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Non-Extendable (3′-Blocked) Primer Oligos — Chain Terminators

Make primers and probes non-extendable by polymerases with 3′ caps and base analogs that remove or mask the 3′‑OH. We provide 3′-inverted bases, 3′-phosphate (reversible), 3′-amine, 3′-spacers, and 3′‑dideoxy caps—delivered with full QC.

3′-Inverted dT / Abasic 3′-Phosphate (Reversible) 3′-Amine (C3/C7) 3′-Spacers (C3/C9) 3′-Dideoxy (ddN)

Overview

Bio-Synthesis designs and manufactures non-extendable (3′-blocked) primer oligonucleotides for dependable polymerase blocking in PCR/qPCR, LAMP, hybrid-capture and surface-immobilization workflows. We help you choose the right chain-terminating strategy—3′-inverted dT or 3′-inverted abasic (permanent), 3′-phosphate (reversible), 3′-amine, C3/C9 spacers, or 3′-dideoxy (ddN)—and optimize placement, spacers, and 5′ end state (±5′-phosphate) to control ligation directionality while blocking extension.

From assay-driven design through RUO→GMP-like manufacturing, we deliver HPLC/UPLC purification, LC-MS confirmation, full COA/documentation, and plate/kitting options for screening. Need reversible gating? We’ll stage workflows with 3′-phosphate or photocleavable 3′ caps; need permanent stop with capture? We’ll pair 3′-inverted caps with 3′-Biotin for SA plates and beads.

Formats
Tubes • 96-well plates
Scale
µmol → multi-gram
QC
UPLC/HPLC • LC-MS
Supply
RUO → GMP-like
Ligation Blockers vs Chain Terminators — Quick Guide
Aspect Ligation Blocker Chain Terminator
Enzyme affected Ligase (seals a nick/junction) Polymerase (extends from 3′‑OH)
Primary goal Prevent sealing/joining at an end Prevent extension of a strand
Requirement disrupted Remove 5′‑phosphate or 3′‑OH at the junction Remove/mask terminal 3′‑OH
Common choices 5′‑OH (no 5′‑P), 3′‑phosphate, 3′‑inverted dT/iSp, 3′‑amine 3′‑inverted dT/iSp, 3′‑dideoxy (ddN), 3′‑amine, 3′‑phosphate, 3′‑O‑Me, C3/C9 spacers
Reversible options 5′‑OH → add 5′‑P (T4 PNK); 3′‑PO4 → remove with 3′‑phosphatase 3′‑PO4 (enzyme), 3′‑photocleavable caps (light)
Notes Choose blockers to control where joining is allowed; directionality via ±5′‑P Choose caps to control whether a strand can be extended

Tip: some 3′ caps (e.g., 3′‑phosphate, 3′‑inverted dT) both block ligation at that end and terminate polymerase extension. Use ±5′‑phosphate on the partner strand to enforce ligation directionality.

What you get with Bio-Synthesis
  • Assay-driven design consult: polymerase context, terminator selection (3′-inv-dT / 3′-PO4 / 3′-NH2 / ddN), spacer/cap geometry, ±5′-phosphate for ligation control.
  • Manufacturing breadth: desalting → HPLC/UPLC; lot-to-lot reproducibility; plate/kitting and barcoding.
  • Analytical package: LC-MS mass confirmation, purity traces, UV260, COA; optional endotoxin/residuals.
  • Documentation & supply: RUO to GMP-like pathways, change control, batch records on request.

Also searched as: 3′-blocked primer, non-extendable primer, 3′-inverted dT oligo, 3′-phosphate oligo, 3′-amine oligo, 3′-dideoxy (ddN) chain terminator, block the 3′ end of an oligo.

Browse Products & Notes Technology • Design • Application Speak to a Scientist

Quick chooser — pick the right 3′ block

Goal Best pick Why / notes
Permanent stop 3′‑inverted dT 3′–3′ linkage; robust across polymerases; resists exonucleases.
Reversible stop 3′‑phosphate Enzyme‑removable 3′ cap; also blocks ligation until dephosphorylated.
Universal termination 3′‑dideoxy (ddN) Classic chain terminator for most polymerases; Sanger‑style stop.
Block + conjugate 3′‑amine Stops extension and adds an amine handle for NHS/maleimide chemistry.
Browse Products & Notes Technology • Design • Application Read FAQs

Products & Notes

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Modification Description Typical use Code
3′‑Inverted dT (3′–3′) Thymidine linked 3′–3′; no 3′‑OH. Permanent chain termination; anti‑tailing. [3′‑inv‑dT]
3′‑Inverted Abasic (iSp) Abasic spacer inverted at 3′. Non‑extendable 3′ cap; minimal base effects. [3′‑inv‑iSp]
3′‑Biotin Biotinylation at 3′ terminus. Blocks extension; capture on SA surfaces. [3′‑Bio]
Technical Notes
  • 3′‑inverted dT/iSp provide polymerase‑proof termination; iSp minimizes base‑specific effects.
  • 3′‑Biotin enables termination and affinity capture (streptavidin plates/beads).
  • Control ligation directionality with the partner strand’s ±5′‑phosphate.

Modification Description Typical use Code
2', 3' Dideoxyadenosine (2,3,ddA) Dideoxy base at the 3′ terminus. Non‑extendable primers/probes; Sanger‑style termination. [2,3ddA]
2',3' Dideoxycytosine (2,3,ddC) Dideoxy base at the 3′ terminus. Non‑extendable primers/probes; Sanger‑style termination. [2,3,ddC]
2',3' Dideoxythymidine (2,3, ddT) Dideoxy base at the 3′ terminus. Non‑extendable primers/probes; Sanger‑style termination. [2,3ddT]]
2',3' Dideoxyguanoisne (2,3 ddG) Dideoxy base at the 3′ terminus. Non‑extendable primers/probes; Sanger‑style termination. [2,3ddG]
3′‑Deoxy (3′‑H) Hydrogen at the 3′ position. Blocks polymerase addition; stable cap. [3′‑H]
3′‑O‑Methyl Methylated 3′‑O blocks elongation. Non‑extendable primer ends under many polymerases. [3′‑OMe]
Technical Notes
  • 3′‑dideoxy (ddN) is a universal chain terminator for most polymerases (Sanger‑style). Only 2'3' ddC can be place at 3' end or 5' end, 2',3'ddA,T,G can only be place at 5' end
  • 3′‑O‑Me termination can be polymerase dependent—validate with your enzyme/buffer set.
  • Pair a 5′‑phosphate with 3′ termination to allow ligation while blocking extension.

Modification Description Typical use Code
3′‑Phosphate 3′‑PO4 cap; no 3′‑OH. Blocks extension/ligation; removable with phosphatase. [3′‑PO4]
3′‑Phosphorothioate 3′‑PS cap; sulfur analog. More nuclease‑resistant termination. [3′‑PS]
Technical Notes
  • Confirm termination by LC‑MS and primer‑extension tests for your polymerase.
  • Combine 3′ caps with the partner’s ±5′‑phosphate to control ligation directionality.

Modification Description Typical use Code
3′‑Photocleavable (PC) Linker 3′ block removed by UV (e.g., o‑nitrobenzyl). Temporal control of extension; spatial patterning. [3′‑PC]
3′‑Phosphate (as above) Enzyme‑removable 3′ cap. Stage‑gated workflows; reversible termination. [3′‑PO4]
Technical Notes
  • Validate UV dose/λ for 3′‑PC linkers and confirm restoration of extension by LC‑MS.
  • Prefer near‑UV where possible; protect capped oligos from ambient light during prep.
  • 3′‑phosphate is an enzyme‑reversible alternative for staged processing.

Modification Description Typical use Code
3′‑Amine (C3/C7) Primary amine at 3′. Termination + conjugation handle (NHS/maleimide). [3′‑NH2]
3′‑Spacer C3 / C9 Short alkyl linkers at 3′. Increase sterics; non‑extendable end. [3′‑C3], [3′‑C9]
Technical Notes
  • 3′‑amine doubles as a conjugation site for NHS‑ester labels while blocking extension.
  • Short C3/C9 spacers increase sterics at the 3′ end with minimal impact on Tm.
  • Add PEG/TEG segments near bulky labels to reduce crowding and preserve hybridization.
Explore related chemistries
Services at a glance
  • Custom design review (polymerase & ligase context)
  • RUO → GMP‑like manufacturing
  • QC: UPLC/HPLC, LC‑MS (COA included)
Need help picking the best terminator?

We’ll recommend the optimal 3′ cap for your polymerase, buffer, and assay format.

Technology • Design • Application

Technology
  • What makes a terminator? Removal/masking of 3′‑OH (3′‑inverted link, ddN, 3′‑PO4, 3′‑NH2, spacers).
  • Cross‑effects: Some caps (3′‑PO4) also block ligation; plan ends accordingly.
  • Reversibility: 3′‑phosphate (enzymes) and 3′‑PC (light) provide temporal control.
Design
  • Choose permanent (3′‑inv‑dT/iSp) for absolute blocking; use ddN for polymerase‑focused termination.
  • For staged workflows, use 3′‑PO4 then remove enzymatically when needed.
  • Add short PEG/TEG/C3 spacers near bulky labels to reduce sterics.
  • Consider polymerase type (proofreading vs non‑proofreading) when selecting caps like 3′‑OMe.
Application
  • Non‑extendable primers/probes for PCR/qPCR, LAMP, hybrid‑capture.
  • Prevent concatemer formation in ligation or TdT‑based workflows.
  • Single‑cycle hybridization capture or surface anchoring with 3′‑Biotin.

Tip: combine a 3′ terminator with a selective 5′ end state (±5′‑phosphate) to control ligation directionality.

FAQ

How do I block the 3′ end of an oligo?

Use 3′-inverted dT/iSp, 3′-phosphate (reversible), 3′-amine, C3/C9 spacers, or 3′-dideoxy (ddN) to remove or mask the 3′‑OH and prevent polymerase extension.

Is 3′‑phosphate reversible?

Yes. 3′‑phosphate can be enzymatically removed to restore a ligation/extension‑competent 3′‑OH; until removed, it also blocks ligation.

Which 3′ cap should I choose for Taq vs. high‑fidelity polymerases?

3′‑inverted dT or 3′‑ddN are broadly effective across non‑proofreading enzymes like Taq. For proofreading/high‑fidelity enzymes (3′→5′ exonuclease), prefer 3′‑inv‑dT/iSp or 3′‑PO4; validate any 3′‑OMe caps in your exact buffer/temperature.

Can a 3′‑blocked oligo still be ligated?

Yes—ligation depends on a 5′‑phosphate on the partner strand and a 3′‑OH on the complementary end being sealed. A 3′ terminator on the far end (e.g., 3′‑inv‑dT or 3′‑amine) still blocks extension but does not prevent ligation at a separate junction. Note: 3′‑phosphate blocks ligation at its own end until dephosphorylated.

How much does a 3′ terminator change Tm?

Typically small (sequence‑ and cap‑dependent). 3′‑spacers (C3/C9) and 3′‑amine have minimal impact; bulky tags may require 1–2 nt length adjustments. When in doubt, measure Tm with your exact buffer and Mg2+.

Can I make termination reversible?

Yes—use 3′‑phosphate (enzyme‑removable) or a 3′‑photocleavable linker (light‑removable). This enables gated extension, staged assembly, and troubleshooting pathways.

What QC confirms that termination works?

LC‑MS mass confirmation plus a functional primer‑extension assay (no extension vs. a native control) are recommended. For reversible caps, confirm before and after deprotection.

How do I combine 3′ termination with capture labels?

Use 3′‑Biotin to terminate while enabling streptavidin capture (plates/beads). If you need a different label, pick 3′‑amine and couple via NHS‑ester or maleimide (with linkers) upstream of the 3′ terminus.

Can I order RNA with a 3′ block?

Yes—many 3′ caps are available on RNA (e.g., 3′‑PO4, 3′‑amine, spacers). Consider nuclease‑resistant backbones or terminal PS if stability is a concern.

Recommended storage and handling?

Store dry at −20 °C, desiccated, protected from light. Avoid repeated freeze–thaw. For PC linkers, minimize ambient light; for 3′‑phosphate, avoid high‑pH buffers that could hydrolyze prematurely.

Speak to a Scientist

Tell us about your chain termination goal. We’ll recommend the right 3′ cap for your polymerase, buffer, and assay format.

Please avoid confidential details; we can arrange an NDA if needed.

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