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Oligonucleotide Reference

Backbone Modifications

Comprehensive overview of phosphodiester variants, orientation changes, mirror-image
scaffolds, and synthetic analogues.

Phosphodiester Alternative Linkage Chirality Analogues Design Notes Services Contact
Backbone Modifications

Backbone-Modified Oligonucleotides for Stability & Precision

Backbone modifications transform standard DNA and RNA into powerful research and therapeutic tools. By altering the phosphate backbone, we deliver enhanced nuclease resistance, improved hybridization, and charge-neutral options that expand applications from diagnostics to FDA-approved antisense therapies.

Stability & Resistance

PS, PS2, PN, boranophosphate.

  • Improved serum half‑life
  • Resists nuclease degradation
  • Ideal for ASO/siRNA therapeutics

Hybridization Control

LNA/BNA, PNA, GNA to tune Tm & specificity.

  • Higher mismatch discrimination
  • Shorter, high‑affinity probes
  • Optimized for qPCR & diagnostics

Charge‑Neutral Options

PMO & PNA backbone with no negative charge.

  • Enhanced uptake & durability
  • Stable in biological fluids
  • Backbones in FDA‑approved ASOs

Phosphodiester-Based Modifications

Product Description Code
Phosphorothioate (PS) One non-bridging oxygen replaced with sulfur; improves nuclease resistance
and RNase H compatibility.		 [PS]
Phosphodithioate Both non-bridging oxygens replaced with sulfur; even greater stability. [PS2]
Methylphosphonate Oxygen replaced by a methyl; neutralizes charge. [MP]
Boranophosphate Borane (BH₃) substitution; altered redox behavior. [BP]
Phosphoramidate / Phosphonamidate P–O replaced with P–N; reduces charge, alters hybridization. [PA]
PN Backbone Fully phosphoramidate-linked analogue with high stability. [PN]
Alkyl/Aryl Phosphotriesters Adds hydrophobicity and stability via alkyl/aryl groups. [PTE-R]

Alternative Linkage & Orientation

Product Description Code
2′,3′-Dideoxynucleosides Lack both 2′ and 3′ hydroxyl groups; chain terminators. [ddN]
2′–5′ Linked Oligonucleotide 2′–5′ phosphodiester linkages; altered enzyme recognition. [2-5]
5′→3′ Synthesis Reverse orientation to control strand polarity. [5→3]

Mirror Image & Chirality

Product Description Code
Left-Hand L-DNA Mirror image of D-DNA; nuclease-resistant, non-immunogenic. [L-DNA]
Left-Hand L-RNA L-RNA enantiomer; stable and immune-evasive. [L-RNA]

Backbone Replacements & Analogues

Product Description Code
Morpholino Backbone Morpholine rings + phosphorodiamidate linkages; used in FDA-approved ASOs. [PMO]
Peptide Nucleic Acid (PNA) Polyamide backbone; charge-neutral, high affinity. [PNA]
Glycol Nucleic Acid (GNA) Minimal glycol backbone; unique geometry. [GNA]
LNA/BNA Bridged nucleic acids; rigidify backbone, raise Tm. [LNA/BNA]
Triazole Linkage Click-chemistry linkage; biocompatible, nuclease-resistant. [TL]

Related Services

siRNA

Custom duplexes with PS/LNA/2′-OMe.

Duplex
ASOs

Gapmers with PS + 2′ mods.

Gapmer
PNA & PMO

Charge-neutral probes and therapeutics.

PNA

Design Considerations for Backbone‑Modified Oligos

Strategy & Architecture

  • Define your goal: RNase H (gapmers), steric block (splicing), or probe diagnostics.
  • Gapmer basics: DNA “gap” with PS linkages; 2′‑mod wings (LNA/BNA, 2′‑OMe/2′‑F).
  • PS patterning: Full or partial PS to balance Tm, potency, viscosity.
  • Orientation: 5′→3′ reverse or 2′–5′ linkages to tune enzyme interactions.
  • Neutral backbones: PMO/PNA for steric‑block or probe workflows.

Tm, Specificity & Length

  • Raise Tm: LNA/BNA in wings; shorten length to keep specificity.
  • PS effect: Slight Tm drop; offset with LNA/BNA placement or length.
  • Mismatch control: PNA & LNA increase discrimination (SNP, clamps).
  • Diagnostics: Triazole linkages (TL) can be ligase‑friendly and nuclease‑resistant.

Chemistry & Manufacturability

  • PS stereochemistry: Mixed Rp/Sp typical; stereodefined optional, app‑dependent.
  • Reagents/setup: L‑oligos, PMO, PNA may need dedicated lines—batch to cut cost.
  • Purification: RP/IEX HPLC or PAGE; conjugates may need affinity/dual HPLC.
  • Formulation: Duplexing, pooling, plates, LNP encapsulation available.

QC & Documentation

  • Identity: ESI‑MS/LC‑MS; optional fragment mapping.
  • Purity & residuals: HPLC traces; solvents/salts/moisture on request.
  • Micro: Endotoxin/bioburden for in vivo; full CoA & traceability.
  • Stability: Accelerated/real‑time; packaging for cold chain.

Tip: For RNase H‑active gapmers, keep a 8–10 nt DNA gap with PS linkages and 2′‑mod wings (LNA/BNA or 2′‑OMe/2′‑F). For steric‑block (splicing), consider PMO or PNA to maximize durability without RNase H.

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