About AR
The AR gene (Androgen Receptor) on chromosome Xq12 Ligand-binding domain mutations in exons 4–8 drive castration-resistant prostate cancer by broadening ligand specificity. Key targets include Exons 1–8 (LBD in exons 4–8) for comprehensive mutation screening.
Mutations: T878A, H874Y, W742C, T877A | GC content: 63% | Target exons: Exons 1–8 (LBD in exons 4–8)
AR Primer Design Challenges
- Very high GC content (63%): AR has one of the highest GC contents among nuclear receptors, requiring 5–10% DMSO for GC-rich exon 1 amplification
- CAG repeat polymorphism: Exon 1 contains a polymorphic CAG trinucleotide repeat affecting translation and confounding primer design
- X-chromosomal hemizygosity: Male single-copy status requires higher PCR sensitivity to avoid allelic dropout artifacts
Recommended Primer Design Parameters for AR
| Parameter | Standard Exons | GC-Rich Regions (≥58%) |
|---|---|---|
| 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 | Add 5–10% DMSO or betaine |
Recommended Primer Sequences for AR
| Target Region | Forward Primer (5′→3′) | Reverse Primer (5′→3′) | Amplicon |
|---|---|---|---|
| Exon 1 (NTD domain) | 5′-GAGCGTACCTGCGTGAAAGA-3′ | 5′-ACAGAGATGCTCTTCAATGG-3′ | 192 bp |
| Exon 5 (LBD T878A) | 5′-TGACTCTGGAGCCCTTTGAA-3′ | 5′-GCTGTGAAGCCTCTCTTCCT-3′ | 215 bp |
Key SNPs to Avoid in Primer Binding Sites
When designing AR primers, avoid these clinically significant variants:
- rs121913659 (T878A) — LBD mutation in exon 5, antiandrogen resistance
- rs121913661 (H874Y) — Exon 5 LBD activating mutation
- rs1042829 (CAG repeat) — Exon 1 polymorphic repeat
Clinical Validation Required
All AR 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 AR Primers Now
Pre-configured with AR-specific parameters. Use our primer design, Tm calculator, and GC content tools for optimal results.