Spacers are incorporated to introduce flexibility and distance between functional groups and the oligonucleotide hybridization region. These inert molecular linkers reduce steric hindrance, enhancing the efficiency of attached moieties such as dyes or affinity tags. Among the diverse DNA spacers for oligonucleotide synthesis, spacer length and composition can significantly influence molecular accessibility and hybridization performance.
Key applications include but are not limited to: FRET optimization, structural biology studies, and reduction of steric hindrance.
Spacers & Linkers Modifications
Spacers and Linkers modifications are essential tools for precisely engineering the physical and functional properties of oligonucleotides. These insertions allow you to adjust the distance between functional groups (e.g., a fluorophore and a quencher) or control the structural flexibility of the molecule. This fine-tuning is critical for optimizing interactions, preventing steric hindrance, and achieving desired biological activity or detection efficiency. In many applications, DNA spacers are incorporated to provide controlled separation while maintaining the structural integrity of the nucleic acid construct.
| Sub-category | Name (full) | Abbreviation / Code | Product Type | Applies to | Position | Function & mechanism (including like products) | Typical applications |
| Carbon spacers | Spacer C3 / C6 / C9 / C12 | Sp C3 / C6 / C12 | Like | DNA / RNA | 5′ / 3′ / Internal | Propyl (C3), hexyl (C6), or dodecyl (C12) carbon chain spacers. Introduce controlled distance between functional groups and the oligonucleotide backbone, reducing steric interference in hybridization or enzyme recognition. A C3 spacer provides minimal separation while preserving efficient molecular interactions. | Probe spacing, linker design, surface immobilization distance control |
| Polyethylene glycol (PEG) spacers | Spacer 9 / 18 / SPC 9 / 12 / 18 | Sp9 / Sp18 | Like | DNA / RNA | 5′ / 3′ / Internal | Triethylene glycol (Sp9) and hexaethylene glycol (Sp18) spacers. Hydrophilic and flexible; more soluble than carbon spacers. Used to improve accessibility of terminal functional groups in solution assays. | Flexible probe design, solution-phase assay optimization, aptamer linker |
| Abasic spacers | dSpacer (abasic site analog) | dSpacer | Like | DNA / RNA | Internal | Synthetic abasic site (tetrahydrofuran-based, dSp). Mimics the natural abasic (AP) site formed after base removal. Used as a substrate for AP endonuclease activity assays and in nick-translation studies. | AP endonuclease assays, DNA repair research, nick-translation substrates |
| Photo-cleavable linkers | PC Linker (Photo-Cleavable Linker) | PC Linker | Like | DNA / RNA | Internal / 5′ | Photolabile nitrobenzyl-based linker that cleaves upon UV irradiation (365 nm). Enables light-controlled release of oligonucleotide payloads or spatiotemporal control of hybridization. | Caged oligos, optogenetics, light-controlled CRISPR, spatiotemporal probe release |
| Branching scaffolds | Trebler (branching unit) | Trebler | Like | RNA | Internal | Introduces a three-way branch point into the oligonucleotide. Allows attachment of three separate sequences or functional groups from a single position — used to create branched DNA/RNA architectures. | Branched nucleic acid nanostructures, signal amplification, multivalent ligand display |
Modification: (dSpacer), 3'Spacer(C3)
Download the order form "Tsingke_DNA_Order Form.1.1.1.250815.csv" for DNA modifications or "Tsingke_RNA_Order Form.1.1.1.250815.csv" for RNA modifications below and email it to info@tsingke.com.cn, or "Send Your Request" to submit your inquiry online. Please refer to "Tsingke_DNA_Modification List_1.1.1.250815.csv" or "Tsingke_RNA_Modification List_1.1.1.250815.csv" sheet to paste special base and internal modification codes in your sequence.
To maintain stability and performance, spacer-modified primers should be stored as follows:
(1) Protect from light: Use opaque or light-blocking containers.
(2) Low temperature: Store at -20°C or below.
(3) Dry conditions: Keep tightly sealed, preferably with a desiccant, to limit moisture and oxidation.
(4) Minimize freeze-thaw cycles: Aliquot upon receipt to avoid repeated freezing and thawing.
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