Epitope Substitution Scans

 Epitope Substitution Scans are the optimal solution if you are interested in:

 

  • Identification of conserved and variable amino acid positions of an epitope
  • Identification of epitope variants and new mimotopes
  • Antibody selectivity and cross-reactivity
  • Peptide vaccine developement
  • Peptide target binder development


On request Epitope Substitution Scans can include selected non-natural amino acids like various D-amino acids or citrulline.

 

 

Specifications of Epitope Single Substitution Scans

Epitope Single Substitution Scans cover the stepwise substitution of all amino acid positions of a given epitope or peptide with all 20 main amino acids and optionally additional non-natural amino acids.

 

PEPperMAP® Epitope Substitution Scan

Epitope Substitution Scan of a 12 aa starting peptide printed in duplicate. The microarray scan (top left) shows a typical exchange pattern that is translated into a heat map (bottom left). The amino acid plot highlights the change in spot intensities upon amino acid exchange with the wild type epitope at 100%. 7 of 12 amino acids are highly conserved with a limited tolerance for exchange. Stained HA (red) and Flag (green) control peptides frame the single substitution of the starting peptide.

 

   Microarray Content:    Gradual exchange of all amino acid positions with all amino acids
   Amino Acids:    20 main amino acids by default, additional non-natural amino acids on demand
   Peptide Length:
   Up to 15 amino acids by default (adjustable)
   Motif Length for Scan:
   Up to 15 amino acids by default (adjustable)
   Peptide Repeats:    Peptide triple spots by default (adjustable)
   Control Peptides:    HA (YPYDVPDYAG) and Flag (DYKDDDDKAS) tags by default
   Microarray Example:    A 12 aa starting peptide will be translated into 12 x 20 = 240 peptides printed in triplicate
   Data Output:    Detailed amino acid plots and substitution matrizes with conserved and variable amino acids

 

 

Specifications of Epitope Double Substitution Scans

In contrast to the stepwise exchanges in the Epitope Single Substitution Scans, Epitope Double Substitution Scans enable the high throughput screening for epitope variants and mimotopes by the exchange of two amino acid positions at once. Epitope Double Substitution Scans are based on PEPperCHIP® Discovery Microarrays.


Epitope Double Substitution Scans are hence a unique solution to discover, develop and optimize peptide vaccines, peptide mimotopes or protein target binders in a single assay with tens of thousands of peptide variants.

 

PEPperMAP® Epitope Double Substitution Scan

Epitope Double Substitution Scan of a 11 aa starting peptide printed in duplicate. The corresponding PEPperCHIP® Discovery Microarray covered 26,400 different peptides for high throughput identification and optimization of peptide variants in a single assay. Stained HA (red) and Flag (green) control peptides frame and segment the microarray with the peptide double substitution scan .

 

 

   Microarray Content:    Double substitutions of all amino acid positions with all amino acids
   Amino Acids:    20 main amino acids by default, additional non-natural amino acids on demand
   Peptide Length:
   Up to 15 amino acids by default, adjustable
   Motif Length for Scan:
   Up to 11 amino acids by default
   Peptide Repeats:    Peptide double spots by default
   Control Peptides:    HA (YPYDVPDYAG) and Flag (DYKDDDDKAS) tags by default
   Microarray Example:    A 11 aa starting peptide will be translated into 26,400 different peptides printed in duplicate
   Data Output:    Detailed intensity data of all peptides with amino acid plots of the top peptide family

 

 

Input Data & Sample Material

  • Starting epitope/peptide sequence for single or double substition scan
  • Epitope Single Substitution Scan: 10-20 µl serum or 10-20 µg purified antibody
  • Epitope Double Substitution Scan: 100 µl serum or 100 µg purified antibody

 


Analysis

PEPperCHIP® Peptide Microarray analysis for Epitope Substitution Scans is straightforward and can be performed in your own lab or covered by a PEPperMAP® Service. Further information about lab requirements for chip analysis can be found here. Epitope Double Substitution Scans based on PEPperCHIP® Discovery Microarrays are exclusively provided in combination with a comprehensive PEPperMAP® Service.

 

 

Further Information

 

 

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