Single-Strand and Multiple Single-Strand RNA customization has never been easier

No pre-designed product to fit your needs? Use our online design tools and extensive synthesis options to create a custom RNA. Numerous combinations of modifications, sizes, and purification options are available for convenient online ordering. Pricing, days to ship and add to cart are immediately available.

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Order Single-strand RNA           Order Multiple Single-strand RNA

If you need a non-standard chemical modification or modified nucleobase that is not available online, please complete our pricing request form and our Scientific Support team will review and respond.

Dharmacon RNA synthesis capabilities are well beyond the industry standard
  • Long RNA oligos
  • Custom RNA inhibitors for the study of microRNA biology
  • Custom phosphoramidites
  • Specialized chemical modifications or modified bases
  • Larger scales for in vivo and preclinical development  

We offer many standard modifications such as 2’O methyl bases, pseudouridine (~U), Cy fluorescent dyes, black hole quenchers (BHQ), and phosphorothioate backbone modifications (*). Custom phosphoramidite production can be requested when the modified base you require is not commercially available or requires a chemical adaptation for our chemistry platform.

Please contact Scientific Support for more information.


Dharmacon RNA oligonucleotides are routinely synthesized at 80 nt and longer with consistency and superior levels of purity.
purified 99 mer

The ability to synthesize longer oligos is highly sequence-dependent due to the potential for secondary structure formation and the inherent difficulty for chemical synthesis of certain sequences.

Reduced overall yield is expected as oligo length increases.



How today's scientists use RNA oligos
Single-strand RNA may be used for Applications for RNA may involve:
Custom microRNA inhibitors in vitro or in vivo applications
Aptamers Virology
Ribozymes miRNA functional studies
tRNAs X-ray crystallography, NMR
FISH/ISH probes RNAi
FRET probes Transcription / translation
RNA/DNA hybrids Assay development
Custom RNA duplexes Microarrays
Dicer substrates RNA-mediated cellular mechanisms
Antisense oligos RNA/protein interactions
Enzyme substrates RNA chemistry

Single-strand RNA can be shipped in its 2' protected form to improve stability.

As a result of chemical RNA synthesis, all oligonucleotides will have chemical protecting groups at the 2' position of each nucleotide.

2'-ACE chemistry is unique among all others because no other chemistry platform offers the option of delivering the product in the protected form. Some of the benefits of working with 2'-protected RNA include:
  • Perform additional chemical manuipulations to the oligo prior to deprotection
  • Achieve an enhanced nuclease resistance conferred to the final product*
  • Maintain water-solubility and stability during long-term storage
  • Easily remove protecting groups under mildly acidic conditions
Protected RNA must be deprotected prior to use. You have two options for deprotecting your RNA oligos:
  1. Perform the deprotection reaction in your lab (default)
    This is a simple 30 minute procedure, and the deprotection buffer will be provided with your order at no charge. The protocol can be found here.
  2. Choose to have your RNA oligo deprotected prior to shipping
    For a small processing fee you will receive your oligo in the "ready-to-use" state following resuspension. If you wish to have your RNA deprotected by us, simply check the box "2'-Deprotect / Desalt" when placing your order. 
  Acid-catalyzed reaction


Dharmacon offers a broad portfolio of dye modifications for fluorescent labeling of your custom siRNA and RNA oligonucleotides.

  • Include a fluorescent tag at the 3', 5' or internal positions of an RNA oligo
  • Potential for multiple labels within a single oligo not limited by position within the sequence
  • Synthesis of most dye-labeled oligos is scalable to gram quantities

Fluorescent dyes available online:

*Some 3' dye labels are only available upon request.
Fluorophore λ max abs (nm) λ max em (nm) Comparable to 5' or 3'
Fluorescein / 6-FAM 494 520 - both*
TAMRA 565 580 - both*
Cy3 547 563 - both*
Cy5 646 662 - both*
Cy5.5 688 707 - both*

We routinely achieve 80-85% purity for unmodified single-strand RNA <35 nt. However, purification may be recommended when chemically synthesized RNA oligonucleotides are:

  • Especially long (>40-50 nt in length)
  • Chemically modified at the 3' end or internally
  • Dually labeled
  • Intended for use in sensitive assays or in vivo applications

Please contact Scientific Support for information regarding recommendations for purification or purity estimates for unpurified material.

Purification and processing options for RNA

  Unprocessed Desalt/Deprotect PAGE HPLC In vivo In vivo HPLC
Deprotected   * *
Desalted   * *
Endotoxin tested        
Sodium counter-ion exchange        
Recommended for 3' or dually labeled RNA      
Recommended for in vivo use        

* PAGE and HPLC purification options can be requested with or without Desalt / Deprotect

Description of RNA Processing Terms

  • Unprocessed: The RNA oligo has not undergone any post-synthesis processing; it is not desalted, deprotected, or purified.
  • Desalted: The RNA oligo has been desalted by either ethanol precipitation or C18 column desalting; column desalting is typically employed for PAGE-purified RNA and RNA <10 nt in length.
  • Deprotected: The 2'-ACE protecting groups of the RNA bases have been removed (deprotected).
  • PAGE: The RNA oligo has been purified by polyacrylamide gel electrophoresis.
  • HPLC: The RNA oligo has undergone ion exchange high performance liquid chromatography for purification.
  • In vivo: The RNA oligo has been processed by counter-ion (Na+) exchange, desalting, sterile filtration, and endotoxin testing.
  • In vivo HPLC: The RNA oligo has undergone both in vivo processing as well as HPLC purification.