Bioorganic synthesis

Group Prof. Dr. Oliver Seitz

Oligonucleotide- and Peptide calculations

PNA, Peptide und PNA-Peptide-Conjugate mass calculation

To calculate the mass of a PNA, a peptide or a PNA-Peptide-conjugate just enter the sequence (separated by blanks) in the corresponding field, select the N- and C-terminal modifications and click on "Calculate!"
You can enter the four PNA-nucleobases (lower case letters!) as well as amino acids (single letter code upper case or three letter code!).
The three letter code is case sensitive! E.g. "gly" would be ignored!
Side chain modifications have to be entered bracketed after the corresponding monomer e.g. Lys(Alloc) or Lys(Biotin). Known modifications right now are the protecting groups Alloc, Fmoc, Boc, Bhoc, Z, Trt, Mmt, Mtt, tBu, Bzl, the fluorophores Dansyl, IAEDANS, Dabcyl, Dabsyl, TAMRA, NBD, EDANS and FAM as well as Biotin.
Furthermore you can enter phosphorylated amino acids by using "p Tyr", "p Ser",... and mark Cystine bridges by using the tilde as side chain modification "Cys(~)" at the relevant positions.

Mol.Wt.:    Exact Mass:
HPLC-MS SIM Ions:   HRMS Ions:
Termination Sequences:


To calculate DNA-properties just enter the sequence (separated by blanks) in the corresponding field, select 3'- and 5'-modification and click on "Calculate!".
Right now you can only enter the four nucleobases A, C, G, T as upper case letters. More terminal and internal modifications like fluorophores will be added later on.