Pcr Cleanup Kit, supplied by Zymo Research, used in various techniques. Bioz Stars score: 96/100, based on 506 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/actin+polymerization+depolymerization+kit/ZR-96+DNA+Clean-Up+Kit+(Shallow+Well)/bio_rxiv__2025__02__12__637932-159-14-17
Average 96 stars, based on 506 article reviews

pcr cleanup kit - by Bioz Stars, 2026-10

96/100 stars

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1) Product Images from "A Generalized Platform for Artificial Intelligence-powered Autonomous Protein Engineering"

Article Title: A Generalized Platform for Artificial Intelligence-powered Autonomous Protein Engineering

Journal: bioRxiv

doi: 10.1101/2025.02.12.637932

Figure Legend Snippet: The site-directed mutagenesis protocol used a 27 bp mutagenic primer (12+3+12) for generating mutations in the ORF. Each mutation site required two mutagenic primers to amplify the adjacent fragments. Another set of primers were used for PCR of vector backbone. The three PCR fragments contained overlapping regions of 27–40 bp. The template plasmids for PCRs were linearized with appropriate restriction enzyme. For ORF PCR, ∼200 pg of template DNA was used per reaction. The PCR reactions were treated with Dpn I to eliminate the original templates, followed by HiFi assembly of the backbone and two adjacent ORF fragments.

Techniques Used: Mutagenesis, Plasmid Preparation

Module 1 of the workflow prepared mutagenesis PCR for 96 mutants in a 96-well PCR plate. The templates and primers for PCR were mixed using worklists on the Tecan Fluent and Echo liquid handler. PCR success was measured by adding 2.5 μL of the PCR reaction to 47.5 μL of 1x Evagreen dye (Biotium #31000) and measuring fluorescence ( λ ex = 498 nm / λ em = 535 nm) with the Tecan Infinite plate reader. 25 μL PCR product was transferred to a new PCR plate, and 1 μL of Dpn I (NEB #R0176) was added, followed by incubation at 37 °C. The Dpn I-treated PCR products were then transferred to a 384-well plate, along with the vector backbone, and a worklist guided the mixing of the correct fragments in the Echo liquid handler for HiFi assembly. After a 30-minute HiFi assembly at 50 °C, competent DH5α cells in a 96-well plate were transformed by heat shock on the Tecan Fluent using onboard heating/cooling blocks. The cells were plated on 8-well omnitray agar plates containing LB + 50 μg/mL kanamycin and incubated overnight at 37 °C in a Cytomat automated shaking incubator.

Figure Legend Snippet: Module 1 of the workflow prepared mutagenesis PCR for 96 mutants in a 96-well PCR plate. The templates and primers for PCR were mixed using worklists on the Tecan Fluent and Echo liquid handler. PCR success was measured by adding 2.5 μL of the PCR reaction to 47.5 μL of 1x Evagreen dye (Biotium #31000) and measuring fluorescence ( λ ex = 498 nm / λ em = 535 nm) with the Tecan Infinite plate reader. 25 μL PCR product was transferred to a new PCR plate, and 1 μL of Dpn I (NEB #R0176) was added, followed by incubation at 37 °C. The Dpn I-treated PCR products were then transferred to a 384-well plate, along with the vector backbone, and a worklist guided the mixing of the correct fragments in the Echo liquid handler for HiFi assembly. After a 30-minute HiFi assembly at 50 °C, competent DH5α cells in a 96-well plate were transformed by heat shock on the Tecan Fluent using onboard heating/cooling blocks. The cells were plated on 8-well omnitray agar plates containing LB + 50 μg/mL kanamycin and incubated overnight at 37 °C in a Cytomat automated shaking incubator.

Techniques Used: Mutagenesis, Fluorescence, Incubation, Plasmid Preparation, Transformation Assay

Purification:

Article Title: Effect of Oceanic Islands on an Insect Symbiont Genome in Transition to a Host-Restricted Lifestyle
Article Snippet: .. The 16S rRNA amplicons were then purified again using the ZR-96 DNA Clean-Up Kit (Zymo Research). .. A total of 18 μL of PCR product from each reaction was normalized using the SequalPrep Normalization Plate Kit (Invitrogen).

Article Title: In vitro and in vivo enzyme activity screening via RNA-based fluorescent biosensors for S-adenosyl-L-homocysteine (SAH)
Article Snippet: In vitro transcription DNA templates for in vitro transcription were prepared through PCR amplification using Phusion DNA polymerase (NEB) from sequence-confirmed plasmids or Ultramer oligonucleotides (for screening experiment only) using primers that added the T7 polymerase promoter sequence. .. PCR products were purified either by a 96-well format ZR-96 DNA Clean-up kit (Zymo Research) for screening experiments or by QIAquick PCR purification kit (Qiagen) for characterization and application experiments. ..

Article Title: Effect of Oceanic Islands on an Insect Symbiont Genome in Transition to a Host-Restricted Lifestyle
Article Snippet: .. The 16S rRNA amplicons were then treated with 5 μL of ExoSAP-IT (Applied Biosystems) and subsequently purified using the ZR-96 DNA Clean-Up Kit (Zymo Research). .. Using the cleaned PCR product as template, a second PCR was performed in a 96-well Illumina DNA/RNA UD Index Set to complete the Illumina sequencing construct.

Article Title: An Optimization to Increase Bacterial DNA Yield in a Lunar Regolith Simulant
Article Snippet: 30 g was then placed in a 50 mL conical tube and topped up with 0.85% saline solution (w/v) to a final volume of 50 mL. (2) Tubes were subjected to vigorous agitation for 30 min and then allowed to rest for 10 min for sedimentation of the substrate. (3) The supernatant was transferred to a new conical tube and centrifuged at 2000 g for 3 min. (4) The new supernatant was discarded, and the precipitate resuspended directly in 100 μL of PrepManTM Ultra Sample Preparation Reagent (Thermo Fisher Scientific, Waltham, MA, USA) by vortexing for 30 s. (5) The suspended bacterial cells were transferred to a 1 mL microcentrifuge tube. (6) The following steps were according to the kit manufacturer: Incubation at 95 °C for 10 min; room temperature for 2 min; microcentrifugation at 14.000 rpm for 2 min. (7) The final supernatant containing DNA was recovered for downstream analyses. .. Purified DNA samples were processed using the ZR-96 DNA Clean-Up KitTM (Zymo Research). ..

Polymerase Chain Reaction:

Article Title: Tank-based bacterial profiling identifies basin-wide white band disease pathogen candidate and no bacterial associations with coral disease resistance
Article Snippet: Each 23 μL PCR reaction was 175 performed using 1 μL DNA, 1.25 μL each 10 mM primer, 12.5 μL 2X Phusion Mix (Thermo Fisher 176 Scientific, Waltham, MA, USA), and 7 μL molecular biology grade water. .. 179 PCR products were then cleaned using a ZR-96 DNA Clean-Up kit (Zymo Research, Irvine, CA, USA). .. 179 PCR products were then cleaned using a ZR-96 DNA Clean-Up kit (Zymo Research, Irvine, CA, USA).

Salting Out:

Article Title: Regional connectivity and viability selection in a range-expanding marine species
Article Snippet: .. DNA was extracted from whelk tissue using a Salting-out protocol (as described in 45), cleaned using the ZR-96 DNA Clean-Up Kit (Zymo Research, USA), and sequenced using the GT-seq panel described below. ..

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