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Custom siRNA synthesis

siRNA customization has never been easier

No pre-designed product to fit your needs? Our Dharmacon™ online design tools and extensive synthesis options make it simple to create a custom siRNA tailored to your specific application. Choose from numerous combinations of modifications, synthesis scales, and purification options - all available for convenient online ordering.

siRNA- Single stranded RNA and antisense oligonucleotides

siRNA Ordering Options

How to use the Dharmacon custom siRNA synthesis tool

Learn how to use the Dharmacon custom siRNA synthesis tool to design and order custom siRNA for your research.

Watch the video

​Unparalleled support to design and create chemically complex siRNA

Design and Flexibility 

  • Expert design assistance

    Access to internal siRNA design specialists for complex projects, new modifications, assymetric designs with our Scientific Support team

  • Flexible modifications

    Choose from phosphorothioate linkages, 2'-O-methyl, 2'-fluoro, conjugation handles and fluorescent labels, and more options to enhance stability and function. A full list of modifications available on our web ordering tools can be found at our Bases and Modifications page.

  • Multiple design options

     Blunt-ended, longer duplexes (>23 nt), mismatched strands, and alternative bases or linkages

Proprietary Dharmacon modification patterns

  • Enhanced specificity

    ON-TARGETplus dual-strand modification dramatically reduces off-target effects

  • Improved stability

    siSTABLE and Accell modifications resist nuclease degradation for in vivo applications

  • Transfection-free delivery

    Accell siRNA enables gene silencing in difficult-to-transfect cells without reagents 

  • Guaranteed strand bias

    ON-TARGET modification ensures correct antisense strand uptake by RISC 

Ordering convenience

  • Convenient online ordering

    Numerous combinations of modifications, sizes, and purification options available.

  • Pre-aliquoted plates

    Custom siRNA delivered in ready-to-use 96-well plates to streamline setup.

  • Custom quote options

    Request tailored quotes for specifications not available through online ordering.

Quality & Support

  • Functionally guaranteed SMARTpools

    Our siRNA design experts can provide custom SMARTpools of 4 siRNAs targeting genes outside of our genome-wide offerings.

  • Confident results

    All oligos made by the Dharmacon Reagents team are examined by mass spectrometry. Additionally, ultra-HPLC analytical data and Mass-spec traces are available on request as an additional service.

  • Custom support available

    Request modifications or customized purification and processing beyond the standard catalog or get design guidance from our team. contact our Scientific Support team.

  • Expert siRNA design assistance
    Our capabilities include a range of alternative siRNA designs to empower your RNAi research

    If you are working in human, mouse or rat models, we may already have what you need as a pre-designed product: Search for your gene in the Search field found in the upper right corner. In addition, our siDESIGN Center is an advanced tool that can help identify functional siRNA for your unique needs and create unique sequences against your target of interest. Learn more about the capabilities of the siDESIGN Center with the User Guide.

    Take advantage of our internal design experts and SMARTpool technology! Order a functionally guaranteed Custom SMARTpool for worry-free customization.

    Alternative siRNA designs that we support include:

    • Blunt-ended

    • Asymmetrical

    • Longer duplexes (>23 nt)

    • Mismatched strands

    • Alternative bases or linkages

    If you can't find what you need or you require additional specifications not available through online order, please request a quote. Need additional help? Please contact Scientific Support


  • Extensive Modification Options

    Extensive modification options:

    We offer a wide selection of chemical modifications, including a variety of fluorophores and functional groups. These can be applied to single-strand RNA, DNA, RNA-DNA chimeras, siRNA, ASO, and microRNA oligos. Modifications available on our web ordering tools can be found at our Bases and Modifications page.

    Standard modifications offered include:

    • Modified bases such as 2'-O-methyl bases

    • Pseudouridine (~U)

    • Fluorescent labels and quenchers

    • Terminal linkers and functional groups for conjugation chemistries

    • Phosphorothioate backbone modifications (*)


    Oligo labeling options:
    • Labeling modifications (internal and/or terminal)
      • Fluorescent, dye, quencher, chromogen modifications
    • Terminal Modifications
      • Non-fluorescent terminal modifications, such as cholesterol or biotin, or chemical groups for conjugation.
    • Terminal linkers for modifications such as PEG, carbon linkers, etc
    • Multiple labels within a single oligo - not limited by position
    • Scalable to gram quantities for most -labeled oligos

    View our web-tool enabled Bases and Modifications

    NOTE: Many other modifications are available upon request. The online ordering tools only include a subset of common modifications. For assistance please contact Scientific Support.

    NOTE: siRNA can be modified at either end of either strand. Multiple modifications can be supported, but availability and feasibility may be dependent upon sequence or other factors. Please contact Scientific Support for more information.

    Sense Antisense image

  • Which Dharmacon siRNA chemical modification pattern is right for your research needs?
    Which Dharmacon siRNA chemical modification pattern is right for your research needs?

    Note: All siRNA modifications, proprietary and other, are available through custom siRNA synthesis webtools.

    ON-TARGET ON-TARGETplus Accell siSTABLE
    Inhibits sense (passenger) strand uptake by RISC ✔ ✔ ✔ ✔
    Antisense strand seed region modified for greater specificity to target ✔
    Resistant to endo-and exonuclease degradation ✔ ✔
    Delivery into cells without transfection reagent ✔
    Also available as Pre-designed siRNA ✔ ✔

    ON-TARGET modification ensures antisense strand bias

     

    Custom Sirna Overview1 Figure Lrg image 

     

     

    The ON-TARGET modification promotes correct strand uptake by blocking the sense (passenger) strand from being taken up by the RISC process. This is a useful method for ensuring antisense (guide) strand processing. All proprietary siRNA modifications (ON-TARGETplus, Accell, siSTABLE) incorporate this sense-strand modification to promote antisense (guide) strand-facilitated silencing.


    ON-TARGET modification ensures antisense strand bias

     

    Otp Reduce Off Target Effects Figure Lrg image

     

     

    A 2006 publication demonstrates that off-target effects are primarily driven by antisense strand seed activity.1 Therefore, sense strand inactivation alone does not decrease the total number of off-target genes. ON-TARGETplus modifications account for both strands:

    • Sense strand is modified to prevent interaction with RISC and favor antisense strand uptake
    • Antisense strand seed region is modified to minimize seed-related off-targeting

    The ON-TARGETplus modification pattern dramatically reduces off-targets. Off-target effects induced by the indicated siRNAs were quantified using microarray analysis. For each target, three different siRNAs were used: unmodified, sense strand-inactivated, and ON TARGETplus-modified. Data shown represents genes down-regulated by two-fold or more. HEK293 cells were transfected with 100 nM siRNA using 0.2 µL of DharmaFECT 1. Data was analyzed at 24 hours.

    1 Jackson, A.L. et al. "Position-specific Chemical Modification Increases Specificity of siRNA-mediated Gene Silencing." RNA 12.7 (2006) 1197-1205.
     
    Accell delivery and gene silencing in cardiomyocytes without a transfection reagent

     

    Sirna Accell Nrvm 1 Figure Lrg image

    Neonatal rat ventricular myocytes were incubated with 1 µM Accell Green (A; Cat# D-001950-01) or Red (B; Cat# D-001960-01) Non-targeting siRNA for 72 hours in Accell delivery media (Cat# B-005000). Nuclei were stained with DAPI (blue). Labeled control uptake showed diffuse cytoplasmic localization in nearly all cells.

    The bar graph indicates the level of gene silencing achieved with Accell GAPD Control siRNA (Cat# D-001930-03) and Pool (Cat# D-001930-30) control reagents when used with neonatal rat ventricular myocyte (NRVM) media or Accell delivery media.

    Myocytes were prepared as described in Maass AH & Buvoli M. Cardiomyocyte preparation, culture, and gene transfer. Methods Mol Biol. 2007;366: 321-30. mRNA expression was determined by QuantiGene branched DNA assay (Panomics).

     
    siSTABLE-modified siRNAs resist degradation by nucleases

     

    Sistable Controls Popup1 Figure Lrg image

     

    Conventional siRNA is degraded within minutes in serum-containing environments, making in vivo use of siRNA problematic. This graph presents evidence that the siSTABLE modification pattern dramatically extends the half-life of siRNA in the presence of 100% human serum as compared to Stealth RNAi (Invitrogen).

    Accell siRNA also includes these stability-enhancing modifications, as well as providing delivery to difficult-to-transfect cells without a transfection reagent.

  • In vivo siRNA considerations

    We want your in vivo experiments to have the best chance of success. To assist you in your experimental planning, we offer the following options and guidance:

    Assess your siRNA sequences in vitro

    • We recommend identifying a highly functional siRNA design in vitro prior to initiating expensive experiments using animal models

    • A predesigned set of 4 siRNA reagents is ideal for testing multiple siRNA sequences

    • Individual duplexes: Four individual siRNAs are pre-designed for every gene in human, mouse and rat. Order 1, 2, 3 or 4.

    • SMARTpool™ format: All four siRNAs are pooled together as a single reagent in one tube.

    • Set of Four: All four siRNAs are provided as individual duplexes in four individual tubes.

    Consider siSTABLE or Accell modification patterns for enhanced nuclease resistance
    • siSTABLE modifications prevent degradation from exo- and endonucleases. siSTABLE is recommended when the siRNA will be exposed to a biological environment rich in nucleases, such as animal serum.
    • Accell modifications incorporate delivery-enhancing properties in addition to stability enhancement. Accell is recommended when target cell or tissue types are not amenable to standard modes of delivery.
    • See a list of recent publications using siSTABLE and Accell modified siRNA for in vivo experimentation.
    Carefully calculate the total siRNA quantity required

    • Consider the number of animals in each cohort, the number of treatments or doses that will be required, and the amount of siRNA required for each dose

    • In vivo experiments typically require a large quantity of siRNA. Synthesis capabilities can accommodate up to 10 grams by request, or up to 100 mg available online

    • Need help converting nmol to mg? Check our siRNA yield table.

    Consider in vivo processing of your siRNA when toxicity to the animal is of concern
    • A specialized post-synthesis siRNA processing procedure including counter-ion (Na+) exchange, sterile filtration, desalting, and endotoxin testing
  • Purification and post-processing
    Purification and processing options for siRNA including In vivo use

    We routinely achieve 80-85% purity for unmodified siRNA strands without additional purification.

    However, purification may be recommended when chemically synthesized siRNAs are:

    • Chemically modified at the 3' end or internally

    • Dually modified on the same strand

    • Intended for use in highly sensitive assays or in vivo applications

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

    siRNA processing options
    Single Strands (A1) Standard (A4) HPLC In vivo In vivo HPLC
    Desalted ✔ ✔ ✔ ✔
    Deprotected ✔ ✔ ✔ ✔
    Duplexed ✔ ✔ ✔ ✔
    Purified ✔ ✔
    Endotoxin tested ✔ ✔
    Sodium counter-ion exchange ✔ ✔
    Recommended for modified siRNA (dyes, etc.) ✔ ✔
    Recommended for in vivo use ✔ ✔
    2'ACE protected single-strands ✔
    Glossary of siRNA processing terms

    • Desalted: The siRNA duplex has been desalted by either ethanol precipitation or C18 column desalting

    • Deprotected: The 2'-ACE protecting groups of the RNA bases have been removed (deprotected)

    • Duplexed: The two complementary siRNA strands have been annealed to form a duplex

    • Single-strand (A1): The siRNA is provided with the sense and antisense strands in separate tubes; individual strands have NOT been desalted or deprotected

    • Standard (A4): The siRNA is provided as a desalted & deprotected duplex, ready to use upon resuspension

    • HPLC: The duplex has undergone ion exchange High Performance Liquid Chromatography for purification

    • In vivo: The duplex has been processed by counter-ion (Na+) exchange, desalting, sterile filtration, and endotoxin testing

    • In vivo HPLC: The duplex has undergone both in vivo processing as well as HPLC purification

  • siRNA synthesis yield
    For unmodified siRNA, the following approximate yields can be expected:
    Standard (A4) Standard (A4) HPLC purified HPLC purified in vivo in vivo in vivo HPLC in vivo HPLC
    nmol mg nmol mg nmol mg nmol mg
    0.025 µmol scale 20 0.25 - - - - - -
    0.05 µmol scale 40 0.5 20 0.25 25 .3 - -
    0.2 µmol scale 150 2 80 1 100 1.3 50 0.65
    0.4 µmol scale 300 4 160 2 200 2.6 100 1.3
    1.0 µmol scale 750 10 320 4 500 6.6 250 3.3
    2.0 µmol scale 1500 20 750 10 1000 13 500 6.6
    5.0 µmol scale 3750 50 1875 25 2500 33 1250 16
    10.0 µmol scale 7500 100 3750 50 5000 66 2500 33
  • Additional resources and webtools
    Technical note | In vivo RNAi: Biodistribution, delivery, and applications

    Learn about important considerations for in vivo studies with RNAi

    Learn more

    Need help entering your sequence using our oligo shortcode?

    Try using our Dharmacon Oligo Sequence Converter. 

    Learn more

    Ordering and calculation tools

    Access our Ordering and calculation tools page for convenient webtools to support everything from designing your own siRNA or CRISPR guide against any organism to analyzing your PCR primers.

    Learn more

  • Revvity's adherence with the United States Framework For Nucleic Acid Synthesis Screening

    Revvity's Dharmacon Reagents team adheres to the guidelines in the United States Framework For Nucleic Acid Synthesis. For more information please see our self-attestation.

Featured technical documents

Product Insert

Option A1 custom siRNA synthesis Option A1 custom siRNA synthesis product insert, containing contents, protocol, shipping and storage conditions, handling precautions, etc.

Product Insert

Option A4 custom siRNA synthesis Option A4 custom siRNA synthesis product insert, containing contents, protocol, shipping and storage conditions, handling precautions, etc.

Product Insert

Option in vivo and in vivo HPLC custom siRNA synthesis Dharmacon option in vivo: The siRNA is shipped as a lyophilized pellet in the 2'- deprotected and duplexed form.

Protocol

TCEP reaction for thiol-modified siRNA/RNA oligonucleotides Protocol to deprotect (reduce) oxidized thiol-modified siRNA and RNA oligonucleotides.

Protocol

Basic siRNA resuspension protocol

Protocol

Ethanol precipitation of RNA oligonucleotides This protocol is for Ethanol Precipitation of RNA Oligonucleotides.

Protocol

Reverse phase cartridge desalting of RNA oligonucleotides Protocol for desalting RNA oligos using reverse phase cartridges, including protocol for cartridge equilibration, washing, and eluting from cartridge.

Recommended reading

Publication list highlighting Dharmacon reagent development and collaborations across CRISPR-Cas9, RNAi and oligo synthesis.

Safety data sheets

North American standard safety data sheet for RNA oligonucleotides.

Safety data sheets

North American standard safety data sheet for deprotection buffer.

Safety data sheets

European Union standard safety data sheet for RNA oligonucleotides.

Safety data sheets

European Union standard safety data sheet for deprotection buffer.

How can we help you?

We are here to answer your questions.

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