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Non-Canonical Structure

Non-Canonical Structure Oligonucleotides

Custom synthesis of G-quadruplex, i-motif, triplex-forming (TFO), Z-DNA/Z-RNA, hairpin & cruciform, Hoogsteen pairing, and R-loop structures with labels, linkers, and stabilization chemistry. Full analytics from RUO to GMP-like.

G-Quadruplex • i-Motif Triplex • Z-DNA/Z-RNA Hairpin • Cruciform Hoogsteen • R-Loop Labels • Linkers • Controls RUO → GMP-like
Get a quote How to order & lead times
Overview Catalog Chooser Technology FAQ Speak

Overview

Non-canonical nucleic acid architectures extend beyond the Watson–Crick helix to enable switchable sensors, gene regulation probes, and therapeutic motifs. Bio-Synthesis engineers sequences and chemistries that reliably fold into target structures under your buffer, pH, ionic strength, and temperature. We integrate stabilizing sugars (2′-OMe, 2′-F, LNA/BNA/cEt), terminal caps, backbone edits (partial PS), and conjugations (fluorophores, quenchers, biotin, PEG, click handles, delivery ligands) to tune performance.

Production spans µmol to multi-gram with UPLC/HPLC purification, LC-MS, and optional CD/UV-thermal melts and gel/PAGE for structure confirmation. Deliverables include COA and RUO → GMP-like pathways.

Formats
Tubes • Plates • Kitting
Scale
µmol → multi-gram
QC
UPLC/HPLC • LC-MS
• CD/melt
Supply
RUO → GMP-like
What you get with Bio-Synthesis
  • Structure-first design: buffer/pH/ionic optimization; sequence tuning and truncation.
  • Stabilization: LNA/BNA/cEt blocks, 2′-OMe/2′-F, terminal caps, partial PS; PEGylation options.
  • Conjugations: dyes & quenchers (FAM/Cy5/ATTO/BHQ), biotin/streptavidin, click (azide/DBCO/TCO), GalNAc, peptide/antibody.
  • Analytics: UPLC/HPLC, LC-MS, optional CD/melt, native PAGE, FRET/turn-on assays.

Also searched as: G4 DNA, i-motif probe, triplex-forming oligo (TFO), Z-DNA oligo, cruciform DNA, hairpin oligo, Hoogsteen pairing oligo, R-loop model.

How to order & lead times

Lead time varies with scale and QC. Typical RUO: 5–10 business days for unlabeled motifs, 10–15 days with labels/FRET; GMP-like timelines quoted on request.

Goal Best pick Why / notes
pH-switchable sensor i-Motif (C-rich) Intercalated C·C+ base pairs; sharp response to mildly acidic pH; great for pH biosensors.
Ligand screening / telomere model G-Quadruplex (G4) Stacked G-tetrads stabilized by K+/Na+; supports FRET/CD assays for small-molecule binders.
Site-specific gene targeting Triplex-forming oligo (TFO) Third-strand Hoogsteen/intermolecular pairing for promoter binding or mutagenesis.
Innate immune/ZBP1 studies Z-DNA / Z-RNA Left-handed helices favored by GC repeats and supercoiling; recognized by Z-domains.
Replication/repair models Hairpin or Cruciform Palindromic/stem-loop designs to probe polymerase and repair pathways.
Transcription collision models R-Loop scaffold RNA:DNA hybrid with displaced ssDNA; used to study R-loop biology and genome stability.
Browse Products & Notes Read FAQs

FAQ

How do I specify buffers for proper folding?

Provide target K+/Na+/Mg2+, pH, temperature, and pre-folding steps (heat-cool, anneal). We match lab folding when we test CD/melt and deliver ready-to-use instructions.

Which stabilizing chemistries are compatible?

We commonly use LNA/BNA blocks and 2′-OMe/2′-F in loops/stems away from the folding core; add partial PS at termini for nuclease resistance.

Can you add labels and linkers without disrupting the structure?

Yes—dyes, quenchers, biotin, PEG, and click handles (azide/DBCO/TCO) are placed on termini or non-critical loop positions with flexible TEG/PEG spacers.

Do you provide structure confirmation data?

Standard QC includes UPLC/HPLC and LC-MS; optional CD spectra, UV-melt and native PAGE snapshots can be added on request.

What inputs help you start quickly?

Motif of interest, buffer/pH/temperature, any known sequences, desired labels/linkers, scale, purification, and required QC.

Products & Notes

Product/Category Description Function Application Code
8-Amino-dG Modified guanine analog. Stabilizes G4 formation. Telomere and aptamer studies. [G4-8AmG]
7-Deaza-8-aza-dG Guanine analog lacking N7. Modulates Hoogsteen pairing. G4 folding mechanism probes. [G4-7d8aG]
8-oxo-dG Oxidized guanine analog. Destabilizes duplex, can favor G4. DNA damage/G4 interplay. [G4-8oxo]
8-Br-dG Brominated guanine analog. Biases syn conformation. Topology (anti vs syn) control. [G4-8Br]
7-deaza-dG G analog missing N7. Reduces Hoogsteen stability. Mechanistic G4 studies. [G4-7dz]
Technical Notes
  • Cations: K+ strongly stabilizes G4 vs. Na+; define assay buffer and pre-folding protocol.
  • Loop edits: LNA/2′-OMe in loops can increase Tm and reduce polymorphism.
  • Readouts: CD (265/295 nm), UV-melt, FRET, native PAGE, and ligand-induced stabilization.

Product/Category Description Function Application Code
2′-F-Ac-C-ANA Modified cytosine analog. Stabilizes C•C+ pairing. pH sensors, i-motif probes. [iM-2FANA]
5-Formyl dC III Cytosine derivative with formyl group. Enhances protonation stability. pH-responsive constructs. [iM-5FdCIII]
Ac-5-Me-dC Acetylated 5-methyl-dC. Fine-tunes folding dynamics. i-Motif sensors. [iM-Ac5MeC]
5-Formyl-dC Formylated cytosine. Modifies i-Motif folding. Regulatory motif probes. [iM-5FdC]
5-Hydroxymethyl-dC II Hydroxymethylated cytosine. Epigenetic mimic; may stabilize. i-Motif stability studies. [iM-5hmdCII]
5-I-dC Iodinated cytosine analog. Increases stacking. Stabilized i-Motif folding. [iM-5IdC]
5-Br-dC Brominated cytosine. Stabilizes structure. pH-responsive probes. [iM-5BrC]
5-Carboxy-dC Carboxylated cytosine. Alters hydrogen bonding. Epigenetic modification mimic. [iM-5CarC]
5-Me-dC Methylated cytosine. Common epigenetic mark. DNA methylation/i-Motif. [iM-5MeC]
Technical Notes
  • Define pH window (on/off) and ionic strength; consider buffering capacity and temperature.
  • Avoid guanine runs that compete with G4 under physiological cations.
  • Validate reversibility and kinetics with CD or stopped-flow fluorescence if needed.

Product/Category Description Function Application Code
8-Amino-dA Modified adenine analog. Stabilizes Hoogsteen binding. Triplex gene targeting. [TFO-8AmA]
8-Amino-dG Modified guanine analog. Improves triplex binding. Triplex stability assays. [TFO-8AmG]
6-thio-dG Sulfur-substituted guanine. Modulates base pairing; crosslinking. Crosslinking & footprinting. [TFO-6tG]
2′-deoxypseudoU Pseudouridine analog. Improves base stacking. Stabilized triplex constructs. [TFO-ψU]
Technical Notes
  • Map G/A tracts in target; avoid interruptions that disrupt triplex binding.
  • pH & Mg2+: tune for Hoogsteen vs. reverse-Hoogsteen preferences.
  • Consider cross-linkers (psoralen) for triplex capture or footprinting assays.

Format Description Typical use Code
Alternating d(CG)n Classical Z-DNA scaffold; salt-promoted B↔Z transitions. ZBP1/ADAR1 studies; transition kinetics. [ZDNA-CG]
Z-RNA motif Alternating r(CG)/r(CU) with divalent cations; stabilized by certain proteins. Innate immune recognition models. [ZRNA]
Labeled B↔Z reporter FRET pair across helical switch; monitors transition in real time. Ligand/mechanics-induced transitions. [Z-FRET]

Format Description Typical use Code
Stem-loop hairpin Defined stem length/GC content; loop edits with LNA/2′-OMe for stability. Polymerase stalling, nuclease mapping. [HP-Std]
Palindromic cruciform Inverted repeats capable of extruding under supercoiling. Cruciform detection; protein binding. [CF-Pal]
Hairpin reporter Dye–quencher across stem; turn-on upon opening or cleavage. Endonuclease or helicase assays. [HP-FRET]

Format Description Typical use Code
R-loop duplex Synthetic RNA:DNA hybrid annealed to target with designed ssDNA displacement. R-loop binding protein assays; footprinting. [RLP-Core]
Labeled R-loop Fluorophore pairs on RNA/DNA strands for FRET or imaging. Resolution/processing studies. [RLP-FRET]
Stabilized R-loop 2′-OMe/2′-F substitutions on RNA strand; terminal caps and partial PS. In-cell or nuclease-rich environments. [RLP-Stab]

Motif Description Typical use Code
Hoogsteen-biased duplex Purine-rich tracts with modified bases or crowding agents in design spec. Protein recognition, NMR/CD studies. [HG-Dx]
Mismatched probes Defined mismatch positions to force alternative hydrogen-bonding. Proofreading and repair assays. [Alt-Pair]

Probe Description Typical use Code
ThT-compatible G4 Sequence tuned for Thioflavin T fluorescence turn-on with G4 ligands. Rapid ligand screens. [G4-ThT]
Topology panel (set) Matched parallel/antiparallel/hybrid G4 oligos with common labels. Ligand selectivity mapping. [G4-Panel]
Competition assay G4 Dual-labeled FRET G4 competing with dsDNA/hairpin controls. Specificity benchmarking. [G4-Comp]

Item Description Typical use Code
Non-folding control Base-shuffled variant preserving composition. Specificity control. [NC-Ctrl]
Topology switch mutant Loop/tract edits that flip topology or disrupt structure. Mechanistic studies. [Topo-Mut]
Positive control set Validated G4/i-motif/TFO exemplars with labels. Assay qualification. [PCS-Set]

Speak to a Scientist

Tell us which structure you need (G4, i-motif, TFO, Z-DNA/Z-RNA, hairpin/cruciform, R-loop), your buffer and labels. We’ll finalize a folding and QC plan.

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

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