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BNA qPCR primers and probes are dual labeled DNA or RNA probes designed for use in the 5' nuclease assays. Spiking oligonucleotide with BNA base in the probes or primers have increase sensitivity in real-time quantitative PCR assay. BNA Probes have increased sensitivity for distinguishing DNA base-pair mismatches, and are commonly used for SNP genotyping assays.

Bio-Synthesis is a sole supplier for BNA dual labeled oligonucleotide probe. All qPCR probes are available at a fixed price per oligonucleotide, within the following parameters:

  • DNA BNA chimeric mix base up 10-25 bases in length
  • up to 6 BNA base insertions
  • Wobbles (non-defined ratio) possible
  • HPLC purified in 10 nmole, 25 nmole up to 1000 nmole
  • QC by MALDI, analytical HPLC and Fluoroscan
  • Deliver lyophilized in tube
  • TAT of 4-6 working days

If any help is needed qPCR primer design or the combination of dyes that should be used on a specific thermocycler, please do not hesitate to contact our scientific support that will be happy to help you.

BNA Enhanced Real-time qPCR Primers and Probes

Bridged Nucleic Acids (BNAs), a novel type of nuclei acid analogs that contains a six-member 2'-O,4'-aminoethylene bridge. This bridge-locked in 3' endo conformation which restricts the flexibility of the ribofuranoise ring and locks the structure into a rigid-bicyclic formation, allowing enhanced hybridization performance and biostability.

Feature of BNA fluorescent probes

  • Higher Tm by BNA modification increases thermal stability and hybridization specificity
  • More accurate gene quantitation and allelic discrimination improve SNP detection assays
  • Shorter NBA probes enable easier and more flexible probe designs for problematic target sequences
  • Compatible with real-time PCR platforms and end-point analytical detection instruments - no additional investment on instrumentation is necessary
  • Compatible with standard DNA and RNA phosphoramdite chemistry - allows the use of the same synthesis and modification protocols as DNA and RNA bases

To overcome certain weakness of standard DNA probe chemistires, choose our range of Bridged Nucleic Acid (BNA) fluorescent probes, this powerful new generation sequence-specific real-time qPCR probes can be use in various PCR probe design:

  • BNA LightCycler FRET Probes
  • BNA dual-labeled fluorogenic probes
  • BNA molecular Beacon

Learn more about Bridged Nucleic Acids (BNAs)

Specifications of BNA real-time qPCR fluorescednt Probes

Quality Control:

All our BNA modified oligonucleotides undergo vigorous process of monitoring and strict quality control. Length and labeling are systematically controlled by PAGE, HPLC or MALDI-TOF mass spectrometry analysis. Quantity is systematically determined and validated by UV Absorbance at 260 nm. Fluorescent probes are systematically quality-checked by analytical ie-HPLC.

Purification

Single purification when labeling at time of the synthesis using phosphoramidite chemistry. Some labeling such as Texas Red, Alexa Flour or ATTO dye series must be labeld post-synthetically by covalently attach a primary amine modified oligonculeotide with dye via NHS ester chemistry. In this case, dual HPLC purified is used to remove failure sequences during first HPLC purification,  after labeling, the second HPLC is performed to remove unlabeled oligonucleotides and excessive dye in order to obtain a full length labeled oligonucleotide.

Bases Assignment

DNA/BNA Chimeras:

  • BNA base (+A, +C, +T, +G) (+ denotes the BNA bases)
  • DNA (A,T,C,G)
  • RNA (rA, rT, rC, rG)

BNA LightCycler FRET Probes can contain up to 6 BNA bases

BNA Molecular beacon can contain up to 8 BNA bases

Contact us for any dyes and quencher combinations not listed below.

5' Reporter Dye Quencher Scale Minimum Guarantee Yield USD
5' 6-FAMTM 3' Black Hole Quencher® 1, BHQ1 100 nmole scale 2 nmole HPLC Purified $225.00
250 nmole scale 8 nmole HPLC purified $475.00
1.0 umole scale 20 nmole HPLC Purified $665.00
5' 6-FAMTM 3' Instant Quencher, IQ4 100 nmole scale 2 nmole HPLC Purified $215.00
250 nmole scale 8 nmole HPLC purified $455.00
1.0 umole scale 20 nmole HPLC Purified $625.00
5' Cy3TM 3' Black Hole Quencher® 2, BHQ2 250 nmole scale 8 nmole HPLC purified $455.00
1.0 umole scale 20 nmole HPLC Purified $625.00
5' Cy3TM 3' Instant Quencher, IQ4 250 nmole scale 8 nmole HPLC purified $475.00
1.0 umole scale 20 nmole HPLC Purified $665.00
5' Cy5TM 3' Black Hole Quencher® 2, BHQ2 250 nmole scale 5 nmole HPLC purified $535.00
1.0 umole scale 10 nmole HPLC Purified $750.00
5' Cy5TM 3' Instant Quencher, IQ4 250 nmole scale 5 nmole HPLC purified $485.00
1.0 umole scale 10 nmole HPLC Purified $680.00
5' HEXTM 3' Black Hole Quencher® 2, BHQ2 250 nmole scale 10 nmole HPLC purified $495.00
1.0 umole scale 20 nmole HPLC Purified $690.00
5' HEXTM 3' Instant Quencher, IQ4 250 nmole scale 10 nmole HPLC purified $450.00
1.0 umole scale 20 nmole HPLC Purified $625.00

Specifications

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).

Purification

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

Length

Length
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

Backbone

Phosphodiester bond

Format

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

Shipment:

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

Pricing:

Please contact your local Bio-Synthesis representative

Ordering:

On-line (contact us), by email (info@biosyn.com) or fax

Ordering & Contact Information

  • Please contact us for additional information or send an email to info@biosyn.com.
  • 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."