Cdk9 CRISPR/Cas9 KO Plasmid (m): sc-430774
- Target species: mouse
- 20 µg of transfection-ready, purified plasmid DNA; Suitable for up to 20 transfections
- Cdk9 CRISPR/Cas9 Knockout (KO) Plasmid (m) is a pool of plasmids, each encoding Cas9 nuclease and a target-specific 20 nt guide RNA (gRNA) designed for maximum knockout efficiency using sequences derived from the GeCKO v2 library
- gRNA sequences direct Cas9 to induce site-specific double-strand breaks (DSBs) in the Cdk9 genomic locus, resulting in gene knockout through non-homologous end joining (NHEJ)
- Cdk9 HDR Plasmid (m) (sc-430774-HDR) is recommended for co-transfection with Cdk9 CRISPR/Cas9 KO Plasmid (m) to enable selection of successfully edited cells through HDR-mediated integration of a puromycin resistance cassette and RFP reporter gene
- Cdk9 HDR Plasmid (m) is a pool of plasmids, each containing a homology-directed repair (HDR) template corresponding to the gRNA target sites in the Cdk9 CRISPR/Cas9 KO Plasmid (m)
- Each HDR plasmid contains two ~800 bp homology arms flanking the puromycin resistance and RFP cassettes, designed to bind genomic DNA sequences surrounding the Cas9-induced double-strand break site and facilitate precise HDR-mediated integration
- The puromycin resistance and RFP genes are flanked by LoxP sites, enabling removal of selection markers via Cre recombinase (Cre Vector: sc-418923) after establishing stable knockout cell lines
- Following transfection, gene knockout efficiency can be assayed by WB, IF or IHC using antibody: Cdk9 Antibody (D-7): sc-13130
Ordering Information
| Product Name | Catalog # | UNIT | Price | Qty | FAVORITES | |
Cdk9 CRISPR/Cas9 KO Plasmid (m) | sc-430774 | 20 µg | $397.00 | |||
Cdk9 HDR Plasmid (m) | sc-430774-HDR | 20 µg | $445.00 |
Overview
Cyclin-dependent kinase 9 (Cdk9) encodes a serine/threonine kinase that forms the catalytic core of positive transcription elongation factor b (P-TEFb), a central regulator of RNA polymerase II pause release and productive transcriptional elongation. By phosphorylating the Pol II C-terminal domain and negative elongation factors, CDK9 coordinates rapid induction of gene expression programs controlling cell-cycle progression, DNA damage responses, differentiation, and stress signaling. In mouse systems, Cdk9-dependent transcriptional control is tightly linked to MYC-driven transcriptional amplification, inflammatory gene expression, and maintenance of proliferative states. Dysregulated CDK9 activity and P-TEFb dynamics are frequently studied in contexts of oncogenic transcription, cardiac and immune pathway remodeling, and virus-host transcriptional dependency, making Cdk9 a key node for mechanistic gene regulation research.
Cdk9 CRISPR/Cas9 KO Plasmid (m) is a pool of plasmids designed for targeted disruption of the Cdk9 gene in mouse cell lines. Each plasmid in the pool co-expresses a unique sgRNA, targeting a distinct site within the Cdk9 locus, alongside the Streptococcus pyogenes Cas9 nuclease, and encodes GFP to enable fluorescent identification and enrichment of successfully transfected cells. This multi-guide strategy increases the likelihood of inducing frameshifts or deletions that produce a functional knockout, offering a more robust alternative to single-guide approaches. DSBs induced at multiple sites are resolved through non-homologous end joining (NHEJ) or, when used with the included HDR donor template, homology-directed repair (HDR) at a defined target site within the locus.
When used in conjunction with the RFP-expressing HDR donor, GFP and RFP fluorescence can be used together to distinguish transfected from edited cell populations, streamlining flow cytometry-based sorting and clone selection workflows.
Homology-Directed Repair (HDR) Donor — Puromycin Cassette with RFP Reporter
For applications requiring confirmed, selectable knockout clones, Cdk9 HDR Plasmid (m) includes an HDR donor construct containing a puromycin resistance cassette (PuroR) and a red fluorescent protein (RFP) reporter, flanked by homology arms specific to a defined Cdk9 target site.
When co-transfected with Cdk9 CRISPR/Cas9 KO Plasmid (m):
- The PuroR-RFP cassette integrates at the Cas9 cut site via HDR, disrupting the Cdk9 open reading frame.
- RFP fluorescence provides an immediate visual indicator of successful integration, enabling fluorescence-based identification or sorting of edited cells prior to or alongside puromycin selection.
- Successfully edited cells are confirmed through puromycin resistance, substantially reducing clone screening burden.
- This selection strategy is ideal for generating stable, clonal KO cell lines for downstream functional studies, drug screening, or model development.
Cre-lox Cassette Removal System
The HDR donor construct features loxP sites flanking the PuroR-RFP selection cassette to allow clean marker removal following clone confirmation. Transient expression of Cre recombinase via the included Cre Vector: sc-418923 excises the cassette, leaving a minimal residual loxP site within the Cdk9 locus and eliminating potential confounding effects on downstream assays.
This two-step approach:
- Minimizes disruption to local chromatin architecture and neighboring regulatory elements
- Restores a near-native genomic context at the edited locus
- Enables reuse of the puromycin selection strategy in the same cell line for additional edits
Key Features
- gRNA targeting Cdk9 exon(s) critical for Cdk9 function
- Co-expression of SpCas9 and sgRNA from a single plasmid for simplified delivery
- HDR donor with puromycin resistance for positive clone selection
- loxP-flanked PuroR cassette with Cre recombinase vector for seamless marker removal
- Supplied ready to use for delivery by transfection
For Research Use Only. Not Intended for Diagnostic or Therapeutic Use.