Oligo Spacer Modification

Oligo Spacer Modification


During oligonucleotide synthesis, spacer arms are introduced into the sequence using spacer phosphoramidites. Multiple additions of different spacer molecules allow control of the exact length of the spacer arm.

  • Spacer C18

Spacer 18 is a hexaethylene glycol chain (also known as HEG spacer) that is 18 atoms long (12 carbons and 6 oxygens) and is used to incorporate a long spacer arm in an oligonucleotide. Spacer 18 can be placed at the 5' end, 3' end, or inside, and it has been used to form bold folds and hairpin loops in oligonucleotides and to immobilize hybrid probes in the solid phase.

  • Spacer C3

Spacer C3 is a short 3-carbon chain (C3). During chemical synthesis, propyl spacer C3 can be added to the inner or both ends of the oligonucleotide, and if a longer spacer is required, spacer C3 can be added sequentially to provide a proper attachment point for linking fluorophores or other pendant motifs.

  • C9Spacer

The C9 spacer is a triethylene glycol chain consisting of nine atoms (six carbons and three oxygens). Due to its chemical properties, this spacer is slightly more hydrophilic than the C3 and C12 spacers. During oligo synthesis, Spacer 9 can be added serially if needed. C9 Spacer has been used to form non-nucleotide bridges in hairpin loops of oligonucleotides, for binding oligonucleotides to epitopes for drug development, and has been applied to solid-phase immobilization of hybridization probes.

  • dSpacer

dSpacer, also known as abasic furan, is a tetrahydrofuran derivative containing a methylene group at the 1 position of 2'-deoxyribose. Similar to C3 spacers, dSpacer is widely used to create a stable abasic site in oligonucleotides. Abasic sites are created by hydrolysis of glycosidic linkages with nucleotide bases (in DNA) or during UV-induced depurination/depyrimidation events (in cells) or as intermediates in the base excision repair (BER) process.

  • rSpacer

rSpacer, also known as an abasic site, is a derivative of tetrahydrofuran (THF) in which methylene occupies the 1 position of the 2'-ribose. Natural RNA abasic sites occur less frequently than DNA abasic sites because RNA is not readily depurinated, but they exhibit higher stability. Although controversial, this feature may have implications for long-lived RNAs, such as tRNA and rRNA.

Our Oligo Spacer Modification Services Specification

Modification typeCode5'Internal3'FunctionPrice
C3 SpacerSpC3Introduce linker arm, prevent enzymatic degradation, a DNA abasic site, an effective chain terminatorInquiry
C6 SpacerSpC6Introduce linker armInquiry
C12 SpacerSpC12Introduce linker armInquiry
Spacer 9Sp9Introduce linker arm, hydrophilic spacerInquiry
Spacer 18 (hexaethyleneglycol)Sp18Introduce linker arm, hydrophilic spacerInquiry
dSpacer (Abasic furan)dSpDNA abasic site, prevent enzymatic degradationInquiry
ribospacer rSpacerrSpRNA abasic site, prevent enzymatic degradationInquiry
Photocleavable PC SpacerPLCphotocleavable spacerInquiry


  • Guaranteed Yield - Guaranteed Minimum Yield for OD
  • Maximum flexibility - Benefit from HPLC purification options for different synthesis scales.
  • High quality - Guarantees the highest demands


  1. Brukner, I; et al. Self-priming arrest by modified random oligonucleotides facilitates the quality control of whole genome amplification. Anal Biochem. 2005. 339(2): p. 345-7.
  2. Dieck, J; et al. Development of bispecific molecules for the in situ detection of protein-protein interactions and protein phosphorylation. Chem Biol. 2014. 21(3): p. 357-68.
* Only for research. Not suitable for any diagnostic or therapeutic use.
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