Dharmacon Custom RNA synthesis

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. 

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   5'-Fluorescein 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. Mol. Wt.: 537.46 Special Note: Light sensitive. Fluorescein is very sensitive to photo bleaching. Absorbance/Fluorescence: 494/520 nm Reference: Science 266: 785-789 (1994), EMBO J. 17: 2378-2391 (1998)	494	520		-	both*
TAMRA   5'-TAMRA-hexyl linker 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. Special Note: Light sensitive Absorbance/Fluorescence: 565/580 nm References: Nucl. Acids. Res. 24: 4535-4542 (1996), Biochem. 39: 14487-14484 (2000)	565	580		-	both*
Cy3   Modification Name: 5’-Cy3 Modification Code: Cy3 Unit Molecular Weight: 507.59 g/mol Cy3 Extinction Coefficient: 136,000 Excitation/Emission Max: 547 nm/563 nm Unit Structure: Modification Name: 3’-Cy3 Modification Code: Cy3-3’ Unit Molecular Weight: 800.85 g/mol Cy3 Extinction Coefficient: 136,000 Excitation/Emission Max: 547 nm/563 nm Unit Structure:	547	563		-	both*
Cy5   Modification Name: 5’-Cy5 Modification Code: Cy5 Unit Molecular Weight: 533.63 g/mol Cy5 Extinction Coefficient: 250,000 Excitation/Emission Max: 646 nm/662 nm Unit Structure: Modification Name: 3’-Cy5 Modification Code: Cy5-3’ Unit Molecular Weight: 826.88 g/mol Cy5 Extinction Coefficient: 250,000 Excitation/Emission Max: 646 nm/662 nm Unit Structure:	646	662		-	both*
Cy5.5   Modification Name: 5’-Cy5.5 Modification Code: Cy5^5 Unit Molecular Weight: 633.75 g/mol Cy5.5 Extinction Coefficient: 209,000 Excitation/Emission Max: 688 nm/707 nm Unit Structure: Modification Name: 3’-Cy5.5 Modification Code: Cy5^5-3’ Unit Molecular Weight: 927.00 g/mol Cy5.5 Extinction Coefficient: 209,000 Excitation/Emission Max: 688 nm/707 nm Unit Structure:	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

* 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.