DNA/RNA Oligonucleotide Synthesis

Product catalog summary

Overview
Bioneer, founded in 1992, is a prominent supplier of synthetic oligonucleotides, providing high-quality DNA and RNA oligos at competitive prices. The company ensures superior quality through in-house production of raw materials and advanced synthesis and purification systems. Their unique Bio-RP purification technology guarantees oligos suitable for PCR and qPCR applications.

AccuOligo® Technology
This technology prevents oligo dislodging and loss during production and shipping by using an adhesive in the tube. It also prevents cross-contamination in plate formats and does not interfere with experimental methods.

Quality Control
Oligos are produced in a clean room environment and undergo rigorous quality control using MALDI-TOF and 96-well CE systems to ensure high purity. The Bio-RP purification system developed by Bioneer removes impurities and failure products, providing oligos nearly at HPLC purity.

Purification Methods

Bio-RP Purification: Offers high purity by isolating n-mer oligos and removing shorter sequences.
HPLC Purification: Provides >90% purity, essential for applications like site-directed mutagenesis.
PAGE Purification: Used for longer oligos, achieving >95% purity.

Standard Oligonucleotide
Bioneer offers synthesis of up to 130 mer oligonucleotides with various purification methods, featuring free Bio-RP purification, quick turnaround, and a broad range of modifications.

HT-Oligo™ (High Throughput Oligonucleotide)
Designed for high throughput use, Bioneer can produce 30,000 oligonucleotides per day, offering high quality at lower costs.

Modified Oligonucleotide
Bioneer provides a wide range of modifications for specialized applications, including real-time detection and mass-scale genotyping projects. Nearly 300 modifications are available, with free Bio-RP purification and competitive pricing.

Fluorescent Dyes
A table provides the excitation and emission maxima, along with the extinction coefficients of various fluorescent dyes such as 6-FAM, Cy3, Cy5, and others. These dyes are crucial for labeling and detecting oligonucleotides in qPCR and other fluorescence-based assays.

Dual-Labeled Probes
These probes have a reporter dye at the 5’ end and a quencher dye at the 3’ end, used for sensitive detection of genes. Bioneer offers a range of dual-labeled probes with various dye and quencher combinations, ensuring high-quality synthesis and competitive pricing.

EBQ Quencher
The EBQ (Excellent Bioneer Quencher) is highlighted as a next-generation dark quencher with a broad wavelength coverage (400-700 nm), offering superior quenching efficiency compared to traditional BHQ quenchers. It is stable across temperature and pH changes and compatible with a wide range of dyes.

Extendamers
These are long oligonucleotides (130-200 bases) synthesized with high coupling efficiency and purified using Bio-RP or PAGE methods. They are ideal for applications like cloning and mutagenesis.

Large Scale Oligonucleotide Synthesis
Bioneer provides large-scale synthesis of DNA and RNA oligos, including modified versions for antisense applications. The document outlines the benefits of phosphorothioate and 2’O-Methyl RNA modifications for increased stability and target affinity.

Custom RNA Synthesis
Bioneer offers high-quality custom RNA synthesis with a variety of modifications and purification options. The document lists guaranteed yields and available modifications for custom RNA oligos.

Quality Control (QC) System
Bioneer employs a MALDI-TOF QC system to ensure the quality of synthesized oligonucleotides. The system is fully automated, providing mass spectrometry data for each sample, ensuring high-quality products and rapid turnaround times.

Quality Control of Oligonucleotides at Bioneer

MALDI-TOF Mass Spectrometry: Used to measure the molecular weight of oligonucleotides, comparing theoretical and actual mass to detect sequence errors, modifications, and contaminants.
HPLC Analysis: Reverse Phase HPLC is used for QC of intermediates and single-stranded DNA, while Ion-exchange chromatography is used for decoy oligonucleotides, crucial for gene therapy QC.
GC Analysis: Checks for residual solvents in oligonucleotides, ensuring concentrations are below 0.1% to prevent side effects.
Specialized QC for Therapeutic Oligonucleotides: Includes HPLC, CE, gel electrophoresis, NMR, and tests for endotoxins, bioburden, moisture, and heavy metals.
NMR Spectroscopy: Used to understand molecular structures, particularly for phosphates in DNA backbones.
Heavy Metal Testing: Ensures oligonucleotides are free from harmful metals like lead and nickel.
Water Content and Bioburden Testing: Measures residual water and ensures sterility by checking for microbial contamination.
Endotoxin Testing: Uses Kinetic Chromogenic Analysis to ensure oligonucleotides are free from endotoxins, with a threshold of less than 0.25 EU/ml.

Oligonucleotide Ordering System
Orders are processed through a main server, with synthesis monitored by an Automatic Oligonucleotide Production System.

FAQs on Handling and Storage
Oligos should be stored at -20°C, preferably in dried form, to prevent degradation. Fluorescent dye-modified oligos require dark storage.

FAQs on Quantity and Concentration
Oligo quantity is determined by UV optical density, and concentration adjustments are provided on data sheets.

FAQs on Synthesis and Order
Details on synthesis processes, including modifications and limitations, are provided.

Oligonucleotide FAQs and Procedures

Quantification and Unit Conversions: Single-stranded oligos with 1 O.D. value contain approximately 33 μg, while double-stranded oligos contain 50 μg.
Molecular Weight Calculation: The molecular weight of an oligonucleotide is calculated using a specific formula involving the number of each nucleotide type and additional constants.
Oligo Quantity Conversion: To convert oligo quantity from nmole to weight, multiply the molecular weight by the number of moles.
Melting Temperature (Tm) Calculation: Tm is the temperature at which 50% of oligonucleotides are in duplex form. The nearest-neighbor method is used for accurate Tm estimation.
Degenerate Bases: Symbols for degenerate bases are provided, such as R for A or G, and N for any base.
Modified Oligos: Information on modified oligos and their structures is available on Bioneer's website.
Synthesis and Order: Oligos do not contain phosphate groups at the 5’ or 3’ positions unless specified.
Synthesis Scale Limitations: Different synthesis scales have specific base length limitations, ranging from 5 to 130 mer depending on the scale.
Oligonucleotide Synthesis Process: The synthesis involves forming 3’-5’ phosphodiester bonds using the phosphite triester method with high coupling efficiency.
User Protocols: Protocols for treating thiol-modified oligonucleotides and annealing complementary oligonucleotides are provided.

Catalog excerpts

DNA/RNA Oligonucleotide Synthesis Oligonucleotide - AccuOligo® QC & Order system Oligonucleotide FAQs User Protocol

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DNA/RNA Oligonucleotide Synthesis Oligonucleotide - AccuOligo® ································································································································3 Standard Oligonucleotide ···········································································································································5 HT-Oligo™ (High Throughput Oligonucleotide) ································································································7 Modified Oligonucleotide ···········································································································································8...

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Oligonucleotide [AccuOligo®) Overview High quality oligos and reasonable price. Founded in 1992, Bioneer is one of leading suppliers of synthetic oligonucleotides in the world (DNA and RNA). In-house production of raw materials (phosphoramidites, reagents & solvents) along with automated oligo synthesis and purification systems result in superior quality oligonucleotides at a reasonable price. Since Bioneer manufactures all the components of our oligonucleotides, we manage the quality control every step of the way - ensuring that you receive only the highest quality product. Bioneer's oligonucleotides...

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Oligonucleotide (AccuOligo®) Bio-RP purification: Phosphoramidite, which serves as the coupling monomer in oligonucleotide synthesis, has a DMT-protected 5’-OH group to prevent repetitive coupling reaction during the individual addition steps of synthesis. Only the n-mer oligos with the expected length, not n-1, n-2, n-3 … mer oligos, have the 5’-DMT group provided DMT was not removed after final round of synthesis (AKA “Trityl-On” mode). Because of this, Bioneer has developed unique Bio-RP resin, which attracts the hydrophobic DMT group, as well as an automated column purification process. In...

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Recommended Purification Methods by Application Synthesis Scale (Guaranteed quantity of starting materials) ■ Description Standard oligonucleotide synthesis service includes synthesis of up to 130 mer oligonucleotides. A variety of synthesis scales, as well as a choice of purification methods, (Bio-RP, HPLC or PAGE), depending on your application, can be selected. ■ Features and Benefits • Free Bio-RP purification: Near HPLC purity at a standard oligo price • Quick turnaround time: 24 - 48 hr from order to shipping in most cases • Broad range of modifications available: Nearly 300 modifications;...

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*Prices are pre-tax. They exclude delivery charges and customs duties and do not include additional charges for installation or activation options. Prices are indicative only and may vary by country, with changes to the cost of raw materials and exchange rates.

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