Spacer C3 phosphoramidite, when incorporated into an oligonucleotide, mimics the three carbon spacing between the 3’ and 5’ hydroxyls of sugar unit. ⁽¹⁾ Although useful where the base at a specific site is unknown, the flexibility of the alkyl chain distorts the sugar-phosphate backbone. This can be alleviated with the use of dSpacer (or “abasic” spacer” since incorporation of this modifier sits directly into the natural sugar-phosphate backbone with no adverse effect. This modifier mimics abasic sites ⁽²⁾ and is useful in the study of mutations resulting from depurination. The inverse abasic modification allows incorporation of this functionality when designing reverse 5'-3’ syntheses to modify the nuclease resistance of the oligonucleotide. Our inverse abasic CPGs are available in a variety of pore sizes and functional loadings.

Ref:

1. Enhancing sequence-specific cleavage of RNA within a duplex region: Incorporation of 1,3-propanediol linkers into oligonucleotide conjugates of serinol-terpyridine, B.N. Trawick, T.A. Osiek and J.K. Bashkin, Bioconjugate Chem., 12, 900-905, 2001.
2. (a) Oligodeoxynucleotides containing synthetic abasic sites model substrates for DNA-polymerases and apurinic apyrimidinic endonucleases, M. Takeshita, C.N. Chang, F. Johnson, S. Will and A.P. Grollman, J. Biol. Chem., 262, 10171-10179, 1987; (b) NMR-studies of abasic sites in DNA duplexes deoxyadenosine stacks into the helix opposite the cyclic analog of 2-deoxyribose, M.W. Kalnik, C.N. Chang, A.P. Grollman and D.J. Patel, Biochemistry, 27, 924-931, 1988.