NOTE: These tools are for ordering RNA and RNA-DNA chimeras only
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.
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.
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.
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.
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.
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.
Dharmacon offers a broad portfolio of dye modifications for fluorescent labeling of your custom siRNA and RNA oligonucleotides.
Some of the dye options listed in the above tables will produce higher oligo yields than others. For assistance in choosing the most appropriate dye label for your application, please contact Technical Support.You can also request a quote online if you already know that an alternative dye will be required for your experiments.
Alexa Fluor® is a registered trademark of Invitrogen Corporation.
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.
We routinely achieve 80-85% purity for unmodified single-strand RNA <35 nt. However, purification may be recommended when chemically synthesized RNA oligonucleotides are:
Please contact Technical Support for information regarding recommendations for purification or purity estimates for unpurified material.
An NHS ester is a reactive group found on the dye that provides the functionality for labeling amino groups found on the oligonucleotide.
Some DyLight dyes are available as phosphoramidites (our standard dyes), and others as NHS esters (our non-standard Alexa alternatives). If applicable, we recommend DyLight dyes as a first choice since this form is most compatible with our 2'-ACE RNA synthesis chemistry and will therefore be more likely to produce higher yields.
Description: Fluorescein is often used in fluorescence experiments to demonstrate the kinetics of folding or substrate binding. Fluorescein is also used as a donor to track optimal changes related to folding or substrate binding to intermolecular interactions.
Reference: Science 266: 785-789 (1994), EMBO J. 17: 2378-2391 (1998)
For more information please contact:Technical Support
00800-222 00 888
+44 (0) 845 3 63 04 25 (UK / EMEA)
Description: TAMRA is a strongly absorbing dye with a wide variety of applications. This modification is coupled from the 5'- or 3'-end of an oligonucleotide to either the 5th or 6th position of the dye.
References: Nucl. Acids. Res. 24: 4535-4542 (1996), Biochem. 39: 14487-14484 (2000)
Modification Code: Cy3
Unit Molecular Weight: 507.59 g/mol
Cy3 Extinction Coefficient: 136,000
Excitation/Emission Max: 547 nm/563 nm
Modification Code: Cy3-3’
Unit Molecular Weight: 800.85 g/mol
Modification Code: Cy5
Unit Molecular Weight: 533.63 g/mol
Cy5 Extinction Coefficient: 250,000
Excitation/Emission Max: 646 nm/662 nm
Modification Code: Cy5-3’
Unit Molecular Weight: 826.88 g/mol
Modification Code: Cy5^5
Unit Molecular Weight: 633.75 g/mol
Cy5.5 Extinction Coefficient: 209,000
Excitation/Emission Max: 688 nm/707 nm
Modification Code: Cy5^5-3’
Unit Molecular Weight: 927.00 g/mol