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 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 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.
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, 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, 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.
| Modification type | Code | 5' | Internal | 3' | Function | Price |
| C3 Spacer | SpC3 | Introduce linker arm, prevent enzymatic degradation, a DNA abasic site, an effective chain terminator | Inquiry | |||
| C6 Spacer | SpC6 | Introduce linker arm | Inquiry | |||
| C12 Spacer | SpC12 | Introduce linker arm | Inquiry | |||
| Spacer 9 | Sp9 | Introduce linker arm, hydrophilic spacer | Inquiry | |||
| Spacer 18 (hexaethyleneglycol) | Sp18 | Introduce linker arm, hydrophilic spacer | Inquiry | |||
| dSpacer (Abasic furan) | dSp | DNA abasic site, prevent enzymatic degradation | Inquiry | |||
| ribospacer rSpacer | rSp | RNA abasic site, prevent enzymatic degradation | Inquiry | |||
| Photocleavable PC Spacer | PLC | photocleavable spacer | Inquiry |
References
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