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Spacers Design and Protocols

Introduction to Spacers Spacers Applications Spacers Design/Protocol Spacers Literature Order Online

Spacers Design / Protocol
Hydrophobic vs Hydrophilic SpacersDesign Considerations

Spacer 9 and Spacer 18 are polyethylene glycol (PEG)-based, and thus hydrophilic, while Spacers C3, C12, PC Linker, and PC Spacer are aliphatic, and thus hydrophobic. Thus, when designing oligos that require one or more Spacer modifications, it is important to consider possible effects of Spacer hydrophobicity/hydrophilicity on the properties of the oligo. For example, post-synthetic labeling of an amino or thiol-modified oligo at the 5-end with a dye, hapten or enzyme is commonly performed in aqueous solution. The active amino or thiol group typically is attached to the oligo via a hydrophobic linker, and when incorporated into long oligos or those with significant secondary structure, poor coupling of the label to the oligos is often observed. Consequently, optimization of the coupling reaction may require incorporation of a hydrophilic spacer (such as Spacer 18 or Spacer 9) next to the amino/thiol linker.

References

(1) 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.
(2) Salunkhe, M., Wu, T.F., Letsinger, R.L. Control of folding and binding of oligonucleotides by use of non-nucleotide linker. J. Am. Chem. Soc. (1992), 114: 8768-8772.
(3) Durand, M., Chevrie, K., Chassignol, M., Thuong, N.T., Maurizot, J. Circular dichroism studies of an oligodeoxyribonucleotide containing a hairpin loop made of a hexaethylene glycol chain : conformation and stability. Nucleic Acids Res. (1990), 18: 6353-6359.
(4) Ju, J., Glazer, A.N., Mathies, R.A. Cassette labeling for facile construction of energy transfer fluorescent primers. Nucleic Acids Res. (1996), 24: 1144-1148.
(5) 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.
(6) Takeshita, M., Chang, C.N., Johnson, F., Will, S., Grollman, A.P. Oligodeoxynucleotides containing synthetic abasic sites. Model substrates for DNA polymerases and apurinic/apyrimidinic endonucleases. J. Biol. Chem. (1987), 262: 10171-10179.
(7) Ordoukhanian, P., Taylor, J-S. Design and synthesis of a versatile photocleavable DNA building block. Application to phototriggered hybridization. J. Am. Chem. Soc. (1995), 117: 9570-9571.

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