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Quikchange primer design software

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The QuikChange Primer Design software is a tool developed by Agilent Technologies to assist users in designing primers for site-directed mutagenesis. The software analyzes DNA sequences and provides recommendations for primer sequences that can be used to introduce specific mutations or changes in a target DNA.

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Lab products found in correlation

Quikchange lightning site directed mutagenesis kit, by Agilent Technologies (3 mentions) Quikchange lightning multi site directed mutagenesis kit, by Agilent Technologies (2 mentions) Pegfp c2, by Thermo Fisher Scientific (1 mentions) Quikchange lightning mutagenesis kit, by Agilent Technologies (1 mentions) Geneart gene synthesis technology, by Thermo Fisher Scientific (1 mentions) Hispeed plasmid maxi kit, by Qiagen (1 mentions) E coli top10 competent cells, by Thermo Fisher Scientific (1 mentions) Quikchange 2 site directed mutagenesis kit, by Agilent Technologies (1 mentions) Pwo dna polymerase, by Merck Group (1 mentions) Qiaquick pcr purification kit, by Qiagen (1 mentions) Kod hot start, by Merck Group (1 mentions)

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QuikChange (236 citations) QuikChange Primer Design (21 citations) QuikChange Primer Design online software (2 citations)

7 protocols using quikchange primer design software

1

Site-Directed Mutagenesis for Amino Acid Substitutions

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Amino acid substitutions were performed with the primers as indicated in key resources table. Primers were designed with the QuikChange Primer Design Software (Agilent Technologies). Single mutants were generated using the QuikChange Lightning Site-Directed Mutagenesis kit (Agilent Technologies) and double mutants were created with the QuikChange Lightning Multi Site-Directed Mutagenesis kit (Agilent Technologies) according to the manufacturer’s instructions. The generated mutants were verified by sequencing to screen against spurious secondary mutations. For primer sequences see Supplementary Table 2.
Sarek G., Kotsantis P., Ruis P., Van Ly D., Margalef P., Borel V., Zheng X.F., Flynn H.R., Snijders A.P., Chowdhury D., Cesare A.J, & Boulton S.J. (2019). CDK phosphorylation of TRF2 controls t-loop dynamics during the cell cycle. Nature, 575(7783), 523-527.
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2

Molecular Cloning of Mouse Palmitoylation Enzymes and SPRY2 Constructs

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Mouse zDHHC17, zDHHC7 and zDHHC3 were subcloned in pEF-BOS HA and kindly provided by Prof. Masaki Fukata (National Institute of Physiological Sciences, Okazaki, Japan; Fukata et al., 2004 (link)), whereas the DHHA17 mutant was generated by site-directed mutagenesis. The cDNA encoding mouse SPRY2 WT was cloned by Gateway Technology into pEGFP-C2 (Lemonidis et al., 2014 (link)) or pmCherry-C1, according to manufacturer's guidelines (Life Technologies, Inc.). All the sprouty-2 mutants described were generated by site-directed mutagenesis. The oligonucleotide primers were designed using QuikChange Primer Design software (Agilent, Santa Clara, CA) and purchased from Sigma (Poole, UK). All plasmids were sequenced by Eurofins Genomics (GATC, Constance, DE).
Locatelli C., Lemonidis K., Salaun C., Tomkinson N.C, & Chamberlain L.H. (2020). Identification of key features required for efficient S-acylation and plasma membrane targeting of sprouty-2. Journal of Cell Science, 133(21), jcs249664.
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3

Thermotoga maritima PlsC Expression and Mutagenesis

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THEMA_05775 is annotated as the putative PlsC gene from Thermotoga maritima (NCBI Bacterial Genome Database). A version of this gene optimized for expression in E. coli was obtained using GeneArt Gene Synthesis Technology (ThermoFisher Scientific). For the complementation and membrane association studies, the gene was cloned into the pPJ131 vector22 (link) via the NdeI (5′) and EcoRI (3′) restriction sites. For the enzyme assay studies, the gene was cloned into the pET21a vector (Novagen) via the NdeI (5′) and EcoRI (3′) restriction sites so as to introduce a C-terminal 6xHis tag. For structural studies, the gene was cloned into the pET28b(+) vector (Novagen) via the NdeI (5′) and XhoI (3′) restriction sites so as to introduce an N-terminal 6xHis tag. Subsequent to the structure determination, several variants of the pPJ131-TmPlsC construct were generated for functional analyses. These included TmPlsC-H1 and TmPlsC-H12 missing one and two N-terminal α-helices, respectively, and point mutants G25A, G25V, G25L, and G25M. The mutations were introduced using the QuikChange Lightning mutagenesis kit (Agilent Technologies), and the mutagenesis primers were designed using the QuikChange Primer Design software (Agilent Technologies). All constructs were verified via Sanger DNA sequencing.
Robertson R.M., Yao J., Gajewski S., Kumar G., Martin E.W., Rock C.O, & White S.W. (2017). A two-helix motif positions the active site of lysophosphatidic acid acyltransferase for catalysis within the membrane bilayer. Nature structural & molecular biology, 24(8), 666-671.
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4

PRRX1 Binding Site Mutagenesis

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The following mutagenesis primers targeting the predicted PRRX1 binding site was designed using Agilent’s QuikChange Primer Design software (https://www.agilent.com/store/primerDesignProgram.jsp): Forward primer, 5′-TTGGTTAACAGAAAACCAAGGCGATTTTTTGCTGGTTTTTCTATTT-3′; reverse primer, 5′-AAATAGAAAAACCAGCAAAAAATCGCCTTGGTTTTCTGTTAACCAA-3′. Bold-Italic letters indicate position of mutation site, flanking the two deleted base pairs (shown in lowercase) from the PRRX1 core binding motif (TTaaTTG). Mutagenesis was performed using the QuikChange II Site-Directed Mutagenesis Kit (Agilent) according to manufacturer’s instructions. Briefly, WT plasmid was amplified by PCR using the mutagenesis primers and a high-fidelity DNA polymerase, followed by DpnI digestion of methylated template DNA. The mutated plasmid was transformed in TOP10 competent E.coli cells (Invitrogen) and isolated using the HiSpeed Plasmid Maxi kit (Qiagen) before verification by sequencing.
Dankel S.N., Grytten E., Bjune J.I., Nielsen H.J., Dietrich A., Blüher M., Sagen J.V, & Mellgren G. (2020). COL6A3 expression in adipose tissue cells is associated with levels of the homeobox transcription factor PRRX1. Scientific Reports, 10, 20164.
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5

Mutagenesis Primer Design and PCR

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Mutagenesis primers were designed using QuikChange Primer Design software (Agilent Technologies). KOD Hot Start or Pwo DNA Polymerase (Merck Millipore) were used according to the manufacturers’ protocols. For Pwo DNA Polymerase elongation periods were extend to 14 min per cycle. The PCR product was purified with the QIAquick PCR purification kit (QIAGEN) and amplified in Escherichia coli.
Siebert A., Gattringer V., Weishaupt J.H, & Behrends C. (2022). ALS-linked loss of Cyclin-F function affects HSP90. Life Science Alliance, 5(12), e202101359.
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6

Site-Directed Mutagenesis for Amino Acid Substitutions

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Amino acid substitutions were performed with the primers as indicated in key resources table. Primers were designed with the QuikChange Primer Design Software (Agilent Technologies). Single mutants were generated using the QuikChange Lightning Site-Directed Mutagenesis kit (Agilent Technologies) and double mutants were created with the QuikChange Lightning Multi Site-Directed Mutagenesis kit (Agilent Technologies) according to the manufacturer’s instructions. The generated mutants were verified by sequencing to screen against spurious secondary mutations. For primer sequences see Supplementary Table 2.
Sarek G., Kotsantis P., Ruis P., Van Ly D., Margalef P., Borel V., Zheng X.F., Flynn H.R., Snijders A.P., Chowdhury D., Cesare A.J, & Boulton S.J. (2019). CDK phosphorylation of TRF2 controls t-loop dynamics during the cell cycle. Nature, 575(7783), 523-527.
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7

Site-Directed Mutagenesis of EGFR and HER2 Binders

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Site-directed mutagenesis of the hEGFR- and hHER2-specific binder scaffolds was performed using the QuikChange Lightning Site-Directed Mutagenesis Kit (Agilent Genomics), according to the manufacturer’s instructions. Mutagenic primers were designed using the QuikChange Primer Design Software (Agilent Genomics) and synthesized by Biomers, Germany. Primer sequences can be found in Supplementary Data 3. In the case of the hHER2-specific binder, the affibody zHER2-AK was generated from the parental affibody zHER2:4, which binds to hHER2 with an affinity of 50 nM45 (link), prior to the alanine scan by introducing mutations N23A and S33K for preventing N-glycosylation66 (link).
Salzer B., Schueller C.M., Zajc C.U., Peters T., Schoeber M.A., Kovacic B., Buri M.C., Lobner E., Dushek O., Huppa J.B., Obinger C., Putz E.M., Holter W., Traxlmayr M.W, & Lehner M. (2020). Engineering AvidCARs for combinatorial antigen recognition and reversible control of CAR function. Nature Communications, 11, 4166.
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