Reagents
| Reagent | Role | Amount |
|---|---|---|
| Carboxylic acid building block | Acyl donor | 20–50 eq |
| DMTMM·PF₆ | Coupling reagent | 20–50 eq |
| NMM or DIPEA | Base | 20–50 eq |
| DNA–amine headpiece | Nucleophile / substrate | 1.0 eq (typically nmol scale) |
Conditions
- Solvent
- DMA/borate buffer (pH 9.4) or DMF/water (4:1)
- Temperature
- Room temperature or 37 °C
- Reaction time
- 2–16 h
- Atmosphere
- Ambient
Procedure
- Prepare DNA–amine headpiece in borate buffer (100 mM, pH 9.4) at the desired concentration (typically 0.5–1.0 mM in DNA).
- Dissolve carboxylic acid building block (20–50 eq) in DMA or DMF.
- Add DMTMM·PF₆ (20–50 eq) to the building block solution. Add base (20–50 eq).
- Combine the activated acid solution with the DNA–amine solution. Vortex to mix. The final organic content should be 40–80% depending on DNA stability tolerance.
- Incubate at RT or 37 °C for 2–16 h (overnight is common for difficult substrates).
- Purify by ethanol precipitation. Analyze by LC-MS for conversion and product identity.
Expected outcome
Published comparisons report higher conversion than HATU for on-DNA amidation, particularly with sterically hindered building blocks (Hosozawa et al., 2024). Broad substrate scope enabling expanded DEL chemical diversity.
Analytical monitoring
LC-MS (oligonucleotide mode) for conversion quantification. UV/Vis for DNA integrity.
Troubleshooting
- Low conversion with a specific building block
- Increase equivalents to 50 eq. Raise temperature to 37 °C. Extend time to 16 h. Try switching solvent system (DMA vs DMF).
- DNA degradation
- Reduce temperature. Decrease organic co-solvent fraction. Check buffer pH. Reduce reaction time.
- Multiple product peaks in LC-MS
- Check for acid chloride formation or anhydride side products. Reduce reagent excess. Ensure building block is pure.
Notes & applicability
- In published on-DNA amidation screens, DMTMM·PF₆ achieved higher conversion than HATU and DMTMM·Cl, particularly for sterically hindered partners (Hosozawa et al., 2024).
- The 20–50 eq stoichiometry reflects optimized protocol conditions from the above study. Many DEL workflows use significantly higher reagent excess (100s–1000s eq). Adjust based on your platform’s standard conditions.
- Screen a small panel of building blocks first to validate conditions before library-scale synthesis.