RNA vs DNA
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.
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.
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.
Following 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.
Author: Brendan Owens is the manager of the technical support group at IDT.
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