Bridged Nucleic Acids (BNA)
Bio-Synthesis provides Molecular Beacon structure probes with large number of dye and quencher combinations. These structure constrained molecular beacon probes are highly sensitive and stronger hybridization specificity than linear probes 1,2. They have greater specificity for mismatch discrimination due to the fact that in the absence of target they form fewer conformations than unstructured probes, resulting in an increase in entropy and the free energy of hybridization.
Incorporate modified base such as BNA or 2'-OMe RNA to your to RNA Molecular Beacons not only have stronger nuclease resistant, but also possess faster hybridization kinetics, and superior binding affinity and specificity toward targets compare to DNA oligonucleotide.
All Bio-Synthesis's Molecular Beacon dual labeled probes are available at a fixed price per oligonucleotide, within the following parameters:
If any help is needed qPCR primer design for Molecular Beacons 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.
Molecular Beacons are hairpin-loop shaped oligonucleotides that contain a probe sequence, a stem with complementary sequence at 5' and 3' end that are modified with a fluorophore and quencher. This key feature of constrained structures is designed so at close proximity the fluorophore and the quencher interact by contact quenching to form a transient "ground-state" heterodimer that is not fluorescent.Upon hybridization with target sequence sequence, the hairpin-loop structure unfolds and separate the 5' end reporter dye from the 3'-end quencher. The quencher is no longer in close proximity to absorb the emission from the reporter dye. The increased emitted flourescence signal be detected by PCR instruments which is directly proportional to the amount of target DNA. If the target DNA sequence does not exactly match the Molecular Beacon probe sequence, hybridization and fluorescence does not occur.
Molecular beacon3 offer greater specificity for mismatch discrimination due to structural constraints. These beacon-based assay are fast, simple, inexpensive, and enable real-time monitoring of nucleic acid reactions both in vivo and in vitro in real-time monitoring of nucleic detection. These stem-loop structure probes have become popular for standard analyses such as quantification of DNA and RNA4. They have also been used for monitoring intracellular mRNA hybridiza-tion,5 RNA processing, 6 and transcription7 in living cells in real-time. They are also ideally suited to SNP/mutation analysis 8 as they can readily detect single nucleotide differences 9,10 and have been reported to be reliable for analysis of G/C-rich sequences. 11 The sensitivity of Molecular Beacons probes permits their use for the accurate detection of mRNA from single cells. 12 They have been used in fourplex assays to discriminate between as few as 10 copies of one retrovirus in the presence of 1 × 105 copies of another retrovirus.13
All our molecular beacon probes are 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.
All molecular beacon probes are dual HPLC purified
BNA LightCycler FRET Probes can contain up to 6 BNA bases
BNA Molecular beacon can contain up to 8 BNA bases
Molecular Beacons are sold under license from the Public Health Research Institute, Newark, NJ. For information on designing Molecular Beacons please refer to The Public Health Research Institute's Molecular Beacons..
Learn more about Bridged Nucleic Acids (BNAs).
All Molecular Beacons dual labeled probes includes 5'-reporter dye, 3'-quencher and dual HPLC purified. Please submit your order or quotation request to the client relations department at firstname.lastname@example.org, fax (972) 420-0442, or you can use our online ordering system.
Please browse our selection below to find a suitable dye and quencher combination, or you may contact us
3' BHQ Modified Molecular Beacon
Minimum Guarantee Yield
3' DABCY Modified Molecular Beacon
Wavelength-shifting molecular beacons are nucleic acid hybridization probes that fluorescence in a variety of different colors, yet are excited by a common light source. These probes contain a harvester fluorophore located at an internal location in its 5' arm that is oposite to the quencher in the hairpin conformation. Harvester fluorophore absorbs strongly in the wavelength range of the monochromatic light source and an emitter fluorophore is chosen so that it can efficiently absorb energy from the available monochromatic light source. In the absence of complementary nucleic acid targets, the probes are dark, whereas in the presence of targets, they fluoresce—not in the emission range of the harvester fluorophore that absorbs the light, but rather in the emission range of the emitter fluorophore. This shift in emission spectrum is due to the transfer of the absorbed energy from the harvester fluorophore to the emitter fluorophore by fluorescence resonance energy transfer, and it only takes place in probes that are bound to targets.
Wavelength-shifting molecular beacons are brighter than conventional molecular beacons of an enhancement in the intensity of the fluorescence of the emitter fluorophore.
In order to ensure that there is no background fluorescence, 100% of the dual labeled probes are purified by single or dual rp-HPLC and ie-HPLC as a standard protocol for all dual–labeled probes which give 90-97% purity. Depending on the type of the probes, one or two purification may performed to ensure the highest purity level
All dual labeled probes are quality checked by MALDI-TOP Mass spectrometry , analytical HPLC and analyze by Fluorometric Scan (ABS/EM) . In addition, the signal-to-background ratio is measured against a target sequence for all molecular beacons.
3-5 Working days
-20 °C to -70 °C
Oligonucleotides are stable in solution at 4°C for up to 2 weeks. Properly reconstituted material stored at -20°C should be stable for at least 6 months. Lyophilized DNA (when kept at -20°C) in a nuclease-free environment should be stable for year
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
Delivered as dried-down product in opaque tubes
Turn-around time is dependent upon successful QC validation and does not include shipping time.
See information on our oligos: storage recommendations
Shipped by mail or express delivery, dry, in individual, opaque tubes
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 may increase turn-around time
Please contact your local Bio-Synthesis representative
On-line (contact us), by email (email@example.com) or fax