02 — Chemistry
Solvent selection for lyophilized peptides
There is no universal solvent that both dissolves every sequence and leaves every assay untouched. Choose from peptide class, then confirm the downstream system.
Always dissolve a small portion before committing the vial. These notes are class-level laboratory practice, not item-specific instructions.
Work from charge and hydrophobicity
| Sequence character | Typical first solvent | Laboratory notes |
|---|---|---|
| Basic / net positive (K, R, H rich) | Water; then 0.1% acetic acid if needed | Acid helps protonate basic residues. |
| Acidic / net negative (D, E rich) | Water; if poor, very dilute aqueous ammonia or bicarbonate | Avoid strong base. Neutralize before most assays. |
| Polar, modest hydrophobicity | Water; then dilute into assay buffer | PBS as a first solvent often reduces solubility because of salt. |
| Hydrophobic / aromatic-rich (L, I, V, F, W) | Minimal DMSO, DMF, or acetonitrile, then dilute | Confirm final organic percentage is tolerated by the assay. |
| Cys, Met, or Trp present | Degassed or low-oxygen aqueous solvents | Avoid DMSO with Cys or Met; DMSO can oxidize sulfur-containing residues. |
| Aggregation-prone | Urea or guanidine HCl only if the assay allows | Chaotropes are last-resort solubilizers, not routine diluents. |
Order of operations
For vial handling before and after solvent is added, see Reconstitution.
- Calculate a concentrated stock required by the assay method. Many published in-vitro methods use stocks in the 1–5 mg/mL range; your system defines the number.
- Add solvent down the vial wall, not as a jet onto the cake.
- Allow the cake to wet. Gentle swirling or rolling. Avoid foaming.
- Brief bath sonication only if solids remain and the sequence is not known to be shear- or heat-sensitive.
- If still incomplete, do not stack unrelated solvents into the same vial.
- Dilute the clear stock into assay buffer immediately before use when stability is unknown.
Assay compatibility
- Cell-based readouts. Residual DMSO, DMF, or acetonitrile is a confounder. Many groups keep final DMSO at or below 0.1% v/v and run solvent-only controls.
- Enzyme assays. pH and ionic strength of the reconstitution solvent carry into the reaction.
- LC-MS. Keep an analytical stock and an assay stock if methods conflict.
- Phosphate and other salts. Useful as working buffers; poor as the first solvent for many lyophilizates.
What “clear” means
A usable stock is optically clear, with no film, gel, or fines. Do not assume concentration from mass/volume if the liquid is not homogeneous.
Small-molecule research reagents do not follow peptide charge rules. Use the CoA and the laboratory’s compound-specific SOP.
General laboratory information for Research Use Only materials. Return to the desk.