Oligonucleotide Tags

Oligonucleotide encoding was reported by-Nielsen and colleagues [19], who used the construct presented in Fig. 2. a-Amino functionality of the serine residue was used as an attachment point for the growing peptide chain, while the (3-hydroxyl of the side chain was used for the encoding oligonucleotide assembly. Therefore, the tag-to-peptide ratio used in this work was 1 1. Synthesis was carried out on controlled porous glass (CPG) beads. 

Oligonucleotide tagging was developed and used successfully for the synthesis of peptides many methodological issues, related mostly to the chemical compatibility of the approach, were solved. However, the compatibility of this encoding strategy with the synthesis of other classes of organic molecules remains limited. 

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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 completion 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. 

In order to develop an artificial restriction enzyme that can cleave a desired sequence, an oligonucleotide tag needs to be attached to the catalysis site. The artificial enzyme shown in Fig. 6.15 has an oligonucleotide tag (the rectangle) connected to a metal-chelate-type catalysis site (the circle). The catalytic site was fixed to a particular site on the substrate upon base pairing between the artificial enzyme and the substrate. When the Lu-chelate site was connected to single-stranded DNA, and the DNA moiety was hybridized to RNA with the complementary sequence, the RNA was hydrolyzed at the desired site. If the DNA sequence in the artificial enzyme is designed appropriately, RNA can be cleaved at any site desired. 

Esch, M. B., Baeumner, A. J., and Durst, R. A. (2001). Detection of Cryptosporidium parvum using oligonucleotide-tagged liposomes in a competitive assay format. Anal. Chem. 73 3162-3167. 

Fan, J. B., et al., Parallel genotyping of human SNPs using generic high-density oligonucleotide tag arrays [In Process Citation]. Genome Res, 2000. 10(6) p. 853-60. 

The most important drawback of oligonucleotide tags is their instability and incompatibility with many classic organic chemistry conditions. Even for peptide chemistry, the reaction conditions have to be carefully adapted to the presence of the nucleotide strands, and this limits significantly the use of this cod-... 

Lynx Therapeutics, Inc. Oligonucleotide synthesis Oligonucleotide tags to identify synthesis products WO9612039 1996... 

Jawalekar AM, Malik S, Verkade JM, Gibson B, Barta NS, Hodges JC, Rowan A, van Delft FL (2013) Oligonucleotide tagging for copper-free click conjugation. Molecules 18(7) 7346-7363. doi 10.3390/moleculesl 8077346... 

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