Oligo Handling, Analysis, and Applications
Support and Educational Content

Long, custom RNA oligos—Ultramer® RNA Oligonucleotides

Ultramer® RNA Oligonucleotides are single-stranded RNA oligos up to 120 bases that are desalted and delivered dry in 6–8 business days. With longer RNA oligos from IDT, you can:

  • Increase flexibility in applications requiring long synthetic RNA, including CRISPR and RNA therapeutics development
  • Create more complex RNA controls and templates
  • Select from guaranteed quantities of 4 nmol, 20 nmol, or 80 nmol
  • Verify the high quality of your oligos with free ESI-MS quality control documentation

Coupling efficiency in oligonucleotide manufacturing refers to the success rate of a synthesizer adding new bases to a growing nucleic acid chain. This measure is especially important in long oligo synthesis, because as the length of an oligo increases, small differences in coupling efficiency have dramatic effects on the amount full-length product produced.

By using Ultramer RNA Oligos, you can take advantage of our optimized, proprietary synthesis methods, which facilitate a narrower, higher range of coupling efficiencies and yield a greater proportion of full-length RNA oligo than standard synthesis methods. The graphs in Figure 1 depict the differences in full-length product produced when using Ultramer RNA Oligo synthesis methodology (coupling efficiencies of 99.0–99.3%; dark blue) and standard RNA oligo synthesis (coupling efficiencies of 98.0–98.5%; light blue).

Figure 1. Ultramer RNA Oligos vs. Standard RNA oligos

Figure 1. Ultramer® synthesis technology provides greater yield of full-length RNA oligos than standard RNA synthesis methods.

ESI (electrospray ionization) mass spectrometry methods are used to confirm the presence of full-length product (Figure 2). You receive free ESI-MS quality documentation for every oligo we synthesize.

Figure 2. QC data 1

Panel A. Ultramer® RNA Oligo, 90mer.

Figure 2. QC data 2

Panel B. Ultramer® RNA Oligo, 120mer.

Figure 2. QC data demonstrates high purity of Ultramer® RNA Oligos.  Molecular weights of a 90mer (A) and 120mer (B) Ultramer RNA Oligo were measured by ESI MS and found to be within 0.01% of their expected molecular weight (determined by their specific sequences).

Ordering long RNA oligos

The RNA Oligo Entry Tool makes ordering long RNA oligos easy. There is even a “Convert to RNA” feature that quickly switches an entire oligo from DNA to RNA.

Upon placing an order, you will receive your Ultramer RNA Oligos in 6–8 business days, delivered dry, in tubes. Ultramer RNA Oligos are desalted to remove small molecular impurities, and are formulated to 4 nmol, 20 nmol, or 80 nmol. As is standard with every IDT oligo, Ultramer RNA Oligos receive complimentary QC via ESI mass spectrometry. Resulting mass spec traces and QC information are available free of charge on the IDT website.

Product focus—Oligos, modifications, dsDNA fragments

Custom DNA and RNA oligonucleotides and primers

You can order up to 1 µmol desalted, custom synthesized DNA oligonucleotides, and they will be shipped to you the next business day (larger scales are available and ship within 5 business days). You can also specify whether to receive them dried down or hydrated, and whether you want them already annealed. Every IDT oligonucleotide is deprotected and desalted to remove small molecule impurities. Your oligos are quantified twice by UV spectrophotometry to provide an accurate measure of yield. Standard oligos are also assessed by mass spectrometry for quality you can count on.

Learn more or order Custom DNA Oligos now.

IDT has the expertise to deliver custom-synthesized RNA with the yield and purity that today's researchers demand. Custom RNA oligos are available in lengths of 5–60 bases. Oligos up to 1 µmol are shipped deprotected and desalted in 2–3 business days or deprotected and purified in 4–6 business days. Please inquire for turnaround on 5 µmol and 10 µmol RNA synthesis.

Learn more or order Custom RNA Oligos now.

Ultramer® RNA Oligonucleotides are single-stranded RNA oligos up to 120 bases that are desalted and delivered dry in 6–8 business days..

Learn more or order Ultramer RNA Oligonucleotides now.

Oligo modifications

Review a list of the common modifications IDT can add to oligonucleotides here. Not finding a modification you need on the IDT website? IDT will consider any modification you need. Just send your request to noncat@idtdna.com.

Custom dsDNA fragments

Rather than annealing oligonucleotides to obtain dsDNA fragments, when your fragment size is 125 bp or longer, it might make more sense to order gBlocks® Gene Fragments. gBlocks Gene Fragments are double-stranded, sequence-verified, DNA genomic blocks, 125–3000 bp in length, that can be shipped in 2–5 working days for affordable and easy gene construction or modification. These dsDNA fragments have been used in a wide range of applications including CRISPR-mediated genome editing, antibody research, codon optimization, mutagenesis, and aptamer expression. They can also be used for generating qPCR standards.

Learn more about gBlocks Gene Fragments at www.idtdna.com/gBlocks.

Related reading

ESI mass spectrometry—why we use it for oligonucleotide quality control—IDT was, and still is, a pioneer in using mass spectrometry for quality control in oligonucleotide synthesis. Learn about why a particular method, electrospray ionization (ESI), is used ubiquitously in our manufacturing processes.

Determining the physical characteristics of your oligos—the OligoAnalyzer Tool—Use this free web tool to determine many of the physical characteristics of your oligonucleotides. By simply inputting your sequence, you can find out its length, GC content, melting temperature range, molecular weight, extinction coefficient, and optical density.

Oligo synthesis: Why IDT leads the oligo industry—Read about the phosphoramidite method of oligonucleotide synthesis that IDT uses in its manufacturing processes. We also highlight additional measures taken to ensure that you receive the highest quality oligos and nucleic acid products in the shortest time possible.

Understanding melting temperature (Tm)—Read this advice from our own thermodynamics specialist, Dr Richard Owczarzy, on the effects of melting temperature (Tm) on hybridization. He provides considerations for better oligo and PCR/qPCR assay design, including oligo concentration, salt, and base pairing mismatch positioning.

Review other DECODED Online newsletter articles on oligo handling and analysis, and oligo modifications.

You can also browse our DECODED Online newsletter for additional application reviews, lab tips, and citation summaries to facilitate your research.

Author: Ellen Prediger, PhD, is a senior scientific writer at IDT.

© 2017 Integrated DNA Technologies. All rights reserved. Trademarks contained herein are the property of Integrated DNA Technologies, Inc. or their respective owners. For specific trademark and licensing information, see www.idtdna.com/trademarks.

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