About ARID1A
The ARID1A gene (AT-Rich Interaction Domain 1A) on chromosome 1p36 Inactivating frameshift and nonsense mutations in ARID1A are common in ovarian clear cell carcinoma and endometrioid cancers. Key targets include Exons 1–20 (ARID domain in exon 1) for comprehensive mutation screening.
Mutations: Frameshift, nonsense mutations | GC content: 48% | Target exons: Exons 1–20 (ARID domain in exon 1)
ARID1A Primer Design Challenges
- Large transcript size: ARID1A spans ~86 kb with 20 exons, requiring systematic tiled amplicon coverage
- AT-rich introns (48% GC): Low GC content in intronic regions may complex with high background in intergenic amplification
- Frameshift mutation detection: Single-nucleotide insertion/deletion mutations require high-resolution amplicon design
Recommended Primer Design Parameters for ARID1A
| Parameter | Standard Exons | Optimized Regions |
|---|---|---|
| Primer length | 20–22 nt | 22–25 nt |
| GC content | 45–55% | 50–60% |
| Tm | 58–62°C | 60–65°C |
| Amplicon size | 150–300 bp | 180–350 bp |
| Annealing temp | 58–60°C | 60–64°C (touchdown) |
| PCR additive | Standard | Optional 3–5% DMSO for problematic regions |
Recommended Primer Sequences for ARID1A
| Target Region | Forward Primer (5′→3′) | Reverse Primer (5′→3′) | Amplicon |
|---|---|---|---|
| Exon 1 (ARID domain) | 5′-CTCTCCCAGCAGTCACTGAA-3′ | 5′-GCTTGCTGAGCTGTCTCTGT-3′ | 188 bp |
| Exon 20 (C-terminal) | 5′-TCCCTACCCCATGTGTGACT-3′ | 5′-ACACCTGGAGCTGTCTCTTG-3′ | 234 bp |
Key SNPs to Avoid in Primer Binding Sites
When designing ARID1A primers, avoid these clinically significant variants:
- rs138486234 (R1989*) — Recurrent nonsense mutation in exon 20
- rs370842097 (Q584*) — Exon 7 truncating mutation in ovarian cancer
Clinical Validation Required
All ARID1A primers designed with VigyanLLM are for research use only. Clinical diagnostic applications require additional wet-lab validation, Sanger sequencing confirmation, and regulatory approval before patient use.
Design ARID1A Primers Now
Pre-configured with ARID1A-specific parameters. Use our primer design, Tm calculator, and GC content tools for optimal results.