PolQi1
Based on 1 Customer Validation
PolQi1 is a selective inhibitor targeting the Polθ domain of DNA polymerase. PolQi1 inhibits the Polθ-mediated microhomology end joining (TMEJ/alt-EJ) pathway, reducing insertion/deletion (Indels) and imprecise editing events during DNA repair. PolQi1 can enhance the efficiency and accuracy of homology-directed repair (HDR) or Prime editing, and reduce off-target effects; and in combination with DNA-PK inhibitor AZD-7648 (HY-111783), exert efficient genome editing capabilities with dual pathway regulation. PolQi1 can be mainly used in gene editing research (such as CRISPR-Cas9 or Prime editing system optimization) to improve the precision editing efficiency of difficult-to-edit cells (such as primary hepatocytes and mouse embryos).
For research use only. We do not sell to patients.
- Purity : 98.42%
- CAS No.: 2607139-80-8
- Formula: C18H14ClF5N4O2
- Molecular Weight:448.77
-
Storage:Powder -20°C, 3 years , 4°C, 2 years ; In solvent -80°C, 6 months , -20°C, 1 month
To place orders, for customer services and technical support, please contact: MedChemExpress USA
Tel: 609-228-6898 E-mail: [email protected] [email protected]
-
Biological Activity
-
Chemical Information
-
Solvent & Solubility
- Protocols
- Purity & Documentation
- References
-
Help & FAQs
All DNA/RNA Synthesis Isoforms
More
Biological Activity
Description
IC50 & Target
|
DNA Polymerase |
In Vitro
PolQi1 (3 μM; 3 h) combines with AZD7648, can enhance homology-directed repair (HDR)-mediated gene knock-in efficiency and reduce insertions/deletions (InDels) in HEK293T and human induced pluripotent stem cells (hiPSCs)[1].
MedChemExpress (MCE) has not independently confirmed the accuracy of these methods. They are for reference only. Further protocols information, click here.
-
Cell Line:HEK293T and hiPSCs (SpCas9-inducible)
-
Concentration:0.3, 3, 10 μM for HEK293T cells; 3 μM for hiPSCs
-
Incubation Time:3 h; combined with AZD7648 (1 μM)
-
Result:Increased HDR-mediated knock-in efficiency by 3.9-fold and reduced InDels by 17.4-fold compared to DMSO controls.
At 10 μM, without significant additional improvement.
Increased HDR efficiency by 6.6-fold and reduced InDels by 2.3-fold compared to DMSO controls.
Chemical Information
-
CAS No. 2607139-80-8
-
Appearance Solid
-
Molecular Weight 448.77
-
Formula C18H14ClF5N4O2
-
Color White to off-white
-
SMILES
CN(C1=C(C(Cl)=C(C=C1)F)F)C([C@H]2N(C3=CC(C(F)(F)F)=CC(C)=N3)C(NC2)=O)=O
-
Shipping
Room temperature in continental US; may vary elsewhere.
-
Storage
Powder -20°C 3 years 4°C 2 years In solvent -80°C 6 months -20°C 1 month
Solvent & Solubility
In Vitro:
DMSO : 100 mg/mL (222.83 mM; Need ultrasonic; Hygroscopic DMSO has a significant impact on the solubility of product, please use newly opened DMSO)
Please refer to the solubility information to select the appropriate solvent. Once prepared, please aliquot and store the solution to prevent product inactivation from repeated freeze-thaw cycles.
Storage method and period of stock solution: -80°C, 6 months; -20°C, 1 month. When stored at -80°C, please use it within 6 months. When stored at -20°C, please use it within 1 month.
Please refer to the solubility information to select the appropriate solvent. Once prepared, please aliquot and store the solution to prevent product inactivation from repeated freeze-thaw cycles.
Storage method and period of stock solution: -80°C, 6 months; -20°C, 1 month. When stored at -80°C, please use it within 6 months. When stored at -20°C, please use it within 1 month.
Concentration (start) × Volume (start) = Concentration (final) × Volume (final)
In Vivo:
Select the appropriate dissolution method based on your experimental animal and administration route.
- For the following dissolution methods, please ensure to first prepare a clear stock solution using an In Vitro approach and then sequentially add co-solvents:
- To ensure reliable experimental results, the clarified stock solution can be appropriately stored based on storage conditions. As for the working solution for In Vivo experiments, it is recommended to prepare freshly and use it on the same day.
- The percentages shown for the solvents indicate their volumetric ratio in the final prepared solution. If precipitation or phase separation occurs during preparation, heat and/or sonication can be used to aid dissolution.
Add each solvent one by one: 10% DMSO 40% PEG300 5% Tween-80 45% Saline
Solubility: ≥ 2.5 mg/mL (5.57 mM); Clear solution
This protocol yields a clear solution of ≥ 2.5 mg/mL (saturation unknown).
Taking 1 mL working solution as an example, add 100 μL DMSO stock solution (25.0 mg/mL) to 400 μL PEG300, and mix evenly; then add 50 μL Tween-80 and mix evenly; then add 450 μL Saline to adjust the volume to 1 mL.
Preparation of Saline: Dissolve 0.9 g sodium chloride in ddH₂O and dilute to 100 mL to obtain a clear Saline solution.
In Vivo Dissolution Calculator
Please enter the basic information of animal experiments:
-
-
-
-
Recommended: Prepare an additional quantity of animals to account for potential losses during experiments.
Please enter your animal formula composition:
-
%DMSO +
Recommended: Keep the proportion of DMSO in working solution below 2% if your animal is weak.
-
%+
-
+%Tween-80 + +
-
%Saline +
The co-solvents required include: DMSO, . All of co-solvents are available by MedChemExpress (MCE). , Tween 80. All of co-solvents are available by MedChemExpress (MCE).
Working solution concentration: 0.22 mg/mL
Method for preparing stock solution: mg drug dissolved in μL DMSO. Stock solution concentration: mg/mL.
1. Take μL DMSO stock solution;
2. Add μL .
μL , mix evenly;
3. Then add μL Tween 80, mix evenly;
4. Then add μL
Please ensure that the stock solution in the first step is dissolved to a clear state, and add co-solvents in sequence. You can use ultrasonic heating (ultrasonic cleaner, recommended frequency 20-40 kHz), vortexing, etc. to assist dissolution.
Protocols
-
Gene Editing
Gene editing modify specific sites within the genome through gene deletions, insertions or conversions to study functionally unknown genes or conduct gene therapy. It is also used to change the biological traits of organisms to establish new varieties. Gene editing techniques include zinc finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN), and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas 9) (CRISPR/Cas9).
-
CRISPR-Cas9 knockout in cultured mammalian cells
CRISPR-Cas9 knockout in cultured mammalian cells uses an sgRNA to direct Cas9 to a complementary genomic sequence adjacent to a compatible PAM; Cas9 creates a targeted DNA double-strand break, and repair by non-homologous end joining can introduce insertions or deletions that disrupt the coding sequence or functional genomic element. The readout of knockout is detection of edited alleles and loss of gene product or phenotype, commonly by PCR/Sanger-sequence trace decomposition, targeted sequencing, immunoblotting, immunostaining, or flow cytometry when the target protein is detectable at the cell surface.
-
CRISPR-Cas9 HDR knock-in/precise editing
CRISPR-Cas9 HDR knock-in uses a guide RNA to direct Cas9 to a genomic target adjacent to a PAM, where Cas9 creates a double-strand break; if a donor DNA template with homology to the cut region is present, cellular HDR can copy the donor sequence into the genome, producing a precise substitution, tag, reporter, or insertion rather than an indel. The readout is the fraction of alleles or cells carrying the intended donor-derived edit, measured by junction PCR, restriction-fragment analysis, Sanger sequencing, amplicon deep sequencing, flow cytometry for reporter knock-in, or clone genotyping; NHEJ indels and partial or non-HDR insertions are measured in parallel because they compete with or confound precise HDR outcomes.
-
CRISPR-Cas9 zebrafish embryo editing
CRISPR-Cas9 zebrafish embryo editing introduces targeted double-strand breaks in genomic DNA by delivering Cas9 nuclease with a guide RNA into one-cell-stage embryos; repair by endogenous DNA-repair pathways produces indels or donor-mediated insertions that can be detected by phenotype, PCR-based genotyping, heteroduplex assays, Sanger sequencing, or amplicon sequencing. The readout reflects the frequency and spectrum of edited alleles in mosaic F0 embryos or transmitted F1 animals; because injected embryos can carry multiple alleles, founder screening and sequence confirmation are required before establishing stable mutant lines.
-
Hepatotoxicity Study
This protocol evaluates hepatotoxicity using complementary in vivo mouse APAP acute liver injury and in vitro hepatocyte-based cytotoxicity readouts. In vivo APAP injury is assessed by serum ALT/AST, liver histology, hepatic glutathione, protein adducts, necrosis, inflammation, and regeneration-related endpoints. In vitro hepatotoxicity is assessed by loss of viability, leakage of ALT/AST/LDH, oxidative-stress markers, mitochondrial function, nuclear morphology, intracellular calcium, and high-content imaging endpoints.
-
Prime editing: A gene-editing technology based on the CRISPR/Cas system
Prime editing is a CRISPR-derived genome editing method that uses a Cas9 H840A nickase fused to an engineered M-MLV reverse transcriptase and a prime-editing guide RNA (pegRNA), where the pegRNA specifies the genomic target through its spacer and encodes the desired edit through a primer-binding site and reverse-transcription template. The editor nicks one DNA strand, the exposed 3' DNA end hybridizes to the pegRNA primer-binding site, reverse transcription copies the edited sequence into a 3' flap, and cellular DNA repair resolves the intermediate to generate substitutions, small insertions, or small deletions without requiring a donor DNA template or a programmed double-strand break. The standard mammalian workflow designs candidate pegRNAs and, when using PE3 or PE3b, an additional nicking sgRNA; delivers prime-editor and guide components into cells; allows editing to occur; extracts genomic DNA; amplifies the target locus; and quantifies precise edits, indels, and byproducts by amp
-
CRISPR/Cas9 Knockout Animal Model
CRISPR/Cas9 knockout animal modeling uses guide RNA to direct Cas9 to a genomic target, where Cas9 creates a DNA double-strand break; repair by error-prone non-homologous end joining generates insertions or deletions that can disrupt coding sequence and produce knockout alleles. Classic animal-model workflows deliver Cas9 mRNA or Cas9 protein with sgRNA into fertilized zygotes by microinjection or electroporation, then transfer edited embryos into pseudopregnant recipients and genotype founders for target-site mutations.
-
CRISPR-Cas9 mouse zygote editing
CRISPR-Cas9 mouse zygote editing introduces Cas9 nuclease and guide RNA into one-cell embryos so that Cas9 creates a guide-directed double-strand break at the target locus; repair by non-homologous end joining can generate indels, while repair with an added donor template can generate defined knock-in or point-mutation alleles. The readout is embryo, pup, or founder genotype, usually assessed by PCR, restriction-fragment analysis, Sanger sequencing, TIDE/sequence-trace analysis, or targeted sequencing; successful editing is interpreted as the presence of indels, intended HDR alleles, or both at the target locus.
-
CRISPR-Cas9 editing of human pluripotent stem cells
CRISPR-Cas9 editing of human pluripotent stem cells uses a guide RNA to direct Cas9 to a genomic target, where Cas9 creates a double-strand break that is repaired mainly by non-homologous end joining for knockout mutations or by homology-directed repair when a donor template is supplied for precise knock-in or sequence correction. The readout is generated by genotyping edited bulk populations or single-cell-derived clones, using PCR, sequencing, restriction-based assays, reporter fluorescence, or allele-specific analysis to distinguish unedited alleles, indels, precise donor-mediated edits, biallelic deletions, and unwanted on-target lesions.
-
CRISPR-Cas9 RNP editing of primary immune cells
CRISPR-Cas9 RNP editing uses preassembled Cas9 protein and guide RNA to direct sequence-specific DNA cleavage at a genomic target, after which cellular DNA repair generates insertions/deletions for knockout or uses an added donor template for knock-in. In primary immune cells, published protocols deliver Cas9 RNPs mainly by electroporation or nucleofection because these methods can introduce protein-RNA complexes into difficult-to-transfect T cells, B cells, NK cells, monocytes, myeloid cells, and innate lymphoid cells without viral Cas9 expression.
Purity & Documentation
-
Data Sheet (280 KB)
-
SDS (252 KB)
- English - EN (252 KB)
- Français - FR (252 KB)
- Deutsch - DE (252 KB)
- Norwegian - NO (252 KB)
- Español - ES (252 KB)
- Swedish - SV (252 KB)
- Italian - IT (252 KB)
- Korean - KR (252 KB)
- Portuguese - PT (252 KB)
-
Handling Instructions (2659 KB)
References
[1]. Wimberger S, et al. Simultaneous inhibition of DNA-PK and Polϴ improves integration efficiency and precision of genome editing. Nat Commun. 2023 Aug 14;14(1):4761. [Content Brief]
[3]. Mentani A, et al. Prime Editing: Mechanistic Insights and DNA Repair Modulation. Cells. 2025 Feb 13;14(4):277. [Content Brief]
Complete Stock Solution Preparation Table
Please refer to the solubility information to select the appropriate solvent. Once prepared, please aliquot and store the solution to prevent product inactivation from repeated freeze-thaw cycles.
Storage method and period of stock solution: -80°C, 6 months; -20°C, 1 month. When stored at -80°C, please use it within 6 months. When stored at -20°C, please use it within 1 month.
| Optional Solvent | Concentration Solvent Mass | 1 mg | 5 mg | 10 mg | 25 mg |
|---|---|---|---|---|---|
| DMSO | 1 mM | 2.2283 mL | 11.1416 mL | 22.2831 mL | 55.7078 mL |
| 5 mM | 0.4457 mL | 2.2283 mL | 4.4566 mL | 11.1416 mL | |
| 10 mM | 0.2228 mL | 1.1142 mL | 2.2283 mL | 5.5708 mL | |
| 15 mM | 0.1486 mL | 0.7428 mL | 1.4855 mL | 3.7139 mL | |
| 20 mM | 0.1114 mL | 0.5571 mL | 1.1142 mL | 2.7854 mL | |
| 25 mM | 0.0891 mL | 0.4457 mL | 0.8913 mL | 2.2283 mL | |
| 30 mM | 0.0743 mL | 0.3714 mL | 0.7428 mL | 1.8569 mL | |
| 40 mM | 0.0557 mL | 0.2785 mL | 0.5571 mL | 1.3927 mL | |
| 50 mM | 0.0446 mL | 0.2228 mL | 0.4457 mL | 1.1142 mL | |
| 60 mM | 0.0371 mL | 0.1857 mL | 0.3714 mL | 0.9285 mL | |
| 80 mM | 0.0279 mL | 0.1393 mL | 0.2785 mL | 0.6963 mL | |
| 100 mM | 0.0223 mL | 0.1114 mL | 0.2228 mL | 0.5571 mL |
PolQi1 Related Classifications
HY-159078 Related Classifications
Powered by Bioz