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Backbone-Modified DNA & RNA Oligonucleotides

Custom backbone-modified DNA and RNA oligonucleotides engineered for nuclease resistance, hybridization control, charge tuning, and advanced therapeutic research applications.

PS / PS2 PN / Phosphoramidate PMO / PNA L-DNA / L-RNA Triazole Linkage ISO 9001:2015 ISO 13485:2016
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Overview Phosphodiester Linkage Chirality Analogues Related Strategy Chemistry & QC FAQ Contact
Overview

Backbone Chemistry for Stability, Charge Control & Hybridization Precision

Backbone modifications transform standard DNA and RNA into more durable, application-specific research tools. By modifying phosphate linkages, orientation, charge, or backbone architecture, researchers can improve nuclease resistance, tune hybridization behavior, and develop charge-neutral or enzyme-resistant oligos for diagnostics, ASO, siRNA, probes, and therapeutic research. Supported chemistries include phosphorothioate (PS), phosphodithioate, methylphosphonate, boranophosphate, PN, PMO, PNA, L-DNA, L-RNA, GNA, LNA/BNA, and triazole linkages.

PS

Stability & Resistance

PS, PS2, PN, and boranophosphate options improve serum half-life and resist nuclease degradation.

TM

Hybridization Control

LNA/BNA, PNA, GNA, and linkage engineering help tune Tm, specificity, and mismatch discrimination.

PMO

Charge-Neutral Options

PMO and PNA backbones reduce or remove negative charge for durable steric-blocking and probe applications.

Phosphodiester-Based Modifications

Phosphodiester-Based Backbone Modifications

Phosphate backbone variants can increase nuclease resistance, alter charge, improve durability, or change redox and hybridization behavior while preserving oligonucleotide sequence programmability.

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 for even greater stability. [PS2]
Methylphosphonate Oxygen replaced by a methyl group; neutralizes backbone charge. [MP]
Boranophosphate Borane (BH3) substitution; alters redox behavior and backbone properties. [BP]
Phosphoramidate / Phosphonamidate P–O replaced with P–N; reduces charge and alters hybridization behavior. [PA]
PN Backbone Fully phosphoramidate-linked analogue with high stability. [PN]
Alkyl / Aryl Phosphotriesters Adds hydrophobicity and stability through alkyl or aryl groups. [PTE-R]
Design note: PS is commonly used in ASO and siRNA workflows to improve nuclease resistance, but dense PS patterning can affect Tm, protein binding, viscosity, and formulation behavior.
Alternative Linkage & Orientation

Alternative Linkage & Orientation Modifications

Orientation and linkage modifications alter strand polarity, enzyme recognition, and chain-extension behavior, supporting chain-termination studies, nuclease-resistant designs, and non-standard oligo architectures.

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

Mirror-Image & Chiral Backbone Architectures

Mirror-image oligos and enantiomeric scaffolds can resist nucleases and alter immune recognition while supporting specialized aptamer, probe, and chirality-focused applications.

Product Description Code
Left-Hand L-DNA Mirror image of D-DNA; nuclease-resistant and non-immunogenic. [L-DNA]
Left-Hand L-RNA L-RNA enantiomer with enhanced stability and immune-evasive properties. [L-RNA]
Backbone Replacements & Analogues

Backbone Replacement & Analogue Chemistries

Synthetic backbone analogues such as PMO, PNA, GNA, bridged nucleic acids, and click-chemistry linkages expand oligonucleotide performance beyond natural phosphate chemistry.

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

Design Strategy for Backbone-Modified Oligos

Strategy & Architecture

  • Define the mechanism: RNase H gapmer, steric-block splice modulation, probe diagnostic, or high-affinity clamp.
  • Gapmer basics: Use a DNA “gap” with PS linkages and 2′-modified wings such as LNA/BNA, 2′-OMe, or 2′-F.
  • PS patterning: Full or partial PS can balance Tm, potency, viscosity, and formulation behavior.
  • Orientation: Reverse 5′→3′ synthesis or 2′–5′ linkages can tune enzyme interactions and architecture.
  • Neutral backbones: PMO and PNA are useful for steric-blocking and probe workflows.

Tm, Specificity & Length

  • Raise Tm: Use LNA/BNA in wings or probe regions; shorten length to maintain specificity.
  • PS effect: PS may slightly reduce Tm; offset with LNA/BNA placement or length adjustment.
  • Mismatch control: PNA and LNA can improve mismatch discrimination for SNP detection and clamp designs.
  • Diagnostics: Triazole linkages can support ligase-friendly and nuclease-resistant probe architectures.
Tip: For RNase H-active gapmers, preserve an 8–10 nt DNA gap with PS linkages and use 2′-modified wings such as LNA/BNA, 2′-OMe, or 2′-F. For steric-blocking applications, consider PMO or PNA when durability without RNase H recruitment is desired.
Chemistry & Quality

Chemistry, Manufacturability & QC Documentation

Chemistry & Manufacturing

  • PS stereochemistry is often mixed Rp/Sp; stereodefined synthesis may be available depending on application.
  • L-oligos, PMO, PNA, and specialized analogues may require dedicated synthesis setup.
  • Batching related constructs can improve efficiency and reduce development cost.

Purification & Formulation

  • RP-HPLC, IEX-HPLC, PAGE, affinity purification, or dual-HPLC may be used depending on construct complexity.
  • Conjugates and neutral backbones may require custom purification development.
  • Duplexing, pooling, plate formatting, formulation, and LNP encapsulation are available.

QC & Documentation

  • Identity by ESI-MS, LC-MS, or optional fragment mapping.
  • Purity documentation with HPLC traces and optional residual solvent, salt, or moisture testing.
  • Endotoxin, bioburden, CoA, traceability, and stability support available on request.
Quality alignment: Bio-Synthesis supports ISO 9001 / ISO 13485-aligned workflows and GLP/GMP-like practices as scoped.

FAQ

What is the purpose of a phosphorothioate backbone?
 Phosphorothioate modification improves nuclease resistance and serum stability by replacing one non-bridging oxygen in the phosphate backbone with sulfur. It is widely used in ASO and siRNA research.
Can PS backbones be combined with 2′ sugar modifications?
 Yes. PS backbones are commonly combined with 2′-OMe, 2′-F, MOE, LNA, BNA, or cEt wings to improve stability, potency, and hybridization behavior.
When should I use PMO or PNA?
 PMO and PNA are charge-neutral backbone systems useful for steric-blocking, splice modulation, high-affinity probes, clamps, and durable diagnostic workflows.
Do backbone modifications affect Tm?
 Yes. Some modifications such as PS can slightly reduce Tm, while LNA/BNA and PNA can increase affinity and mismatch discrimination. The final effect depends on placement and sequence context.
What QC is recommended for backbone-modified oligos?
 Recommended QC can include mass spectrometry, analytical HPLC, purity traces, residual salt or solvent analysis, endotoxin testing for in vivo research, and a certificate of analysis.
What information should I provide for a quote?
 Include sequence, backbone chemistry, modification placement, oligo type, scale, purification target, conjugates, QC requirements, and intended application.
More FAQ'sAll FAQ's
Contact & Quote Request

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