Custom RNA synthesis

Create and order RNA molecules with a wide variety of chemical modifications or learn about our capabilities for long RNA oligos, dye labeling and custom amidites. These tools are for ordering RNA and RNA-DNA chimeras only. Order custom DNA from here.

Single-strand RNA Synthesis

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  

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 Technical Support for more information.

Dharmacon routinely synthesizes RNA oligonucleotides of 80 nt and longer and consistently obtains superior levels of purity.

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.

Purified 99-mer with 5'-Fluorescein

Dharmacon RNA synthesis capabilities support the routine synthesis of long, chemically modified RNA oligonucleotides. UPLC and LC-MS analysis demonstrate the standard level of purity obtained.

The chemistry experts at Dharmacon can customize RNA phosphoramidites to accommodate your unique requests.

When you need a non-standard chemical modification or modified nucleobase that is not available online, we may still be able to help.

To learn more about our capabilities for custom amidite synthesis and to determine feasibility for your project, please contact Technical Support. You may also request a quote using our online submission form.

If contacting our scientists by email, please consider including a chemical structure or an attached publication where your request is described - this will help our chemists determine feasibility and will help to facilitate a more timely response.

How today's scientists use RNA oligos:

Single-strand RNA may be used for:
Custom microRNA inhibitors
Aptamers
Ribozymes
tRNAs
FISH/ISH probes
FRET probes
RNA/DNA hybrids
Custom RNA duplexes
Dicer substrates
Antisense oligos
Enzyme substrates
Applications for RNA may involve:
in vitro or in vivo applications
Virology
miRNA functional studies
X-ray crystallography, NMR
RNAi
Transcription / translation
Assay development
Microarrays
RNA-mediated cellular mechanisms
RNA/protein interactions
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 for deprotection of 2'-ACE protected RNA.

The 2'-protecting groups are completely removed using aqueous buffers in less than 30 minutes. Please see our deprotection protocol for step-by-step instructions.

*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*
DY547 548 562 Cy3, Alexa 546, Alexa 555 both*
TAMRA 565 580 - both*
DY647 645 662 Cy5, Alexa 647 both*
DY677 684 698 CY5.5, Alexa 680 both*
Cy3 547 563 - both*
Cy5 646 662 - both*
Cy5.5 688 707 - both*

In addition to fluorescent dyes, we offer a broad portfolio of other chemical modifications that can be applied to both siRNA and single-strand RNA.

NOTE: Not all modifications are available through online ordering tool.
For assistance please contact Technical Support.

We offer a wide array of oligonucleotide modifications for your specific custom synthesis applications. Scroll through RNA type and position below for online ordering availability.

NOTE: Not all modifications are available through online ordering tool. For assistance please contact Technical Support.

Filter by:

  • siRNA
  • ssRNA
  • ssRNA-3'
  • ssRNA-Internal
  • ssRNA-5'
  • miRNA
  • SHOW ALL

Showing modifications available for:

  • siRNA
  • ssRNA
  • ssRNA-3'
  • ssRNA-Internal
  • ssRNA-5'
  • miRNA
  • All
Standard RNA Bases Short Code 0.05 µmol 0.2 µmol 0.4 µmol 1.0 µmol 2.0 µmol
(A,C,G,U) A,C,G,U $6.10 $7.75 $12.90 $17.00 $26.00
2'-Omethyl RNA Bases Short Code 0.05 µmol 0.2 µmol 0.4 µmol 1.0 µmol 2.0 µmol
2'-OMe RNA Bases (A, C, G, U) mA,mC,mG,mU $6.10 $7.75 $12.90 $17.00 $26.00
Standard DNA Bases Short Code 0.05 µmol 0.2 µmol 0.4 µmol 1.0 µmol 2.0 µmol
2'-Deoxy Bases (A, C, G, T) dA,dC, dG, dT $6.10 $7.75 $12.90 $17.00 $26.00
Base Modifications Short Code 0.05 µmol 0.2 µmol 0.4 µmol 1.0 µmol 2.0 µmol
1-Methyl-guanosine m1G $73.00 $80.00 $90.00 $115.00 $200.00
2,6-Diaminopurine DAP $90.00 $95.00 $105.00 $135.00 $230.00
2-Methyl-adenosine m2A $75.00 $93.00 $105.00 $130.00 $230.00
2-Aminopurine 2AP $75.00 $93.00 $105.00 $130.00 $230.00
4-Thio-uridine 4-S-U $100.00 $130.00 $145.00 $180.00 $320.00
5-Bromo-Uridine U[5Br] $73.00 $80.00 $90.00 $115.00 $200.00
5-Fluoro-cytidine C[5F] $73.00 $80.00 $90.00 $115.00 $200.00
5-Fluoro-uridine U[5F] $73.00 $80.00 $90.00 $115.00 $200.00
5-Iodo-uridine U[5I] $73.00 $80.00 $90.00 $115.00 $200.00
5-Methyl-cytidine 5-M-C $73.00 $80.00 $90.00 $115.00 $200.00
5-Methyl-Deoxycytidine 5-M-dC $73.00 $80.00 $90.00 $115.00 $200.00
5-Methyl-uridine rT $73.00 $80.00 $90.00 $115.00 $200.00
Inosine I $30.00 $32.00 $42.00 $58.00 $100.00
N2-Methyl-guanosine m2G $250.00 $350.00 $550.00 $900.00 $1600.00
N3-Methyl-uridine 3-M-U $73.00 $80.00 $90.00 $115.00 $200.00
N6,N6-Dimethyl-adenosine DMA $75.00 $93.00 $105.00 $130.00 $230.00
N6-Methyl-adenosine m6A $73.00 $80.00 $90.00 $115.00 $200.00
O6-Methyl-guanosine O6mG $85.00 $105.00 $125.00 $145.00 $270.00
Pseudouridine ~U $90.00 $95.00 $105.00 $135.00 $230.00
Purine ribonucleoside Pu $73.00 $80.00 $90.00 $115.00 $200.00
Pyrrolo-cytidine pC $90.00 $95.00 $105.00 $135.00 $230.00
Ribavirin RBV $73.00 $80.00 $90.00 $115.00 $200.00
Backbone modifications Short Code 0.05 µmol 0.2 µmol 0.4 µmol 1.0 µmol 2.0 µmol
Phosphorothioate * $8.00 $13.00 $15.00 $20.00 $29.00
Phosphorylation Short Code 0.05 µmol 0.2 µmol 0.4 µmol 1.0 µmol 2.0 µmol
5'-Phosphate 5'-P $45.00 $52.00 $63.00 $78.00 $135.00
2'-Modifications Short Code 0.05 µmol 0.2 µmol 0.4 µmol 1.0 µmol 2.0 µmol
2'-Amino-butyryl-pyrene-uridine 2'-P-U $100.00 $130.00 $145.00 $180.00 $320.00
2'-Amino-cytidine 2'-N-C $75.00 $93.00 $105.00 $130.00 $230.00
2'-Amino-uridine 2'-N-U $73.00 $80.00 $90.00 $115.00 $200.00
2'-Deoxy-uridine dU $30.00 $32.00 $42.00 $58.00 $100.00
2'-Fluoro-adenosine 2'-F-A $58.00 $60.00 $85.00 $87.00 $160.00
2'-Fluoro-cytidine 2'-F-C $40.00 $43.00 $57.00 $65.00 $100.00
2'-Fluoro-guanosine 2'-F-G $58.00 $60.00 $85.00 $87.00 $160.00
2'-Fluoro-uridine 2'-F-U $40.00 $43.00 $57.00 $65.00 $100.00
2'-OMe-inosine mI $73.00 $80.00 $90.00 $115.00 $200.00
Amino Modifiers Short Code 0.05 µmol 0.2 µmol 0.4 µmol 1.0 µmol 2.0 µmol
3'-Amino modifier C12 N12-3' $100.00 $130.00 $145.00 $180.00 $320.00
3'-Amino modifier C6 N6-3' $100.00 $130.00 $145.00 $180.00 $320.00
3'-Amino modifier C3 N3-3' $45.00 $52.00 $63.00 $78.00 $135.00
5'-Amino modifier C12 N12 $75.00 $93.00 $105.00 $130.00 $230.00
5'-Amino modifier C3 N3 $73.00 $80.00 $90.00 $115.00 $200.00
5'-Amino modifier C5 N5 $73.00 $80.00 $90.00 $115.00 $200.00
5'-Amino modifier C6 N6 $73.00 $80.00 $90.00 $115.00 $200.00
5-Aminohexylacrylamino-uridine 5-LC-N-U $100.00 $130.00 $145.00 $180.00 $320.00
Thiol Modifiers Short Code 0.05 µmol 0.2 µmol 0.4 µmol 1.0 µmol 2.0 µmol
3'-Disulfide thiol-modifier S-S-3' $100.00 $130.00 $145.00 $180.00 $320.00
5'-Disulfide thiol-modifier S-S $100.00 $130.00 $145.00 $180.00 $320.00
Spacer Modifiers Short Code 0.05 µmol 0.2 µmol 0.4 µmol 1.0 µmol 2.0 µmol
C18 Spacer 18S $30.00 $32.00 $42.00 $58.00 $100.00
C3 Spacer C3 $30.00 $32.00 $42.00 $58.00 $100.00
C9 Spacer 9S $30.00 $32.00 $42.00 $58.00 $100.00
dSpacer dab $75.00 $93.00 $105.00 $130.00 $230.00
rSpacer rab $75.00 $93.00 $105.00 $130.00 $230.00
Chain Terminators Short Code 0.05 µmol 0.2 µmol 0.4 µmol 1.0 µmol 2.0 µmol
3' Inverted abasic b $45.00 $52.00 $63.00 $78.00 $135.00
3' Inverted deoxy-thymidine idT-3' $45.00 $52.00 $63.00 $78.00 $135.00
3'-Terminal 3'-Deoxy-Guanosine 3'dG $55.00 $80.00 $90.00 $120.00 $180.00
3'-Terminal dideoxy-cytidine ddC $75.00 $93.00 $105.00 $130.00 $230.00
5' Inverted deoxy-thymidine idT $30.00 $32.00 $42.00 $58.00 $100.00
5' Terminal 5'-deoxy-ribo-adenosine 5'dA $30.00 $32.00 $42.00 $58.00 $100.00
5' Terminal 5'-deoxy-ribo-cytidine 5'dC $30.00 $32.00 $42.00 $58.00 $100.00
5' Terminal 5'-deoxy-ribo-guanosine 5'dG $30.00 $32.00 $42.00 $58.00 $100.00
5' Terminal 5'-deoxy-ribo-uridine 5'dU $30.00 $32.00 $42.00 $58.00 $100.00
Labeling Short Code 0.05 µmol 0.2 µmol 0.4 µmol 1.0 µmol 2.0 µmol
3-Biotin 3'-Bi $75.00 $95.00 $105.00 $130.00 $190.00
3'-Cholesterol 3'-Chl $110.00 $145.00 $165.00 $210.00 $365.00
3'-Cy3 Cy3-3' $85.00 $105.00 $125.00 $145.00 $270.00
3'-Cy5 Cy5-3' $85.00 $105.00 $125.00 $145.00 $270.00
3'-Cy5.5 Cy5^5-3' $85.00 $105.00 $125.00 $145.00 $270.00
3'-DY547 (Cy3 Alternative) DY547-3' $145.00 $160.00 $215.00 $250.00 $400.00
3'-Fluorescein 3'-Fl $75.00 $93.00 $105.00 $130.00 $230.00
3'-Biotin LC 3'-LCBi $110.00 $145.00 $165.00 $210.00 $365.00
3'-Biotin LC LC 3'-2LCBi $110.00 $145.00 $165.00 $210.00 $365.00
3'-Puromycin Pmn $45.00 $52.00 $63.00 $78.00 $135.00
3'-TAMRA 3'-TAM $165.00 $200.00 $240.00 $265.00 $460.00
5'-Biotin Bi $90.00 $95.00 $105.00 $155.00 $270.00
5'-Cholesterol Chl $110.00 $145.00 $165.00 $210.00 $365.00
5'-Cy3 Cy3 $75.00 $95.00 $115.00 $135.00 $250.00
5'-Cy5 Cy5 $75.00 $95.00 $115.00 $135.00 $250.00
5'-Cy5.5 Cy5^5 $75.00 $95.00 $115.00 $135.00 $250.00
5'-Dabcyl Dabcyl $100.00 $130.00 $145.00 $180.00 $320.00
5-DY547 (Cy3 Alternative) DY547 $125.00 $135.00 $150.00 $190.00 $325.00
5'-DY647 (Cy5 Alternative) DY647 $145.00 $160.00 $185.00 $270.00 $465.00
5'-DY677 (Cy5.5 Alternative) DY677 $200.00 $225.00 $245.00 $300.00 $500.00
5'-Fluorescein Fl $90.00 $95.00 $105.00 $135.00 $230.00
5'-Pyrene 5'-Pyr $115.00 $155.00 $190.00 $240.00 $460.00
5'-TAMRA TAM $165.00 $200.00 $240.00 $265.00 $460.00
5'-TET TET $75.00 $93.00 $105.00 $130.00 $230.00
Degenerate Bases Short Code 0.05 µmol 0.2 µmol 0.4 µmol 1.0 µmol 2.0 µmol
Pricing shown is for first degenerate base coupling, subsequent additions at standard base pricing
dN dN $45.00 $52.00 $63.00 $78.00 $135.00
dS dS $45.00 $52.00 $63.00 $78.00 $135.00
dW dW $45.00 $52.00 $63.00 $78.00 $135.00
mN mN $45.00 $52.00 $63.00 $78.00 $135.00
rN rN $45.00 $52.00 $63.00 $78.00 $135.00
rS rS $45.00 $52.00 $63.00 $78.00 $135.00
rW rW $45.00 $52.00 $63.00 $78.00 $135.00

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 Technical 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.