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A wide variety of spacers can be incorporated into oligonucleotides, both at the 3´- and 5´-ends, or internally in the nucleotide chain. The ethylene glycol-based spacers (Spacer18 = hexaethylene glycol, HEG and
Spacer9 = triethylene glycol) are somewhat more hydrophilic than the pure alkyl chains (Spacer C3, Spacer C6 and Spacer C12). The addition of a Spacer C3 (3 hydrocarbons) to the 3´-end of an oligonucleotide can prevent e.g. its elongation during a PCR without influencing its annealing properties in any meaningful way. Such a modification is therefore well suited for hybridisation probes used in a PCR reaction.
The dSpacer, also referred to as the abasic site, tetrahydrofuran (THF) or apurinic/apyrimidinic (AP) site, is a non-nucleobase deoxyribose building block, thus the spacing ratios in the oligonucleotide chain remain largely unchanged.

biomers.net offers different terminal and internal spacers:

  • Spacer C3, Spacer C6, Spacer C12
  • Spacer9, Spacer12, Spacer18
  • dSpacer
      Modification                5´                 3´                        internal
           Spacer C3 x x x
           Spacer C6 x x x
           Spacer C12 x x x
           Spacer9 x x x
           Spacer12 x x x
           Spacer18 x x x
           dSpacer x - x
 

   terminal and internal Spacer