Table 6.2 The use of oligonucleotides to encode amino acids in peptide synthesisAmino acid Structure Oligonucleotide codeGlycine
(Gly) CH 2 COOHNH 2 CACATGMethionine
(Met)NH 2CH 3 SCH 2 CH 2 CHCOOHACGGTAMany peptide libraries have been encoded using single stranded DNA oligo-
nucleotides as tags. Each oligonucleotide acts as the code for one amino acid
(Table 6.2). Furthermore, a polymerase chain reaction (PCR) primer is usually
attached to the tag site so that at the end of the combinatorial synthesis the
concentration of the completed tag DNA-oligonucleotide molecule may be
increased using theTaqpolymerase procedure. This amplification of the yield
of the tag makes it easier to identify the sequence of bases, which leads to a more
accurate decoding.
At each stage in the peptide synthesis a second parallel synthesis is carried out
on the same bead to attach the oligonucleotide tag (Figure 6.11). In other words,
two alternating parallel syntheses are carried out at the same time. On comple-
tion of the peptide synthesis, the oligonucleotide tag is isolated from the bead
and its base sequence determined and decoded to give the sequence of amino
acid residues in the peptide.
Peptides have also been used as tags (Figure 6.12) in a similar manner to
DNA oligo nucleotides. The sequence of amino acids in the encoding peptide is
determined using the Edman sequencing method. This amino acid sequence is
used to determine the history of the formation and hence the structure of the
product found on that bead.
6.3.2 Still’s binary code tag system
A unique approach by Still was to give each building block its own chemical
equivalent of a binary code for each stage of the synthesis using inert aryl halides
(Figure 6.13(a) ). One or more of these tags are directly attached to the resin
using a photolabile linker at the appropriate points in the synthesis. They
indicate the nature of the building block and the stage at which it was incorpor-
ated into the solid support (Table 6.3). Aryl halide tags are used because they
can be detected in very small amounts by GC. They are selected on the basis that
their retention times are roughly equally spaced (Figure 6.13(b) ). At the end of
124 COMBINATORIAL CHEMISTRY