Oligo Handling, Analysis, and Applications
Support and Educational Content

Unraveling RNA—the importance of a 2' hydroxyl

2′ Hydroxyl


On paper, the small structural differences between RNA and DNA may not look substantial but, in practice, these small differences have major significance for the biological role of RNA. The additional 2’ hydroxyl (OH) group present in RNA, but lacking in DNA, has effects that range from the biogenesis of life on earth to how RNA oligonucleotides should be stored.  Importantly, the addition of the 2’ OH group increases melting temperature (Tm) and stability by locking an RNA duplex into a compact A-form helix that is more stable than DNA’s standard B-form helix.

RNA stability

Tm is a measure of duplex stability, commonly defined as a function of how many hydrogen bonds are present in a duplex. But these cross strand hydrogen bonds are not the only stabilizing force in a duplex.  As two single strands form a duplex, each base of a single strand forms van der Waals interactions with neighboring bases on the same strand.  These significant stabilizing forces are stronger in RNA due to the A-form helix which stacks neighboring bases in a more stable lattice.

Self-folding structures

Many RNAs, including tRNA, rRNA, and snoRNA, form self-folding structures in which part of the RNA is single-stranded and part is bound to itself, forming duplexed regions. These duplexed regions tend to be under 10 bp and, at that short length the unique base stacking interactions of RNA are vital in making them stable. The remaining single-stranded regions rely on the reactive 2’ OH groups to bind to proteins, creating RNA-protein complexes that have critical roles in processes such as DNA and protein synthesis.

Structure begets enzymatic activity

The increased stability of RNA duplexes allows for highly diverse secondary and tertiary structures including triplexes, pseudoknots, loops, and junctions. This array of potential secondary and tertiary structures enable RNA to fold into enzymatically active molecules such as RNAse P, which cleave tRNA to their mature length.  Artificial ribozymes have also been developed in labs with an array of functionality including self replication. RNA is so versatile that it is widely believed that in early life, before DNA and proteins, RNA alone performed both information storage and catalytic functions, establishing life’s singular dependence on nucleic acids.  

2' HydroxylFollowing the removal of the 2’ OH protecting group in post-synthesis processing, a new vulnerability begins.  RNA is susceptible to alkaline hydrolysis which cleaves the backbone at the phosphodiester bond. These combined factors make the manufacture of RNA unique and contribute to differences between RNA and DNA in pricing and availability of both modifications and oligo lengths.

Compared to DNA, the unique manufacturing process required with RNA further demonstrates the significant impact of RNA’s 2’ OH group, which is also seen in nature. Expanded interest and study concerning RNA’s central role in biology has spurred innovation in RNA synthesis, and the two fields of RNA research and RNA synthesis will continue to advance in conjunction with each other, both with a focus on RNA’s dynamic 2’ OH.

Product focus—Custom RNA Oligos, RNAi products

Custom RNA Oligos

IDT has the expertise to deliver custom-synthesized RNA with the yield and purity that today's researcher demands. Use IDT RNA products for CRISPR, as Dicer substrates, aptamers, and microRNA inhibitors, and for many other applications.

RNA oligos are available from 10–90 bases for 100 nmole, 5–90 bases for 250 nmole and 1 µmole, and 5–50 bases for 5 µmole and 10 µmole. RNA oligos are also available with a range of modifications. See the IDT modifications portfolio for more information.

Standard custom RNA is shipped deprotected and desalted in 2–3 business days or deprotected and purified in 4–6 business days. Please inquire for turnaround on 5 µmole and 10 µmole RNA synthesis.

Learn more or order Custom RNA Oligos.

DsiRNAs for RNAi

Dicer-substrate short interfering RNAs (DsiRNAs) are chemically synthesized 27mer duplex RNAs that have increased potency in RNA interference compared to traditional, 21mer siRNAs.

  • Achieve sustained knockdown of cytoplasmic RNA, such as mRNA and some lncRNA, using low levels of DsiRNA (typically, 1–10 nmol)
  • Choose Predesigned DsiRNAs targeting human, mouse, or rat transcripts
    • Select from over 322,000 Predesigned DsiRNAs covering the complete transcriptomes
    • Conveniently order TriFECTa RNAi Kits (3 Predesigned DsiRNAs for the same target, 3 Control DsiRNAs, and Duplex Buffer), which are guaranteed to work*
  • Easily generate Custom DsiRNAs to sequences from any species

Learn more about DsiRNAs.

Additional reading

Oligonucleotide modifications: Choosing the right mod for your needs—Learn about our broad family of oligonucleotide modifications, and get suggestions for selecting modifications that can help you in your research.

My oligos have arrived: Now what?—Review these recommendations for resuspension and storage of newly received oligonucleotides.

Calculations: Converting from nanograms to copy number—Calculation often used when creating a qPCR standard curve. Link to free, online tool that will do it for you.

Troubleshooting polyacrylamide gel electrophoresis (PAGE)—Review this extensive troubleshooting guide for the PAGE issues our gel electrophoresis team has encountered during their work.

Review other articles on oligonucleotide handling and oligonucleotide modification.

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

Author: Brendan Owens is the manager of the technical support group at IDT.

© 2011, 2016 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.


  1. 12 Kirschbaum 09 Apr
    Howdy! I know this is kinda off topic however I'd figured I'd ask. Would you be interested in exchanging links or maybe guest writing a blog post or vice-versa? My site addresses a lot of the same topics as yours and I believe we could greatly benefit from each other. If you are interested feel free to shoot me an email. I look forward to hearing from you! Terrific blog by the way!
  2. 11 Heady 22 May
    The high graphic games that we play οn our computer ɑre all efforts οf these tedams annd organizations. Τɦiѕ cɑn channelize ߋut tο bе a real outgo operative adventure оn the mօve of tthe application developer. Ӊowever the question stіll remains іf they will stand their ߋwn on tҺe console market.
  3. 10 Gann 22 May
    Also, playing thesе games on a ѕmall screen mіght seem much lеss appealing fߋr thoѕe ԝho агe used to high-quality graphics and playing on a muϲh larger TV օr PC screen. Ιt іs haas alгeady Ƅecome a great market hitter аnd is a business industry macho. Ңowever tthe quesstion ѕtill remains іf thеy will stand thеir own оn the console market.
  4. 9 Malizia 23 May
    NUMΒER #6: ASSASSIN'S CREED BROTHERHOOD (RELEASED NOVEMBER 16, 2010). Ԝe ϲan play our оwn favorite games, оn оur very own Mobile Phones. Ƭhis game hаs to gеt а rating 4 out of 5 fоr a retro experience ѡith а modern twist.
  5. 8 Threlkeld 23 May
    Hello my loved one! I wish to say that this article is awesome, nice written and include almost all significant infos. I'd like to peer extra posts like this .
  6. 7 McMurray 30 May
    However, many websites have forgoten this fact and made intricate designs outt of it, such as using darrk font colors aagainst dark background or white font color with light background. My office products store was one of those twelve thousand office supply stores. Therefore, it iss eminent for all online entities to develop their website in the most user friendly manner.
  7. 6 Cardin 31 May
    Those whoo are looking for the ultimate experience can traavel furtther offsite to engage in corporate team building. Our Website Design Delhi packages are nominal combining all the best web services along witth the excellent technical supportt for any queries. Be it hand-sketch designing, computer-generated layout or snapped photograph, the image gallery should seamlessly integrate with corporate identity and enhance its brand appeal.
  8. 5 Kemper 02 Jun
    Aw, this was an exceptionally nice post. Spending some time and actual effort to create a very good article… but what ccan I say… I procrastinate a whole lot and nerver manage to get anything done.
  9. 4 Ely 05 Jun
    Thanks for your personal marvelous posting! I definitely enjoyed reading it, you may be a great author.I will make certain to bookmark your blog and will often come back someday. I want to encourage continue your great work, have a nice holiday weekend!
  10. 3 Knaggs 07 Jun
    For most recent news you have to go to see web and on the web I found this site as a finest website for most recent updates.
  11. 2 Villagomez 09 Jun
    Truly no matter if someone doesn't know afterward its up to other people that they will assist, so here it takes place.
  12. 1 Kaleski 14 Jun
    During the 2008 presidential campaign, Barack Obama described his proposed federal income tax cuts for the middle class as 'sharing the wealth' Taxation is a form of government interference in the market. The industry or business, who have to send lots of parcels and containers according to orders, then these printers may become a big help for them. Lisa Lia scanned her satellite link, downloaded a poem from a Yahoo site in Hong Kong, and erased the link.

The OligoAnalyzer® Tool

Learn everything you need to know about your primers—Tm, hairpins, mismatches, and more.

Try it now ≫

Related Articles

DNA Oligonucleotide Resuspension and Storage

Guidelines and recommendations for how to resuspend and store newly synthesized oligonucleotides.

Read more ≫

Annealing Oligonucleotides

Tips on making double-stranded DNA from single-stranded, complementary oligonucleotides.

Read more ≫

Calculation Tips for Resuspending and Diluting Nucleic Acids

Easy guidelines for making a 100 µM solution; calculating nmoles, µg, copy number, and concentration; and determining concentration equivalencies.

Read more ≫

Calculations: Converting from Nanograms to Copy Number

Link to a free, online tool that will help you do this calculation often used when creating a qPCR standard curve.

Read more ≫

Understanding Melting Temperature

Advice on considerations for better oligo design: oligo concentration, salt, and SNPs.

Read more ≫