Spacer C3 is a three-carbon spacer that is used to incorporate a short spacer arm into an oligonucleotide. Spacer C3 can be incorporated in consecutive additions if a longer spacer is required. Spacer C3-modified oligos have been used in a number of different applications, including protein-RNA functional studies (1), as a DNA abasic site mimic to study the utility of small synthetic ligands (such as pteridines) for nucleotide recognition in SNP typing applications (2), and for solid-phase immobilization of hybridization probes (3). Spacer C3 incorporated at the 3’-end of an oligo functions as an effective blocking agent against polymerase extension at that end in PCR reactions (4).
1. Pritchard, C.E., Grasby, J.A., Harny, F., Zacharek, A.M., Singh, M., Karn, J., Gait, M.J. Methylphosphonate mapping of phosphate contacts critical for RNA recognition by the human immunodeficiency virus tat and rev proteins. Nucleic Acids Res. (1994), 22: 2592-2600.
2. Dai, Q., Xu, C-Y., Sato, Y., Yoshimoto, K., Nishizawa, S., Teramae, N. Enhancement of the Binding Ability of a Ligand for Nucleobase Recognition by Introducing a Methyl Group. Anal. Sci. (Japan) (2006), 22: 201-203.
3. Li, H., McGall, G. Photoactivatable Silanes: Synthesis and Uses in Biopolymer Array Fabrication on Glass Substrates. In Frontiers in Biochip Technology, X, W-L., Cheng, J. (Ed.). Springer Science+Business Media, Inc. (2006). pp. 176-190.
4. Zhou, L., Myers, A.N., Vandersteen, J.G., Wang, L, Wittwer, C.T. Closed-Tube Genotyping with Unlabeled Oligonucleotide Probes and a Saturating DNA Dye. Clin. Chem. (2004), 50: 1328-1335.