BNA Oligos: Optimized Binding, Built for Therapeutic

Request a Quote Today Speak to a Scientist

Rapid. Reliable. Secure

Custom BNA Synthesis

Locked-sugar oligonucleotides with high affinity, specificity, and nuclease resistance for demanding assays.

Overview

Bridged Nucleic Acids (BNAs) are RNA/DNA analogs in which the ribose sugar is “locked” by a covalent bridge (typically between the 2′-O and 4′-C). This rigidifies the sugar into a C3′-endo conformation that promotes exceptionally stable duplex formation with complementary DNA or RNA.

Bio-Synthesis provides end-to-end custom BNA oligonucleotide synthesis—from sequence design through labeling and conjugation—delivered with comprehensive QC documentation.

Speak to a Scientist

At-a-Glance

  • Length: 8–30 mer (longer on review)
  • Purification: HPLC standard; IE-HPLC/PAGE optional
  • Chemistry: BNA-DNA mixmers, BNA-RNA mixmers, fully BNA segments
  • Labels: dyes, biotin, haptens; spacers/PEG; click-ready handles
  • Formats: Lyophilized or buffered; plates or tubes
  • QC: MS + analytical HPLC; optional Tm/hybridization data

Key Advantages

Enhanced Affinity

Higher Tm versus DNA/RNA of the same length enables shorter probes with stronger binding.

High Specificity

Improved single-base mismatch discrimination for SNP and mutation targeting.

Stability & Resistance

Locked sugars increase resistance to nuclease degradation and harsh conditions.

Applications

  • Molecular diagnostics & SNP genotyping
  • Allele-specific PCR / qPCR probes
  • Antisense & miRNA modulation (research)
  • Hybridization assays & NGS sample prep
  • In situ hybridization
  • CRISPR guide and off-target studies
  • Short, high-affinity capture probes
  • Biosensors & nanotech assemblies
  • Stability-demanding environments

Custom Synthesis Options

Parameter Options
Length 8–30 mer (custom longer upon review)
Composition BNA mixmers with DNA/RNA; full BNA segments on request
Purification RP-HPLC (standard); IE-HPLC/PAGE optional
Scales 1 mg to gram quantities
Delivery Lyophilized or in buffer; single tubes or 96-well plates
QC Package MS (MALDI/ESI), analytical HPLC; optional Tm/hybridization

Popular Modifications & Linkers

Category Examples Common Uses
Fluorescent Dyes FAM, HEX, JOE, TAMRA, ROX, Cy3/Cy5, ATTO, Alexa Fluor® series qPCR/ASO probes, FISH/ISH, imaging
Affinity Tags Biotin (TEG/long), Digoxigenin, DNP Capture, pull-down, immunodetection
Reactive Handles Amine, Thiol, Azide/Alkyne (CuAAC/SPAAC), Maleimide Bioconjugation to peptides, proteins, surfaces
Spacers / PEG Ahx, AEEA, miniPEG, PEG(n), C6/C12 Reduce sterics; tune distance/solubility
Quenchers BHQ-1/2/3, Iowa Black, Eclipse Quenched probes & molecular beacons

Quality Assurance

  • Mass spectrometry for MW confirmation
  • Analytical HPLC purity profile
  • Optional: UV-melting (Tm), hybridization/functional tests
  • Documentation suitable for RUO; GLP/cGMP support on request

Typical Turnaround

Standard labeled BNA: 2–3 weeks from order confirmation. Complex mixmers or multi-label probes may require additional time.

Lead time is sequence- and modification-dependent; rush options may be available.

How to Order

  1. Provide your sequence or request design assistance.
  2. Select labels, spacers, and any conjugations.
  3. Choose scale, purification, and optional tests.
  4. Receive a same-day quote and timeline.

Panels or RFPs welcome—attach details in the form.

Specifications Checklist

  • Sequence (5′→3′), length, target, and desired Tm
  • Mixmer pattern (BNA/DNA/RNA) and positions
  • Labels/linkers and conjugation partner (if any)
  • Scale, purification, and QC requirements

BNA Technology & Benefits

What is BNA? Bridged Nucleic Acids (BNAs) are nucleic-acid analogs in which the ribose is “locked” by a covalent bridge (typically 2′-O to 4′-C). This conformational lock enforces a C3′-endo sugar pucker, pre-organizing the backbone for A-form–like duplexes and yielding markedly higher affinity and specificity to complementary DNA or RNA.

  • Pre-organization: Reduced entropic penalty at binding, increasing on-rates.
  • Higher Tm per residue: BNA mixmers often raise duplex Tm vs. DNA of the same length, enabling shorter probes with equal—or better—stability.
  • Sharper mismatch penalties: Single-base mismatches reduce Tm more strongly than in DNA probes, improving discrimination.
  • Nuclease resistance: Locked sugars hinder endo/exonuclease attack for greater stability in biological matrices.

Design Notes (Practical)

  • Mixmers: Interleave BNA with DNA/RNA to tune Tm and maintain synthesis yield/solubility.
  • Length: 12–20-mers work well for most targets; shorter is feasible due to higher affinity.
  • Placement: Enrich BNA near predicted weak regions (A/T-rich) or at termini for added stability.
  • Buffers: BNAs tolerate broader ionic strengths; verify conditions for your assay format.

Benefits at a Glance

  • Higher affinity to DNA/RNA (elevated Tm)
  • Superior specificity (single-nucleotide discrimination)
  • Greater stability (enhanced nuclease resistance)
  • Shorter probes with equal performance → better synthesis yield and cleaner analytics
  • Versatile labeling (dyes, quenchers, biotin, haptens; click-ready handles)
  • Broader applications: SNP genotyping, allele-specific PCR/qPCR, ISH/FISH, capture assays, antisense (research)

Compatibility

  • Works as BNA/DNA or BNA/RNA mixmers
  • Pairs with common backbone chemistries (e.g., phosphorothioate for antisense studies)
  • Supports dual-labeled probes, molecular beacons, and capture constructs

Note: Extremely high BNA content can elevate Tm beyond desired windows and reduce solubility. We can optimize the BNA pattern for your assay.

Use Case Why BNA Helps Typical Setup
SNP / rare variant detection Sharper mismatch penalties improve single-base discrimination Short BNA mixmer probe; optional quencher/dye for qPCR
Allele-specific PCR/qPCR Higher Tm yields tighter clamping and cleaner curves BNA in probe or primer hot-spots; optimize %BNA to target Tm
ISH/FISH probes High affinity & nuclease resistance in complex samples Dye-labeled BNA mixmers with spacers to reduce sterics
Capture/enrichment Short, strong binders reduce off-targets Biotinylated BNA with PEG spacer; streptavidin capture
Optimize My BNA Design

FAQ

What length works best for BNAs?

Most probes use 12–20-mers. Shorter designs are feasible thanks to the higher Tm of BNA mixmers.

Can BNAs be combined with DNA or RNA?

Yes—mixmers (BNA with DNA/RNA) allow fine control of Tm, affinity, and specificity.

Do BNAs improve mismatch discrimination?

Yes. The locked conformation typically increases single-base discrimination compared to DNA probes.

Do you support GMP production?

We support RUO through cGMP with appropriate QA oversight. Include your regulatory needs in the request.

Speak to a Scientist

Complete the form to receive a tailored quote. Your request will be emailed to info@biosyn.com and logged to your CRM endpoint (configure below).

Full Name *
Email *
Company / Institution *
Phone *
BNA Sequence(s)
Labels / Linkers / Conjugations
Scale *
Purification
Notes / Requirements

By submitting, you agree to be contacted regarding your request.

Why Choose Bio-Synthesis

Trusted by biotech leaders worldwide for over 40+ years of delivering high quality, fast and scalable synthetic biology solutions.