CTCF CRISPR/Cas9 KO Plasmid (h2): sc-401245-KO-2

Overview

CTCF (CCCTC-binding factor) is a ubiquitously expressed zinc-finger DNA-binding protein that functions as a master regulator of chromatin architecture and transcriptional insulation. By mediating long-range chromatin looping and defining topologically associating domain (TAD) boundaries, CTCF coordinates enhancer–promoter communication and contributes to epigenetic regulation in conjunction with cohesin. It influences key processes including transcriptional control, replication timing, and DNA damage responses, and its disruption can lead to widespread changes in gene expression programs. Altered CTCF dosage or boundary function has been linked to genome instability and dysregulated developmental and oncogenic pathways, making it a high-value target for mechanistic studies of 3D genome organization and gene regulation.

CTCF CRISPR/Cas9 KO Plasmid (h2) is a pool of plasmids designed for targeted disruption of the CTCF gene in human cell lines. Each plasmid in the pool co-expresses a unique sgRNA, targeting a distinct site within the CTCF 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, CTCF HDR Plasmid (h2) 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 CTCF target site.
When co-transfected with CTCF CRISPR/Cas9 KO Plasmid (h2):

• The PuroR-RFP cassette integrates at the Cas9 cut site via HDR, disrupting the CTCF 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 CTCF 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 CTCF exon(s) critical for CTCF 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.