FAQs RNA longmers
The current maximum length of standard RNA oligonucleotides is 140 bases. For RNA oligos longer than 140 bases, please inquire.
Synthesis scale refers to the amount of starting CPG (controlled-pore glass) support-bound monomer used to initiate the DNA synthesis, not the amount of final material synthesized. This is the same for all manufacturers of synthetic DNA using standard phosphoramidite chemistry. When a synthesis scale of 40 nmole is specified, approximately 40 nmoles of the first base are added to the DNA synthesizer. For an average 25-mer, at least 25% of this starting material will result in failure sequences; hence it is not possible to produce 40 nmoles of full-length product from a 40 nmole scale synthesis. The losses occur during synthesis, post-synthetic processing, transfer of material, and quality control. Final yield is the actual amount that we guarantee to deliver.
Please note that OD260 values are a measure of total nucleotides´ optical density. Hence, neither purity nor amount of ordered substance are transparently reflected. For simplification and exemplification reasons look at the following:
1 OD of the 20mer 5´CAT CGT ATT CGA TGC TAC GT 3´
translates into approximately 5 nmol.
1 OD of the 40mer 5´CAT CGT ATT CGA TGC TAC GT CAT CGT ATT CGA TGC TAC GT 3´
translates into approximately 2.5 nmol.
Therefore, a 1 OD guaranteed amount of delivered product can vary significantly, while metabion´s commitment to delivered yields in nmol does not allow for ambiguity in terms of what you expect and pay for.
Our default delivery form is dry. This ensures maximum stability during transport and storage.
Yes, we do! Please, visit our dedicated page
RNA longmers are usually processed within 8-15 business days including purification and quality control, depending on sequence length/complexity and modification level.
Freight forwarders delivery time to the final destination is not included. In terms of "counting" working days, orders placed past 15:00 (Munich time) are considered to be next day's order. Be assured that we try to process your order as quickly as possible without compromising on quality!
DNA synthesis is a complicated process, which has improved significantly over the last years. Despite these improvements, all manufacturers have an inherent failure rate. We are constantly developing our processes and systems to minimize these losses; however, it is inevitable that we will occasionally have to re-synthesize some oligos. Please note that metabion performs strict quality controls on each and every oligo synthesized. If an oligo does not pass our quality tests, it will be resynthesized.
Metabion is dedicated to reliably deliver high quality products. While every production step is performed in light of achieving best quality, the product is released only if it passes our final inspection. Mass Spectrometry has become the state-of-the-art technology for verifying the integrity of oligonucleotides, and metabion has been the first custom oligo house who introduced routine mass checks into its operations. Each and every oligo is characterized by either MALDI- or ESI-ToF and stringent release criteria are applied.
Mass Spectrometry allows for the most sensitive detection of low-level by-products/impurities such as
- n-1/n-x oligos
- Incomplete Deprotection
- Acrylonitrile adducts
- High Salt Content Identification
Moreover, it is the fastest and most efficient way to identify potential product mix-ups.
We run two different types of Mass Spectrometry (MS) instruments in order to cope best with quality and quantity/throughput issues determined by the specifications of the respective oligo/analyte. While each instrument type precisely characterizes oligonucleotides in terms of composition through direct molecular weight measurement, their field of application is diligently adjusted to suitability considerations.
MALDI-ToF instruments typically have a higher throughput, while the limits of using this technique become manifest, if it comes to analyzing long oligonucleotides, or oligos carrying certain photo-labile modifications (e.g.common quenchers like BHQ®s, Dabcyl used in DLPs).
ESI-ToF is less efficient in terms of throughput but perfectly compensates for resolution issues with long oligos as well as for a potential detrimental laser impact on labile/photosensitive modifications – thus being a "natural" complement to MALDI-ToF analysis.
|Comparison MALDI-ToF and ESI-ToF|
|< 60 nts||+||+|
|> 60 nts||-||++|
|Photosensitive Modified Oligos||-||+|
Synthetic oligonucleotide purification is particularly challenging because of the small differences in size, charge and hydrophobicity between the full-length product and impurities, which often co-elute.
For improved analysis of complex samples like long and/or multiple labeled oligos, metabion offers liquid chromatography (LC) coupled with electrospray ionization mass spectrometry (ESI-MS). The mass spectrometer is connected to a high pressure liquid chromatography (HPLC) system, which allows premium analyte characterization via chromatographical separation, followed by respective molecular weight determination. With this system, the mass of oligonucleotides between 2 and 220 bases can be analysed with high accuracy, resolution and sensitivity. Our expert production team will take care of the method (MALDI or ESI ToF) that best applies to your sample.
Preparative High Pressure Liquid Chromatography (HPLC) deals with isolating the separated components of a sample, and can be done on small-, mid- and large scale operations. In other words, the objective of a preparative HPLC is isolating and purifying a product. Practically, the sample goes from the detector into a fraction collector or it is collected manually.
Analytical HPLC refers to the processes of separating and identifying the components of a sample. It is usually a small-scale process, whose objective is the qualitative and quantitative determination of a compound. The sample goes from the detector into waste.
metabion offers analytical HPLC as an additional (optional) quality control method, complementing our Mass-Check QC, which is performed by default on all our oligos.
For product/quality documentation please see FAQ: What kind of documentation do I get with my RNA oligos?
The chemistry of RNA synthesis is identical to the DNA synthesis except for the presence of an additional protecting group at the 2' hydroxyl position of ribose. This position is protected with silyl groups (usually TBDMS), which are stable throughout the synthesis. The remaining positions on both the sugar and the bases are protected in the same fashion as in DNA. Please visit our DNA FAQs for more information.
For RNA oligonucleotide between 5-40 nts and for a quantity delivered between 10-100 nmol, we offer RNA oligonucleotides desalted as well as HPLC purified. Over 100 nmol and 40 nts our default purity is HPLC! Such RNA require HPLC purification to guarantee the top quality required for your experiments. For such RNA oligonucleotides, HPLC purification is included in our price per base/probe/duplex. Visit our Standard Portfolio.
Synthesis is monitored through trityl analysis. Quality check by mass spectrometry further ensure top quality. Please visit our DNA FAQs page for more information.
The label on the oligo tube shows basic information like oligo name, name of person who ordered, oligo sequence including modifications, oligo ID, amount of RNA (OD260 and nmol), Tm, and molecular weight.
In addition, you will receive a synthesis report containing more detailed information on the physical-chemical properties of the oligo, such as base composition, base count, purification grade, amount of RNA (OD260 and nmol), Tm and molecular weight.
Each and every oligo produced and delivered is analyzed by either MALDI- or ESI-ToF before release, and Mass-Check documentation/traces will be provided upon additional charges (desalted RNA) or free of charge (HPLC purified RNA). The following terminology is used for differentiating between offered QC:
For desalted RNA:
Standard quality control performed on each and every oligo. Either MALDI- or ESI-ToF, subject to the "nature of the oligo", and metabion internal procedures. This service is free of charge and no printed/pdf documentation is provided.
Explicitly ordered and performed MALDI-ToF check. Product delivered with MALDI-ToF traces. Additional charges apply.
Explicitly ordered and performed ESI-ToF check. Product delivered with ESI-ToF traces. Additional charges apply.
Performed Mass Check and Analytical HPLC (see FAQ: What´s the difference between preparative and analytical HPLC?). Product delivered with analytical HPLC but without MS traces. Additional charges apply.
Mass Check + Analytical HPLC
Explicitly ordered and performed Mass Check (MALDI-ToF or ESI-ToF subject to the "nature of the oligo" and metabion internal procedures) and Analytical HPLC (see FAQ: What´s the difference between preparative and analytical HPLC?). Product delivered with analytical HPLC and MS traces. Additional charges apply.
For HPLC purified RNA:
Standard quality control performed on each and every oligo. Either MALDI- or ESI-ToF, subject to the "nature of the oligo", and metabion internal procedures. This service is free of charge and will always be delivered with hard copies of the Mass Check trace for all our HPLC purified RNA products.
Mass Check (MALDI-ToF or ESI-ToF subject to the "nature of the oligo" and metabion internal procedures) and explicitly ordered Analytical HPLC (please read FAQ: What´s the difference between preparative and analytical HPLC?). Product delivered with analytical HPLC and MS traces. Additional charges apply.
There are two ways of ordering:
- The preferred way is order transmission through our Web Order Portal for most convenient online shopping. Online ordering is the most convenient way.
Jump on our Web Order Portal (WOP; https://wop.metabion.com/), look for the product category “RNA Oligos” under “RNA Custom Synthesis”, open the respective order form and enter your oligo. Options provided are self-explanatory. The system shall guide you through the ordering process. For more information click here
If you want to connect your eProcurement System with our Web Order Portal (e.g. OCI - Open Catalog Interface), please simply contact our Customer Service (email@example.com).
- You can order by sending us an e-mail with our pre-formatted excel order file as attachment. Download respective Order Form
When you write your email, please make sure to address the following questions in the excel template:
RNA Oligo Order download xls » Also available in our web order system (WOP)
- Name of the RNA oligo?
- Sequence of the RNA oligo in 5’-3’ orientation?
- Yield range
If you are a new customer, please additionally provide us with
- Your shipping and billing address
- Any other information like Purchase Order number, VAT number (VAT only for customers resident in the EU) etc
In case you opt to transmit orders via email using your own format(s), we need to alert you that above mentioned information are obligatory for processing your order. Due to extra efforts necessary for individual order format transfer into our system, order processing will take longer as compared to preferred web orders and pre-formatted emails.
Online orders or email orders which indicate an email address will be confirmed by email.
Our default shipping mode is sending by Express service overnight at EURO 4.20 per shipment within Germany. If the value of your order is > EURO 125,00 shipping within Germany is free of charge!
Average in-house turnover times (freight forwarders delivery time not included):
- Desalted RNA in single tube format: 3-5 working days
For RNA in plates, expected turnover time is 5-7 business days
HPLC-purified, unmodified or single-labelled RNA oligonucleotides from our standard portfolio are usually processed within 5-10 business days including purification and quality control.
Duplex oligos take about 10-15 days to be produced, purified and QCed
- For RNA dlps you should consider 10-15 days as a realistic turnaround time and for RNA longmers depending on sequence length/complexity and modification level 8-15 business days
Above mentioned estimated turnover times are only indications and refer to our standard portfolio. In terms of "counting" working days, orders placed past 15:00 (Munich time) are considered to be next day's order. Major deviations will be communicated timely. Be assured that we try to process your order as quick as possible without compromising on quality!
All our products are offered according to our terms and conditions.
A comprehensive Synthesis Report comes along with each order, indicating oligo name and sequence, composition of bases, modification, base count, purification, yield in ODs, nmol, Tm and molecular weight.
Yes, we do! This is part of our standard RNA portfolio! Delivery/shipping condition of dsRNA like for all our RNA oligos is “dry”. Simply dissolve the pellet in annealing buffer and apply a suitable annealing protocol. For your convenience we recommend to follow our guidelines prepared for download.
The best way to store RNA is as a dry pellet at -20°C to -80°C and to avoid frequent freeze-thaw cycles. If you want to store your RNA in solution re-suspend the delivered pellet in an RNAse-free solution buffered at pH 7.4 - 7.6 and store at -20°C or less. We recommend that RNAs are re-suspended at a convenient stock concentration and stored in small aliquots to avoid multiple freeze thaw cycles.
For modified oligonucleotides – especially for fluorescent dye labelled oligos – you should minimize the probe’s exposure to light because of its bleaching effect. Additionally, we recommend storing dye labelled oligos highly concentrated, rather than in working dilutions, if you don’t use them immediately. The higher the dilution factor the faster the fluorescent activity decreases/fluorescence fades away. Therefore, try to store highly concentrated aliquots frozen, thaw them only once, and dilute them just before usage. Click here to download our guidelines for handling RNA.
We recommend to dissolve single stranded RNAs in 1x TE buffer (10 mM TrisCl, pH7.5, 0.1 mM EDTA; prepared under RNase-free conditions). This buffers the pH and chelates metal ions, which may contribute to RNA degradation. RNase-free water is also acceptable.
metabion's RNA oligonucleotides are delivered deprotected and purified – ready to use. They are RNAse free, but as RNA is highly susceptible to degradation by exogenous RNAses introduced during handling, it is essential that you conduct all handling steps under sterile, RNAse free conditions. Never handle RNA without wearing gloves. RNAse free reagents, barrier pipette tips and tubes should be used!
For more information, please read FAQ: How should siRNA oligonucleotides be stored?
We recommend that each aliquot of RNA should not be stressed by more than 4 - 5 freeze-thaw cycles to ensure product integrity.
All oligonucleotides, whether single-stranded or double-stranded oligos, are provided as dried pellets and shipped at ambient temperature. While being stable at room temperature for 2-4 weeks, they should be placed at -20°C or at lower temperature upon receipt.
RNA duplexes are significantly more resistant to nucleases than a single strand RNA oligonucleotide. However, maintaining sterile, RNAse free conditions is always recommended as a precaution. Dried pellets are stable at room temperature for 2-4 weeks, but should be placed at -20°C or -80°C for long term storage. Under these conditions, dry RNA is stable for at least one year.