Photo-Crosslinking Calculator

About the Photo-Crosslinking Calculator

The Photo-Crosslinking Calculator is a free, scientifically accurate online tool designed for researchers working with photo-reactive amino acid crosslinkers in protein-protein interaction studies, mapping binding interfaces, and structural biology. This calculator follows established, peer-reviewed photochemical principles and reagent specifications from leading manufacturers and publications.

What is Photo-Crosslinking?

Photo-crosslinking is a powerful chemical biology technique that uses light to covalently trap transient or weak protein-protein, protein-peptide, protein-DNA, and protein-ligand interactions in living cells or in vitro. Upon irradiation with UV light (typically 254–365 nm), photo-reactive groups generate highly reactive intermediates (nitrene, carbene, or diradical) that insert into nearby C–H, N–H, or X–H bonds within ~3–15 Å, forming irreversible covalent bonds.

Most Common Photo-Reactive Groups

• Aryl Azides (e.g., Sulfo-SANPAH) → generate nitrenes at 254–300 nm
• Benzophenones → generate diradicals at 350–365 nm, highly reusable (multiple activation cycles)
• Aliphatic Diazirines → generate carbenes at 350–370 nm, smallest size, longest-lived reactive species

Importance of Photo-Crosslinking

Photo-crosslinking is essential in:

• Mapping protein-protein interaction interfaces at amino-acid resolution
• In vivo crosslinking (CLMS, XL-MS) using genetically encoded photo-amino acids (photo-Leu, photo-Met)
• Drug-target identification and PROTAC validation
• Structural proteomics and integrative modeling with AlphaFold-Multimer
• Studying membrane protein complexes and GPCR signaling

Scientific Basis & Formulas Used in This Calculator

All calculations follow standard formulas used in peer-reviewed literature:

• Amount of crosslinker (nmol) = Concentration (mM) × Volume (µL)
• Mass of crosslinker (µg) = nmol × MW / 1000
• Molar ratio = nmol crosslinker / nmol protein

When and Why You Should Use This Calculator

Use the Photo-Crosslinking Calculator when you:

• Need to prepare precise stock solutions of Sulfo-SANPAH, SDA, LC-SDA, or benzophenone derivatives
• Want to calculate optimal UV exposure time to avoid over-crosslinking and protein damage
• Are designing photo-crosslinking mass spectrometry (photo-CLMS) experiments
• Teaching chemical biology or proteomics courses

User Guidelines

1. Select your photo-crosslinker from the dropdown (MW auto-updates).
2. Enter desired final concentration and reaction volume.
3. Input protein concentration and volume if you want molar ratios.
4. Choose UV wavelength and exposure time (365 nm is safest for proteins).
5. Click “Calculate” – get exact pipetting instructions and safety notes.

This free Photo-Crosslinking Calculator is proudly brought to you by Agri Care Hub. For detailed photoreactive crosslinker chemistry and reactivity tables, visit Thermo Fisher’s Photo-Crosslinking Guide.

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