Spacers Design and Protocols

Spacers Design / Protocol

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

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