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Custom BNA & LNA Modified Oligonucleotides

High-affinity BNA bridged nucleic acid, BNAClamp™, LNA, PNA, and modified oligo synthesis for PCR clamping, mutation detection, SNP discrimination, miRNA analysis, ISH/FISH, antisense research, and diagnostic assay development.

BNA / 2’,4’-BNANC BNAClamp™ PCR LNA Supported SNP Discrimination Mutation Detection miRNA Detection ISH / FISH Probes HPLC / MS QC
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Overview Comparison BNAClamp Applications Specs FAQ Reading Literature Contact
Overview

BNA bridged nucleic acids for high-affinity target recognition

BNA / 2’,4’-BNANC is a third-generation bridged nucleic acid chemistry with a six-membered bridged structure that restricts sugar conformation and promotes stronger Watson-Crick binding to DNA or RNA targets. Bio-Synthesis positions BNA as the primary modified oligo platform while also supporting LNA and other nucleic acid analogs.

PBNA-A, BNA-mC, BNA-G, and BNA-T bridged nucleic acid structures

BNA Platform Advantages

Designed for strong target binding, nuclease resistance, and high sequence discrimination.

Higher Tm

Each BNA addition can increase duplex Tm, supporting shorter and more specific probes.

Labeling Options

Improves DNA/RNA binding and triplex formation for advanced targeting.

Biostability

Enhanced resistance against exo- and endonuclease degradation.

Best-Fit Uses

Ideal when assay success depends on high affinity, mismatch discrimination, and robust detection.

BNAClamp™ PCR

Wild-type suppression and mutant allele enrichment.

miRNA / ISH

Short high-affinity probes for short RNA and tissue detection workflows.

SNP assays

Single-nucleotide mismatch discrimination and allele-specific detection.

Comparison Table

BNA, LNA, PNA, and DNA/RNA comparison

BNA is optimized for high-affinity hybridization, mismatch discrimination, and diagnostic assay performance. LNA and PNA provide alternative modified oligo strategies depending on polymerase compatibility, probe format, and targeting requirements.

Feature BNA LNA PNA DNA/RNA
Binding Affinity Very High High High Standard
Tm Increase +2 to +9°C +2 to +8°C Moderate–High —
Mismatch Discrimination Excellent Very Good High Moderate
Nuclease Resistance Excellent Excellent Excellent Poor
PCR Compatibility Excellent Good Limited Standard
Best Applications PCR Clamp, SNP, miRNA qPCR, Antisense FISH, Capture, Clamp General Molecular Biology

Why BNA? BNA provides strong duplex stability, mismatch discrimination, and PCR clamp performance while maintaining compatibility with many molecular biology and diagnostic workflows.

BNAClamp™ PCR Technology

BNAClamp™ for rare mutation enrichment and wild-type suppression

BNAClamp™ probes bind strongly to wild-type sequences and suppress their PCR amplification, allowing rare mutant targets to amplify preferentially.

Wild-Type DNA

Pol

BNAClamp™ binds the wild-type sequence and blocks polymerase extension.

→
↓

Mutant DNA

Pol

Mismatch prevents strong clamp binding, allowing mutant amplification.

→
↓

Mutation Enrichment

Mutant signal enriched

Rare mutation signal becomes easier to detect in qPCR or mutation assays.

Applications

BNA and LNA modified oligo applications

BNA can be incorporated with DNA, RNA, LNA and other analogs to support diagnostic, therapeutic research, and molecular biology workflows requiring stronger binding and stability.

Mutation Detection

BNAClamp™ and BNA probes for wild-type suppression, rare variant enrichment, and mutation-sensitive assays.

SNP Discrimination

High-affinity probes supporting single-base mismatch discrimination and allele-specific assay development.

miRNA Detection

Short high-affinity probes for robust detection of microRNA targets regardless of GC content.

ISH / FISH Probes

BNA-enhanced probes for short transcripts, preserved tissue sections, cell preparations, and imaging assays.

Antisense & RNA Targeting

Duplex/triplex stabilization for RNA targeting, gene silencing research, antigene, and antisense workflows.

Aptamer Capping

BNA incorporation can improve aptamer stability while preserving target-binding properties.

Synthesis Options

Custom BNA oligonucleotide synthesis specifications

Bio-Synthesis supports custom BNA, LNA, PNA, DNA/RNA analogs, labels, linkers, purification options, and QC documentation for research and diagnostic development programs.

Parameter Available Options
Length Up to 200 bases depending on sequence, chemistry, modification density, and purification requirements
Scale Microgram through multi-gram project quantities
Bases / Linkages BNA, BNA3/DNA, RNA, LNA, PNA, analogs, phosphodiester and phosphorothioate options
Modifications Dyes, quenchers, biotin, spacers, linkers, affinity tags, conjugates, and 100+ available modifications
Purification RP-HPLC, PAGE, ion-exchange HPLC, dual HPLC/PAGE, RNase-free HPLC/PAGE by project need
QC MALDI-TOF MS, ESI MS or LC-MS, analytical HPLC, UV quantitation and technical data support
Format Dried, in solution, annealed, mixed, 2 mL tube, 96-well plate or 384-well plate formats
Design & Modification Support

BNA, LNA, labels, linkers, and purification strategy

Modified oligos often require design review around BNA content, target length, Tm balancing, salt form, purification, and analytical release testing.

BNA Probe Design

affinity, Tm, and specificity tuning

BNA can be spiked into DNA or RNA oligonucleotides to tune duplex stability, probe length, mismatch discrimination, and nuclease resistance.

Tm Control
Adjust BNA content to narrow Tm ranges across targets with different GC content.
Mismatch Sensitivity
Useful for SNP, mutation, and allele-specific detection.[1]
Purification
HPLC is strongly recommended for many heavily modified BNA oligos.

Supported Modifications

LNA, labels, conjugates, and delivery formats

Bio-Synthesis supports BNA and LNA modified oligos with standard and specialized modifications for assay development.

Labels
FAM, TAMRA, Cy dyes, quenchers, biotin and assay-specific labels.
Linkers
Spacers, reactive handles, conjugation groups and affinity tags.
Formats
Lyophilized, solution, annealed, mixed, plate-based, and custom formats.
Recommended Reading

BNA probe design guides and comparison resources

Review the BNA brochure and comparison resource for chemistry background, performance characteristics, BNAClamp™ technology, applications, and synthesis options.

BNA Bridged Nucleic Acid Brochure

Bio-Synthesis brochure describing BNA / 2’,4’-BNANC chemistry, BNAClamp™ PCR, miRNA detection, SNP discrimination, synthesis options, purification, and QC.

View Brochure →

BNA, PNA, LNA, and DNA Comparison

Comparison resource for choosing BNA, LNA, PNA, or DNA probes based on affinity, stability, compatibility, probe length, and diagnostic application needs.

View Comparison →

BNA Probe Design Guidelines

Design recommendations for BNA-based oligonucleotide probes including mismatch discrimination, Tm balancing, probe length, target selection, and diagnostic assay optimization.

View Design Guidelines →

BNA/LNA Gapmer Design Guidelines

Technical guidance for designing antisense gapmers including wing chemistry selection, central DNA gap length, RNase H activation, mismatch discrimination, and target optimization strategies.

Read Gapmer Design Guide →

Antisense & Gapmer Literature

Selected BNA antisense and gapmer references

BNA and bridged nucleic acid chemistries have been investigated for antisense, gapmer, cholesterol-lowering, and RNA targeting applications due to their enhanced affinity, nuclease resistance, and mismatch discrimination properties.

Cholesterol-lowering Action of BNA-based Antisense Oligonucleotides Targeting PCSK9

Wang E. et al. evaluated BNA-based antisense oligonucleotides targeting PCSK9 in diet-induced hypercholesterolemic mice and demonstrated cholesterol-lowering activity.

View Article →

BNANC Gapmer Antisense Oligonucleotides

Study describing bridged nucleic acid gapmer design strategies, RNase H activation, and antisense activity optimization.

View Article →

Antisense Effects of 2’,4’-BNA/LNA-based Oligonucleotides

Reference discussing high-affinity bridged nucleic acid antisense oligonucleotides, stability enhancement, and RNA targeting performance.

View Article →

BNA-modified Antisense Oligonucleotides for Therapeutic Applications

Review article covering BNA/LNA chemistry, gapmer architecture, nuclease resistance, and therapeutic antisense development.

View Article →

Related applications: BNA gapmer and antisense designs are commonly explored for RNase H-mediated silencing, splice modulation, miRNA targeting, cholesterol regulation, and mutation-selective RNA targeting workflows.

Frequently asked questions about BNA and LNA modified oligos

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.
More FAQ'sAll FAQ's
Contact & Quote Request

Ready to discuss your BNA or LNA modified oligo project?

For faster technical review, share your sequence, target type, desired BNA/LNA content, application, label or conjugation needs, purification preference, scale, delivery format, and QC documentation requirements.
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Email: Info@Biosyn.com
Phone: +001-972-420-8505 (INT)
Phone: 800-227-0627 (US/CAN)

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Fast Quote Checklist

Include sequence, BNA/LNA placement, target, scale, purification, labels, linkers, format, and QC needs.

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Why Choose Bio-Synthesis

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Greetings Researchers,

Please be advised that any information, guidelines, writeups, and oral/video/graphic content on our website are intended solely as general guidelines.
It is the researcher's sole responsibility to conduct thorough research on the designs of the products intended for their experiments before submitting
their designs to Biosynthesis for review of production feasibility.
Thank you for your understanding.

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