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Conjugation Chemistry

Spacer & Linker Oligonucleotide Modifications

Enhance oligonucleotide performance with custom spacer & linker modifications - Backed by expert design and full QC from research to GMP-like supply.

Overview All Spacers & Linkers Technology & Applications Related Services FAQ

Overview

Bio-Synthesis provides end-to-end spacer and linker oligonucleotide modification services. We help you select the right architecture—short C2–C6 or extended C9–C12 alkyl linkers, flexible Sp18/HEG, or hydrophilic PEG/azido-PEG for click chemistry. For specialized applications, we offer photocleavable PC spacers for light-triggered release and d/rAbasic sites for structural or enzymatic studies. All projects include design consultation, scalable synthesis (from nmol to gram), and comprehensive QC (HPLC, ESI-MS/MALDI, SEC optional) with full CoA documentation.

Steric Control Hybridization Tuning Conjugation Geometry Click-Ready (Azido-PEG) Photocleavable

Spacers & Linkers

Availability by position is indicative (✔ = commonly supported). Ask if you need a position not listed.

Hide Table & Notes
Product 5′ Int 3′ Function Application Code
Abasic Site (dSpacer abasic furan-THF) ✔ ✔ ✔ Non-informational gap; enzyme/repair studies Structural mapping; controlled mismatches [dSpacer]
Photocleavable PC Spacer ✔ ✔ ✔ Light-triggered cleavage Photo-controlled capture/release [PC-Spacer]
PC Spacer C3 (photocleavable) ✔ ✔ ✔ Short PC linker with compact spacing Solid-phase or solution cleavage workflows [PC Sp3]
rAbasic Site (rSpacer abasic furan) ✔ ✔ ✔ RNA abasic analog; non-informational gap RNA structure/repair, enzyme probing [rAbasic]
Spacer 18 (hexaethyleneglycol, HEG) ✔ ✔ ✔ Flexible hydrophilic spacing; steric relief Conjugation geometry; hybridization tuning [Sp18]
Spacer 9 ✔ ✔ ✔ Medium alkyl spacer Distance control; reduce quenching [Sp9]
Spacer C12 ✔ ✔ ✔ Longer alkyl spacer; added reach Bulky labels; surface/particle attachment [SpC12]
Spacer C2 ✔ ✔ ✔ Very short alkyl spacer Fine geometry control [SpC2]
Spacer C3 ✔ ✔ ✔ Short alkyl spacer Compact separation for labels [SpC3]
Spacer C4 ✔ ✔ ✔ Short-medium alkyl spacer Distance/sterics tuning [SpC4]
Spacer C6 ✔ ✔ ✔ Medium alkyl spacer; common default Conjugation and surface chemistries [SpC6]
Spacer C9 ✔ ✔ ✔ Medium-long alkyl spacer Reduce sterics; broaden reach [Spc9]
ribo rSpacer ✔ ✔ ✔ RNA-compatible spacer RNA constructs; structural spacing [rSp]
Azido PEG12 ✔ ✔ ✔ Click-ready PEG spacer SPAAC/CuAAC bioorthogonal labeling [Azido PEG12]
Azido PEG24 ✔ ✔ ✔ Longer PEG for added reach/solubility Large payloads; surfaces/NPs [Azido PEG24]
Azido PEG3 ✔ ✔ ✔ Short PEG; compact click handle Minimal perturbation conjugation [Azido PEG3]
Technical Notes
  • Placement: Use 5′/3′ termini for conjugation; internal placements benefit from flexible PEG/HEG to preserve Tm.
  • Length selection: C2–C6 for compact spacing; C12–Sp18/PEG for bulky labels or surfaces.
  • Photocleavage: PC spacers enable reversible capture and on-demand release with UV/visible light (assay-dependent).
  • Click chemistry: Azido-PEG spacers are compatible with SPAAC/CuAAC; maintain copper-free conditions for sensitive targets.
  • Tm impact: Flexible, hydrophilic spacers (PEG/HEG) generally preserve duplex stability better than short rigid linkers.
  • QC: Identity by ESI-MS/MALDI and purity by HPLC; optional SEC for high-MW conjugates.
Speak to a Scientist

Need help choosing the right spacer or linker?

Our scientists will recommend the best C2–C12, Sp18/HEG, PEG/azido-PEG, or PC spacer to fit your assay, conjugation strategy, or delivery needs — and guide you from design through QC.

Speak to a Scientist Browse All Modifications

Technology & Applications

Technology

  • Geometry & sterics: Choose C2–C6 for compact spacing; C9–C12 or Sp18/PEG for bulky cargo or surfaces.
  • Hydrophilicity: PEG/HEG improves solubility and reduces aggregation vs alkyl spacers.
  • Orthogonality: Azido-PEG spacers enable click workflows without disturbing other handles.
  • Photo-control: PC spacers allow on-demand release or capture with light (wavelength/conditions assay-specific).
  • Abasic sites: d/rAbasic create programmable gaps for structural enzymology and repair studies.

Applications

  • Conjugation positioning: Tune label distance from the helix to minimize quenching or steric hindrance.
  • Surface & nanoparticle assembly: Provide reach and mobility for chips, beads, and NPs.
  • Probe & assay design: Photocleavable spacers for capture/release; abasic gaps for enzyme mapping.
  • Bioorthogonal labeling: Azido-PEG spacers for clean, selective attachment of dyes, peptides, or lipids.

We deliver modeling guidance (distance, reach, flexibility) and validate with Tm/functional assays as needed.

FAQ

How do I choose between alkyl, HEG/Sp18, and PEG spacers?

Use alkyl for compact, inert spacing; HEG/Sp18 for flexible hydrophilic reach; PEG when you need both reach and solubility or a click-ready handle (Azido-PEG).

Do spacers change duplex stability?

Short rigid spacers near hybridization sites may slightly affect Tm. Flexible PEG/HEG typically preserves duplex behavior—verify with a short pilot if the site is critical.

When should I use a photocleavable spacer?

When you need reversible capture or time-resolved release. Select wavelength and conditions compatible with your labels and sample matrix.

What QC is provided?

Standard QC includes ESI-MS/MALDI identity and HPLC purity; optional SEC for high-MW constructs. We can add photo/cleavage verification upon request.

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