In general terms, a spacer is introduced into an oligonucleotide to add distance between the oligonucleotide and a modifier. This reduces the possibility of any adverse interaction between the modifier and the sequence. For instance, G-rich sequences are known to quench fluorescein therefore the use of a suitable spacer will remove the dye label from the proximity of the oligonucleotide minimising the quenching effect.
Although useful where the base at a specific site is unknown, the flexibility of a C3 alkyl chain distorts the sugar-phosphate backbone. This can be alleviated with the use of dSpacer (LK2146/BA0033) since incorporation of this modifier sits directly into the natural sugar-phosphate backbone with no adverse effect. This modifier mimics abasic sites⁽¹⁾ and is useful in the study of mutations resulting from depurination. Similarly, we offer the 2-deoxy (BA0333) and rSpacer (BA0248) analogues for related studies.

Ref:

1. (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.