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Our BNA Genotyping Probes are dual-labeled DNA probes designed with 5' nuclease assays. BNA enhanced oligonucleotide are ideal when studying short or very similar sequences. The high affinity of an BNA oligo to its complementary sequence results in improved specificity and sensitivity compared to traditional DNA or RNA oligonucletoides, it is an idea solution for SNP genotyping assays.

BNA Probes

Bridged Nucleic Acids (BNAs) bases can significantly increase Tm of an oligonucleotide when incorporated into dual-labeled probe. BNA probes can be designed with shorter lengths than standard dual labeled probes. Shorter probe design permits better quenching, increased signal to noise ratio and are there more, more sensitive. These probes offer an improved ability to discriminate mutation or closely related sequences. BNA enhanced dual labeled probe can have a Tm > 15oC between perfect-match and mismatch hybridization. Ability to modulate Tm greatly increase accuracy of allele determination in real-time PCR or other detection system which require differential hybridization to discriminate closely related sequences.

  • BNATM-enhanced primer, probes or clamps increase the detection of polymorphisms with unmatched specificity
  • Strong discrimination power for the detection of single nucleotide polymorphism (SNP)
  • Superior sensitivity to detect difficult targets
  • Compatible with all dyes

Design Considerations

When designing allele-specific primers or probes for SNP detection, vary the length and BNA™ positioning to obtain comparable melting temperatures ( Tm) for the alleles, while keeping the difference in melting temperatures ( Δ Tm) between the perfect match and mismatch binding as high as possible.

SNP probe design

  • Capture probes length of approximately 12 nt in length.
  • 2-3 BNA™ bases should be positioned directly at the SNP site.
  • The position of the mismatch in the capture probe is flexible. However, the SNP should ideally be positioned centrally.
  • A T m of approximately 65 oC is recommended.
  • No BNA™ bases should be positioned in palindrome sequences (GC base pairs are more critical than AT base pairs).

Clamp design

BNATM-enhanced clamps are oligonucleotides that compete with probes and primers for binding. They are very similar to the primers or probes they compete with, but are designed to perfectly match undesired PCR products or templates that should not be amplified.

  • Modified of 3’ BNA probe with inversed T or phosphorylation to prevent PCR extension
  • BNA probe length should be approximatly13-18 bases with >60%-80% BNA bases.

Allele-specific primer design

  • Avoid placing BNA base at the extreme 3' end of the primers to prevent low PCR efficiency.
  • BNA base should be positioned at the location of the polymorphism and/or immediately 5' of the polymorphism.

Custom Dual Labeled BNA Probes

Select your own BNA SNP probe using service package below or design your own using different dyes and quencher combination. Our BNA genotyping probes includes:

  • Synthesis of the custom oligo (10-25 nt), up to 6 BNA base insertions, reporter, quencher, and HPLC purification
  • Scale: 0.5 nmoles, 10 nmoles, 20 nmoles
  • Q.C by MALDI-TOP mass spectrometry, and analytical HPLC
  • BNA probes are lyophilized and shipped in 4–6 business days

5' Reporter Dyes3' Quencher
5' 6 FAM Black Hole Quencher 1,2,3
5' Cy3™ TAMRA
5' Cy5™ Eclipse Dark Quencher
5' HEX
5' Alexa
5' JOE
5' ROX
5' Rhodamine-6G
5' Texas Red
5' Yakima Yellow
5' Drgonfly Orange
5' Dyomic Dye
5' DyeLight


Quality control:

Every oligo is quality checked by MALDI-TOF mass spectrometry, electrospray ionization mass spectrometry (ESI-MS), capillary electrophoresis (CE), and/or polyacrylamide gel electrophoresis (PAGE).


Fully deprotected and desalted. Purified by PAGE or RP-HPLC


LightCycler probes 15 to 40 mers (optimal length: 20 to 30 mers)
Dual-labeled fluorogenic probes: 15 to 40 mers
Molecular Beacons 15 to 40 mers
Scorpions probes 30 to 60 mers (uni-probe)
15 to 45 mers (bi-probe)
Plexor up to 30 mers


Phosphodiester bond


Delivered as dried-down product in opaque tubes

Turn-around time:

Turn-around time
LightCycler probes 4 to 5 working days
Dual-labeled fluorogenic probes: 5 to 6 working days
Molecular Beacons 5 to 6 working days
Scorpions probes 7 to 10 working days

Turn-around time is dependent upon successful QC validation and does not include shipping time.

Storage and stability:

See information on our oligos: storage recommendations


Shipped by mail or express delivery, dry, in individual, opaque tubes

Technical Documentation:

Oligonucleotides are delivered with an OligonucleotideTechnical Data Sheet, which includes oligonucleotide name, sequence, concentration, precise quantity in OD and nmols, Tm, MW, length, extinction coefficient and purification data.

Additional Services:

  • Probe design services
  • High-throughput screening formats (microplates, etc)
  • Aliquoting

Additional services may increase turn-around time


Please contact your local Bio-Synthesis representative


On-line (contact us), by email ( or fax

Ordering & Contact Information

  • Please contact us for additional information or send an email to
  • You may also request an online quote.
  • To contact us by phone, please call 1-972-420-8505 or Fax at 1-972-420-0442
  • Orders may be placed using a purchase order (PO) or by credit card through our secure online ordering system.
  • When using a credit card ( creditcard ) it will be billed under "Bio-Synthesis, Inc."