About DNMT3A
The DNMT3A gene (DNA Methyltransferase 3 Alpha) on chromosome 2p23 Recurrent R882 hotspot mutations in the methyltransferase domain occur in ~25% of cytogenetically normal AML cases and clonal hematopoiesis. Key targets include Exons 2–23 (MTase domain in exons 10–23) for comprehensive mutation screening.
Mutations: R882H, R882C, frameshift, nonsense | GC content: 52% | Target exons: Exons 2–23 (MTase domain in exons 10–23)
DNMT3A Primer Design Challenges
- R882 hotspot mutations: Arginine 882 mutations in exon 23 cluster at the tetramerization interface requiring specific flanking primers
- Two major domains: Proline-rich N-terminus (exons 2–9) and methyltransferase domain (exons 10–23) require separate targeting strategies
- Clonal hematopoiesis detection: Age-related DNMT3A mutations require highly sensitive (0.5–1% VAF) deep sequencing primer design
Recommended Primer Design Parameters for DNMT3A
| 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 DNMT3A
| Target Region | Forward Primer (5′→3′) | Reverse Primer (5′→3′) | Amplicon |
|---|---|---|---|
| Exon 23 (R882) | 5′-CTGTGGAGAGAGCCTCTCCT-3′ | 5′-CACCTCCACAAACCTCAACC-3′ | 212 bp |
| Exon 10 (MTase start) | 5′-GAGCAAGGAGTCCCACATCA-3′ | 5′-GGAGGTGGACACATTGTGCT-3′ | 185 bp |
Key SNPs to Avoid in Primer Binding Sites
When designing DNMT3A primers, avoid these clinically significant variants:
- rs387906912 (R882H) — Exon 23 hotspot in AML
- rs144469610 (R882C) — Exon 23 C>T transition in clonal hematopoiesis
Clinical Validation Required
All DNMT3A 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 DNMT3A Primers Now
Pre-configured with DNMT3A-specific parameters. Use our primer design, Tm calculator, and GC content tools for optimal results.