Table 1 Degenerate codons and their corresponding amino acid sequences of CDR libraries designed for affinity maturation.

From: Targeting mutant p53-expressing tumours with a T cell receptor-like antibody specific for a wild-type antigen

Heavy CDR1

 Original seq.

S

G

G

Y

Y

W

S

       

 Degenerate codon

K M T

G G T

G G T

K M T

K M T

T G G

K M T

       

 Encoded amino acid

Y/A/D/S

G

G

Y/A/D/S

Y/A/D/S

W

Y/A/D/S

       

Heavy CDR3

 Original seq.

E

N

F

G

A

F

D

H

      

 Degenerate codon

K M W

D M T

K H T

G G A

K M T

K H T

K M T

B M T

      

 Encoded amino acid

Y/A/D/S/E

Y/A/D/S/N/T

Y/A/D/S/F/V

G

Y/A/D/S

Y/A/D/S/F/V

Y/A/D/S

Y/A/D/S/H/P

      

Light CDR1

 Original seq.

T

G

S

S

S

N

I

G

A

D

Y

E

T

H

 Degenerate codon

D M T

G G G

K M T

K M T

K M T

D M T

D H T

G G G

K M T

K M T

K M T

K M W

D M T

B M T

 Encoded amino acid

Y/A/D/S/N/T

G

Y/A/D/S

Y/A/D/S

Y/A/D/S

Y/A/D/S/N/T

Y/A/D/S/D/T/I/V/F

G

Y/A/D/S

Y/A/D/S

Y/A/D/S

Y/A/D/S/E

Y/A/D/S/T/N

Y/A/D/S/H/P

Light CDR3

 Original seq.

Q

S

Y

D

S

N

L

S

A

W

V

   

 Degenerate codon

B M W

K M T

K M T

K M T

K M T

D M T

B H T

K M T

K M T

T G G

K H T

   

 Encoded amino acid

Y/A/D/S/Q/H/P/E

Y/A/D/S

Y/A/D/S

Y/A/D/S

Y/A/D/S

Y/A/D/S/N/T

Y/A/D/S/L/H/P/V/F

Y/A/D/S

Y/A/D/S

W

Y/A/D/S/F/V

   
  1. Diversity of CDR1 and CDR3 libraries of the heavy and light chains of P1C1. Residues of the respective CDR loops were identified by Kabat definition and randomized with degenerate codons encoding for the original amino acid or a limited diversity consisting of Ala, Ser, Tyr or Asp. Gly and Typ were left unchanged to preserve structural integrity. Theoretical diversity of the heavy-chain CDR1, 3 and light-chain CDR1, 3 libraries are calculated to be 256, 1.6 × 105, 3.8 × 108 and 1.6 × 107
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