Biochemistry · Synthetic Biology · Chemical Design
Beyond the Twenty Non-Natural Amino Acids
Explore real non-natural amino acids used in research, and design your own. From click-chemistry handles to photocages to radiohalogen labels — the expanded alphabet of protein building blocks.
200+
Non-natural amino acids synthesized to date
▶ Catalog
+ Designer
● Context
The Expanded Alphabet
A curated library of non-natural amino acids actively used in chemical biology, drug development, and protein engineering.
All
Bioorthogonal
Photocaged
UV-removable
Light-activated protein
Conditional function
Fluorinated
Metal-binding
Helix stapling
Constrained
Design Your Own Amino Acid
No single non-natural amino acid does everything. Combine a core chemistry with reporter groups, radiohalogen labels, and design constraints to propose a multi-functional probe tailored to your imaging or biochemical goal.
Design Parameters
Core chemistry
Reporter chemistry (combine with core)
Radiohalogen labeling (nuclear imaging)
Pharmacokinetic profile
Design constraints
General
✓
Metabolically stable in caged form (resists premature degradation)
✓
Water-soluble at physiological pH (IV injection compatible)
✓
Cell-permeable (MW < 500 Da, minimal H-bond donors)
✓
Bioorthogonal in caged form (no off-target reactivity in blood)
✓
SPPS-compatible (Fmoc solid-phase synthesis)
✓
Compatible with amber suppression (genetic incorporation)
Photochemical
✓
UV-removable cage (365 nm, one-way — cage not regenerated)
✓
Two-photon activated (NIR 700–900 nm, deep tissue compatible)
✓
Visible-light compatible (≥400 nm, no UV — safer for live cells)
✓
Reversible photoswitch (fatigue-resistant, cage not consumed)
Aromatic ring accessible for electrophilic radioiodination (¹²³I / ¹³¹I)
✓
Electron-rich ring for regioselective iodination at 3-position
✓
Aromatic ring suitable for ¹⁸F-fluorination (SNAr or electrophilic)
✓
Contains chelator site for radiometal (⁶⁸Ga / ⁶⁴Cu / ⁹⁹ᵐTc)
✓
Radiolabel site orthogonal to cage — labeling does not block uncaging
✓
Radiolabeled form retains LAT1 / NIS transport substrate recognition
✓
Stable to in vivo deiodination (metabolic dehalogenation resistance)
Conditional function trigger
✓
Conditional function trigger: light
✓
Conditional function trigger: pH (tumor microenvironment ~6.5)
✓
Conditional function trigger: redox (GSH-activated in tumor cytoplasm)
✓
Conditional function trigger: enzyme (TPO / tyrosinase / kinase)
NH₂
Configure parameters and design
Designing your amino acid…
Combined chemistry
Reporter / labeling notes
Orthogonality assessment
Scientific Context
Non-natural amino acids (nnAAs) expand the chemical space of proteins beyond the 20 canonical residues. They are incorporated via chemical synthesis (SPPS) or through genetic code expansion using engineered aminoacyl-tRNA synthetase / tRNA pairs.
The 22 Naturally Encoded Amino Acids
Selenocysteine (Sec, U) and pyrrolysine (Pyl, O) are the 21st and 22nd amino acids — encoded by UGA and UAG stop codons respectively in specific organisms. They are the only naturally occurring additions to the standard 20.
The three major strategies for incorporating nnAAs into proteins each have distinct trade-offs between site specificity, yield, and chemical diversity:
Strategy
Method
Scale
Limitation
SPPS
Chemical synthesis, Fmoc / Boc
~50 residues
Chain length, ligation needed for proteins
Amber suppression
Engineered aaRS / tRNA pair, UAG codon
Full-length proteins
Incorporation efficiency ~20–60%
Cell-free
Reconstituted PURE system or cell extract
Milligram scale
Cost, cannot scale to grams easily
NCL / EPL
Native chemical ligation, expressed protein ligation
Semi-synthetic proteins
Requires Cys at ligation junction
Bioorthogonal Chemistry Pairs
The most powerful nnAA applications pair reactive handles: azide (pAzF) + DBCO for SPAAC; propargyl + azide for CuAAC; BCN + tetrazine for IEDDA. Reaction rates span 10⁻³ to 10⁶ M⁻¹s⁻¹ — tetrazine ligation is the fastest.
Key research groups who pioneered genetic code expansion include Peter Schultz (Scripps), Jason Chin (MRC LMB), and Nobelist Carolyn Bertozzi (Stanford) for bioorthogonal chemistry in living systems.