Custom RNA synthesis

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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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.

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Need Custom DNA?

Use our convenient tools to order the custom DNA oligo that fits your needs.

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.

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:

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.
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*

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Standard RNA Bases	Short Code	0.05 µmol	0.2 µmol	0.4 µmol	1.0 µmol	2.0 µmol
(A,C,G,U) Standard RNA Bases (A, C, G, U) Modification Code: rA, rC, rG, rU Unit Structure: Unit Molecular Weight: rA (329.21) rG (345.21) rC (305.18) rU (306.17)	A,C,G,U	$6.63	$8.36	$13.97	$18.36	$28.15
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) 2'-OMe RNA Bases (A, C, G, U) Modification Code: mA, mC, mG, mU Description: The naturally occurring 2'-O-methyl (2'-OMe) modification is the first and most extensively tested 2'-substitutions; 2'-OMe slightly enhances the binding affinity toward RNA (Tm increase of 0.5-0.7°C per modification). 2'-OMe modification has been extensively used to generate fully functional siRNAs with higher nuclease resistance, reduced siRNA immunogenicity, and less off-targeting. Unit Structure: Unit Molecular Weight: mA (343.24) mC (319.21) mG (359.23) mU (320.19) References: Soutschek, J. et al. Therapeutic silencing of an endogenous gene by systemic administration of modified siRNAs. Nature, 432, 173-178 (2004). Allerson, C. R. et al. Fully 2'-modified oligonucleotide duplexes with improved in vitro potency and stability compared to unmodified small interfering RNA. J. Med. Chem, 48, 901-904 (2005).	mA,mC,mG,mU	$6.63	$8.36	$13.97	$18.36	$28.15
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) 2'-Deoxy Bases (A, C, G, T) Modification Code: dA, dC, dG, dT Description: DNA modification, typically dTdT, has long been the industry standard for modifying siRNA 3'-overhang, while conferring nuclease resistance and preserving siRNA potency. DNA is well-tolerated in the passage strand with little effects on siRNA potency. Only partially DNA substituted guide strands are functional, whereas alternating the DNA modification with 2'-f has created fully substituted, active guide strands. Unit Structure: Unit Molecular Weight: dA (313.21) dC (289.18) dG (329.21) dT (304.19) References: Elbashir, S. M. et al. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. I, 411, 494-498 (2001). Chiu, Y. L. and Rana, T. M. siRNA function in RNAi: a chemical modification analysis. RNA, 9, 1034-1048 (2003).	dA,dC, dG, dT	$1.15	$2.30	$3.20	$5.10	$8.30
Base Modifications	Short Code	0.05 µmol	0.2 µmol	0.4 µmol	1.0 µmol	2.0 µmol
1-Methyl-guanosine 1-Methyl-guanosine Modification Code: m1G Unit Structure: Unit Molecular Weight: 359.23 References: Agris, P. F. et al. Site-selective introduction of modified purine and pyrimidine ribonucleosides into RNA by automated phosphoramidite chemistry. Biochimie 77, 125-134 (1995).	m1G	$74.46	$81.60	$91.80	$117.30	$204.00
2,6-Diaminopurine 2,6-Diaminopurine Modification Code: DAP Description: 2,6-Diaminopurine (2-aminoadenine, DAP) is an adenine analog which can be found in S-2L cyanophage DNA where 2,6-diaminopurine is completely substituted for adenine. Studies have shown that DAP in DNA is compatible with normal DNA function. The DAP-T base pair possesses an extra hydrogen bond compared with A-T because of the additional -NH₂ pointing toward the minor groove of DNA. DAP is a common tool in nucleic acid chemistry which can be used to study molecular recognition between DNA or RNA and ligands, both small and large. Double-stranded siRNAs having DAP modification incorporated into the antisense strand were capable of inducing RNAi activity. Unit Structure: Unit Molecular Weight: 344.22 References: Cheong, C. et al. Thermodynamic studies of base pairing involcing 2,6-diaminopurine. Nucleic Acids Res. 16, 5115-5122 (1988). Bailey, C and Waring, M. J. The use of diaminopurine to investigate structural properties of nucleic acids and molecular recognition between ligands and DNA. Nucleic Acids Res. 26, 4309-4314 (1998). Chiu, Y. and Rana, T. M. siRNA function in RNAi: a chemical modification analysis. RNA 9, 1034-1048 (2003).	DAP	$91.80	$96.90	$107.10	$137.70	$234.60
2-Methyl-adenosine 2-Methyl-adenosine Modification Code: m2A Unit Structure: Unit Molecular Weight: 343.24 References: Agris, P. F. et al. Site-selective introduction of modified purine and pyrimidine ribonucleosides into RNA by automated phosphoramidite chemistry. Biochimie 77, 125-134 (1995).	m2A	$76.50	$94.86	$107.10	$132.60	$234.60
2-Aminopurine 2-Aminopurine Modification Code: 2AP Description: 2-Aminopurine (2AP) is a fluorescent analog of guanosine and adenosine. Because 2AP can base pair with uridine, it can replace normal A:U pairs without substantial deformation of duplexes. 2-Aminopurine is widely used in biochemical settings as a site-specific fluorescent probe of DNA and RNA structure and base-flipping and -folding. Unit Structure: Unit Molecular Weight: 329.21 References: Hall, K. B. 2-Aminopurine as a probe of RNA conformational transition. Methods Enzymol. 469, 269-285 (2009).	2AP	$76.50	$94.86	$107.10	$132.60	$234.60
4-Thio-uridine 4-Thio-uridine Modification Code: 4-S-U Description: 4-Thio-uridine (s4U) is a thiol-modified ribonucleoside, and is typically used to modify oligos slated for RNA, or RNA-protein, structural studies. Because 4-thio-rU is photoreactive, 4-thio-rU modified RNA oligonucleotides can be used as photoaffinity probes in the role of substrate analogs for characterizing the enzyme:substrate complex. In addition, because the thiol group is chemically reactive, other moieties can be conjugated at the thiol group of 4-thio-rU. Such a strategy was used to introduce spin labels to 4-thio-rU-containing RNA oligonucleotides. Unit Structure: Unit Molecular Weight: 322.23 References: Kumar R. K. and Davis, D. R. Synthesis and studies on the effect of 2-thiouridine and 4-thiouridine on sugar conformation and RNA duplex stability. Nucleic Acids Res. 25, 1272-1280 (1997). Yu, Y. T. Site-specific 4-thiouridine incorporation into RNA molecules. Methods Enzymol. 318, 71-88 (2000). Rublack, N. et al. Synthesis of specifically modified oligonucleotides for application in structural and functional analysis of RNA. J. Nucleic Acids 1-19 (2011).	4-S-U	$102.00	$132.60	$147.90	$183.600	$326.40
5-Bromo-Uridine 5-Bromo-uridine Modification Code: U[5Br] Description: Halogenated nucleosides are used to crosslink oligonucleotides to DNA, RNA, and proteins. They are also used to investigate structures via x-ray diffraction and NMR. Modifications such as 5-bromo-uridine that stabilize base-pairing interactions can be used in designing siRNAs for various applications. Unit Structure: Unit Molecular Weight: 385.06 References: Zeng, Y. and Wang, Y. Sequence-dependent formation of intrastrand crosslink products from the UVB irradiation of duplex DNA containing a 5-bromo-2'-deoxyuridine or 5-bromo-2'-deoxycytidine. Nucleic Acids Res. 34, 6521-6529 (2006). Javed, A. et al. In situ immunofluorescence analysis: analyzing RNA synthesis by 5-bromouridine-5'-triphosphate labeling. Methods Mol. Biol. 285, 29-31 (2004). Chiu, Y. and Rana, T. M. siRNA function in RNAi: a chemical modification analysis. RNA 9, 1034-1048 (2003).	U[5Br]	$74.46	$81.60	$91.80	$117.30	$204.00
5-Fluoro-cytidine 5-Fluoro-cytidine Modification Code: C[5F] Description: Halogenated nucleosides are used to crosslink oligonucleotides to DNA, RNA, and proteins. They are also used to investigate structures via x-ray diffraction and NMR. Unit Structure: Unit Molecular Weight: 323.17 References: Puffer, B. et al. 5-Fluoro pyrimidines: labels to probe DNA and RNA secondary structures by 1D 19F NMR spectroscopy. Nucleic Acids Res. 37, 7728-7740 (2009).	C[5F]	$74.46	$81.60	$91.80	$117.30	$204.00
5-Fluoro-uridine 5-Fluoro-uridine Modification Code: U[5F] Description: Halogenated nucleosides are used to crosslink oligonucleotides to DNA, RNA, and proteins. They are also used to investigate structures via x-ray diffraction and NMR. Unit Structure: Unit Molecular Weight: 324.16 References: Ferrer-Orta, C. et al. Sequential structures provide insight into the fidelity of RNA replication. Proc. Natl. Acad. Sci. USA 104, 9463-9468 (2007). Puffer, B. et al. 5-Fluoro pyrimidines: labels to probe DNA and RNA secondary structures by 1D ¹⁹F NMR spectroscopy. Nucleic Acids Res. 37, 7728-7740 (2009).	U[5F]	$74.46	$81.60	$91.80	$117.30	$204.00
5-Iodo-uridine 5-Iodo-uridine Modification Code: U[5I] Description: Halogenated nucleosides are used to crosslink oligonucleotides to DNA, RNA, and proteins. They are also used to investigate structures via x-ray diffraction and NMR. Modifications such as 5-iodo-uridine that stabilize base-pairing interactions can be used in designing siRNAs for various applications. Unit Structure: Unit Molecular Weight: 432.06 References: Stump, W. T. and Hall, K. B. Crosslinking of an iodo-uridine-RNA hairpin to a single site on the human U1A N-terminal RNA binding domain. RNA 1, 55-63 (1995). Chiu, Y. and Rana, T. M. siRNA function in RNAi: a chemical modification analysis. RNA 9, 1034-1048 (2003).	U[5I]	$74.46	$81.60	$91.80	$117.30	$204.00
5-Methyl-cytidine 5-Methyl-cytidine Modification Code: 5-M-C Description: The nucleobase modification 5-methylcytosine (5-mC) is widespread both in DNA and different cellular RNAs. In tRNA, 5-mC sites are typically located around the variable region and anticodon loop and research has shown that tRNA methylation stabilizes tRNA secondary structure, affects aminoacylation and codon recognition, and confers metabolic stability. Additionally, ribosomal RNA methylation was shown to be involved in translational fidelity and tRNA recognition. 5-Methyl-cytosine enhances DNA or RNA duplex stability by elevating melting temperature 0.5 - 1.3°C per addition. Unit Structure: Unit Molecular Weight: 319.21 References: Motorin, Y. et al. 5-Methylcytosine in RNA: detection, enzymatic formation and biological functions. Nucleic Acids Res. 38, 1415-1430 (2010). Squires, J. E. et al. Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA. Nucleic Acids Res. 40, 5023-5033 (2012).	5-M-C	$74.46	$81.60	$91.80	$117.30	$204.00
5-Methyl-Deoxycytidine 5-Methyl-deoxycytidine Modification Code: 5-M-dC Description: The nucleobase modification 5-methylcytosine (5-mC) is widespread both in DNA and different cellular RNAs. 5-Methyl-cytosine enhances DNA or RNA duplex stability by elevating melting temperature 0.5 - 1.3°C per addition. Unit Structure: Unit Molecular Weight: 303.21 References: Freier, S. M. and Altmann, K.-H. The ups and downs of nucleic acid duplex stability: structure-stability studies on chemically modified DNA:RNA duplexes. Nucleic Acid Res. 25, 4429-4443 (1997).	5-M-dC	$74.46	$81.60	$91.80	$117.30	$204.00
5-Methyl-uridine 5-Methyl-uridine Modification Code: rT Description: 5-Methyluridine, also called ribothymidine, is the ribonucleoside counterpart to the deoxythymidine. Substitution of 5-methyluridine in siRNA guide strand results in gene silencing activities comparable to or better than that of wide-type siRNA. Such major groove modifications also increase the serum stability of siRNAs. Unit Structure: Unit Molecular Weight: 335.23 References: Motorin, Y. and Helm, M. RNA nucleotide methylation. Wiley Interdiscip. Rev. RNA 2, 611-631 (2011). Terrazas, M. and Kool, E. T. RNA major groove modifications improve siRNA stability and biological activity. Nucleic Acid Res. 37, 346-353 (2009).	rT	$74.46	$81.60	$91.80	$117.30	$204.00
Inosine Inosine Modification Code: I Description: The most commonly used degenerate modified base is inosine, which serves as a more-or-less universal base, as it is capable of pairing with all four natural nucleotides, though not with equal affinity (I-C >I-A>I-T~I-G>I-I). Even so, inosine continues to be successfully used in this role in a variety of applications requiring degeneracy at certain base positions of primers and probes, particularly at wobble positions, where degeneracy might be needed to permit annealing to many different, but closely related, sequences. Unit Structure: Unit Molecular Weight: 330.19 References: Loakes, D. The applications of universal DNA base analogues. Nucleic Acids Res. 29, 2437-2447 (2001). Alseth, I. et al. Inosine in DNA and RNA. Cur. Opi. Genetics and Dev. 26, 116-123 (2014).	I	$30.60	$32.64	$42.84	$59.16	$102.00
N3-Methyl-uridine N3-Methyl-uridine Modification Code: 3-M-U Unit Structure: Unit Molecular Weight: 320.19 References: Micura, R. et al. Methylation of the nucleobases in RNA oligonucleotides mediates duplex-hairpin conversion. Nucleic Acids Res. 29, 3997-4005 (2001). Chui, H. M. P. et al. Synthesis of a 3-methyluridine phosphoramidite to investigate the role of methylation in a ribosomal RNA hairpin. Bioorg. Med. Chem. 10, 325-332 (2002).	3-M-U	$74.46	$81.60	$91.80	$117.30	$204.00
N6,N6-Dimethyl-adenosine N6,N6-Dimethyl-adenosine Modification Code: DMA Description: N6,N6-Dimethyl-adenosine (m⁶₂A) is a minor RNA modification found primarily in rRNA, and recently, in Mycobacterium tRNA. N6-dimethyl rA appears to play a structural role in rRNA. Unit Structure: Unit Molecular Weight: 357.26 References: Politz, S. M. and Glitz, D. G. Ribosome structure: localization of N6,N6-dimethyladenosine by electron microscopy of a ribosome-antibody complex. Proc. Natl. Acad. Sci. USA 74, 1468-1472 (1997). Rife, J. P. et al. The synthesis of RNA containing the modified nucleotides N2-methylguanosine and N6,N6-dimethyladenosine. Nucleosides and Nucleotides 17, 2281-2288 (1998). Micura, R. et al. Methylation of the nucleobases in RNA oligonucleotides mediates duplex-hairpin conversion. Nucleic Acids Res. 29, 3997-4005 (2001).	DMA	$76.50	$94.86	$107.10	$132.60	$234.60
N6-Methyl-adenosine N6-Methyl-adenosine Modification Code: m6A Description: N6-methyl-adenosine (m⁶A) is the most abundant modification in mammalian mRNA and long non-coding RNA. First discovered in the 1970s, m⁶A modification has been proposed to function in mRNA splicing, export, stability, and immune tolerance. Unit Structure: Unit Molecular Weight: 343.24 References: Pan, T. N6-Methyl-adenosine modification in messenger and long non-coding RNA. Trends Biochem. Sci. 38, 204-209 (2013).	m6A	$74.46	$81.60	$91.80	$117.30	$204.00
Pseudouridine Pseudouridine Modification Code: ~U Description: Pseudouridine (ψ) is one of the most abundant post-transcriptionally modified nucleotides in various stable RNAs of all organisms. Pseudouridine is derived from uridine via base-specific isomerization, resulting in an extra hydrogen-bond donor that distinguishes it from other nucleotides. Pseudouridine-modified RNA can be used as research tools for studies into the roles of this residue in RNA structure and function in the cell. Unit Structure: Unit Molecular Weight: 306.17 References: Sipa, K. et al. Effect of base modifications on structure, thermodynamic stability, and gene silencing activity of short interfering RNA. RNA 13, 1301-1316 (2007). Ge, J and Yu, Y. T. RNA pesudouridylation: new insights into an old modification. Trends Biochem. Sci. 38, 210-208 (2013).	~U	$91.80	$96.90	$107.10	$137.70	$234.60
Purine ribonucleoside Purine ribonucleoside Modification Code: Pu Description: Purine ribonucleoside (Nebularine) lacks exocyclic functional groups and offers an altered hydrogen bonding scheme while retaining base stacking ability. It can be viewed as an adenosine analog with the hydrogen bond donor deleted. Unit Structure: Unit Molecular Weight: 314.19 References: Lucia, J. S. et al. Functional group substitutions as probes of hydrogen bonding between GA mismatches in RNA internal loops. J. Am. Chem. Soc. 113, 4313-4322 (1991).	Pu	$74.46	$81.60	$91.80	$117.30	$204.00
Pyrrolo-cytidine Pyrrolo-cytidine Modification Code: pC Description: Pyrrolo-cytidine is a fluorescent bicyclic analog of cytidine that base pairs specifically with guanosine (but not A, C, or U). Its excitation and emission maxima are 350 nm and 450 nm, respectively. Because these values are significantly different from the UV absorption maxima of DNA/RNA (260 nm) and protein (280 nm), pyrrolo-C is useful for probing the structures of DNA/RNA or protein-nucleic acid complexes. Unit Structure: Unit Molecular Weight: 343.23 References: Berry, D. A. et al. Pyrrolo-dC and pyrrolo-C: fluorescent analogs of cytidine and 2'-deoxycytidine for the study of oligonucleotides. Tetrahedron Lett. 45, 2457-2461 (2004). Tinsley, R. A. and Walter, N. G. Pyrrolo-C as a fluorescent probe for monitoring RNA secondary structure formation. RNA 12, 522-529 (2006).	pC	$91.80	$96.90	$107.10	$137.70	$234.60
Ribavirin Ribavirin Modification Code: RBV Description: Ribavirin is a guanosine ribonucleoside analog used to stop viral RNA synthesis and viral mRNA capping. It displays broad-spectrum anti-viral activity and is currently used for the treatment of some viral infections. Unit Structure: Unit Molecular Weight: 306.17 References: Cameron C. E. and Castro C. The mechanism of action of ribavirin: lethal mutagenesis of RNA virus genomes mediated by the viral RNA-dependent RNA polymerase. Curr. Opin. Infect. Dis. 14, 757-764 (2001).	RBV	$74.46	$81.60	$91.80	$117.30	$204.00
Backbone modifications	Short Code	0.05 µmol	0.2 µmol	0.4 µmol	1.0 µmol	2.0 µmol
Phosphorothioate Phosphorothioate Modification Code: * Description: A classic and popular phosphate backbone modification is the phosphorothioate (PS) modification where one of the non-bridging phosphate oxygens is replaced with sulfur. Phosphorothioates have been widely used in antisense and siRNA applications. The majority of therapeutic oligonucleotides contain this modification which is introduced to increase nuclease resistance and facilitate cellular uptake and bioavailability in vivo. Unit Structure: Unit Molecular Weight: 15.97 (additional MW where sulfur replacing oxygen) References: Kurreck, J. The role of backbone modifications in oligonucleotide-based strategies, in Therapeutic Oligonucleotides (Kurreck, J. ed.), RSC Publishing, pp 1-22 (2008). Eckstein, F. Phosphorothioates, essential components of therapeutic oligonucleotides. Nucleic Acid Ther. 24, 274-287 (2014).	*	$8.16	$13.26	$15.30	$20.40	$29.58
Phosphorylation	Short Code	0.05 µmol	0.2 µmol	0.4 µmol	1.0 µmol	2.0 µmol
5'-Phosphate 5'-Phosphate Modification Code: 5'-P Unit Structure: Unit Molecular Weight: 80.99	5'-P	$45.90	$53.04	$64.26	$79.56	$137.70
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'-Amino-butyryl-pyrene-uridine Modification Code: 2'-P-U Description: Pyrene is a polycyclic aromatic hydrocarbon (PAH) consisting of four fused benzene rings. Because pyrene can be chemically modified in various ways and its fluorescence quantum efficiencies are high in both monomers and excimer emissions, pyrene-modified olignucleotides have been exploited as fluorescent probes of DNA and RNA in hybridization assays. In addition, pyrene fluorescence is largely affected by environmental factors, such as solvent and nearby nucleotide bases, which has led to its development as a potential probe for nucleic acid structures. Unit Structure: Unit Molecular Weight: 575.51 Pyrene Extinction Coefficient: 54,000 Excitation/Emission Max: 335 nm/381 nm References: Yamana, K. et al. 2'-Pyrene modified oligonucleotide provides a highly sensitive probe of RNA. Nucleic Acids Res. 27, 2387-2392 (1999). Du, H. et al. PhotochemCAD: A computer-aided design and research tools in photochemistry. Photochem. Photobiol. 68, 141-142 (1998).	2'-P-U	$102.00	$132.60	$147.90	$183.60	$326.40
2'-Amino-cytidine 2'-Amino-cytidine Modification Code: 2'-N-C Description: The thermal stability of duplexes containing 2'-amino-RNA has been determined and it was reported that 2'-amino-C substitutions destabilized by about 4Â° relative to RNA C. It was also further reported that 2'-amino-RNA linkages are nuclease-resistant. The pKa of the 2'-amino group is quite low at 6.2 but this retains sufficient nucleophilicity to allow conjugation reactions to take place. It is therefore possible to label a 2'-amino group with a fluorophore. Unit Structure: Unit Molecular Weight: 304.20 References: Smalley, M. K. and Silverman, S. K. Site-specific fluorescent labeling of large RNA with pyrene, in Current Protocols in Nucleic Acids Chemistry Chapter 11, Unit 11.11 (2004).	2'-N-C	$76.50	$94.86	$107.10	$132.60	$234.60
2'-Amino-uridine 2'-Amino-uridine Modification Code: 2'-N-U Description: The thermal stability of duplexes containing 2'-amino-RNA has been determined and it was reported that 2'-amino-C substitutions destabilized by about 4° relative to RNA C. It was also further reported that 2'-amino-RNA linkages are nuclease-resistant. The pKa of the 2'-amino group is quite low at 6.2 but this retains sufficient nucleophilicity to allow conjugation reactions to take place. It is therefore possible to label a 2'-amino group with a fluorophore. Unit Structure: Unit Molecular Weight: 305.18 References: Smalley, M. K. and Silverman, S. K. Site-specific fluorescent labeling of large RNA with pyrene, in Current Protocols in Nucleic Acids Chemistry Chapter 11, Unit 11.11 (2004).	2'-N-U	$74.46	$81.60	$91.80	$117.30	$204.00
2'-Deoxy-uridine 2'-Deoxy-uridine Modification Code: dU Description: DNA modification has long been the industry standard for modifying siRNA 3'-overhang, while conferring nuclease resistance and preserving siRNA potency. DNA is well-tolerated in the passage strand with little effects on siRNA potency. Only partially DNA substituted guide strands are functional, whereas alternating the DNA modification with 2'-f has created fully substituted, active guide strands. Unit Structure: Unit Molecular Weight: 290.17 References: Elbashir, S. M. et al. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature, 411, 494-498 (2001). Chiu, Y. L. and Rana, T. M. siRNA function in RNAi: a chemical modification analysis. RNA, 9, 1034-1048 (2003).	dU	$30.60	$32.64	$42.84	$59.16	$102.00
2'-Fluoro-adenosine 2'-Fluoro-adenosine Modification Code: 2'-F-A Description: 2'-Fluoro-nucleosides adopt an RNA-type sugar conformation, presumably due to the high electronegativity of fluorine. Fluorine substitution (2'-F) slightly stabilizes dsRNA duplex (~1°C in Tm per modification). 2'-F substitution is among the best tolerated modification types and therefore allows the creation of highly modified, active siRNAs, both strands tolerate 2'-F modifications at most positions and substitution of all siRNA pyrimidines was reported to greatly enhance serum stability and to effective support silencing in vitro and in vivo. Unit Structure: Unit Molecular Weight: 331.20 References: Chiu, Y. L. and Rana, T. M. siRNA function in RNAi: a chemical modification analysis. RNA, 9, 1034-1048 (2003).	2'-F-A	$59.16	$61.20	$86.70	$88.74	$163.20
2'-Fluoro-cytidine 2'-Fluoro-cytidine Modification Code: 2'-F-C Description: 2'-Fluoro-nucleosides adopt an RNA-type sugar conformation, presumably due to the high electronegativity of fluorine. Fluorine substitution (2'-F) slightly stabilizes dsRNA duplex (~1 °C in Tm per modification). 2'-F substitution is among the best tolerated modification types and therefore allows the creation of highly modified, active siRNAs, both strands tolerate 2'-F modifications at most positions and substitution of all siRNA pyrimidines was reported to greatly enhance serum stability and to effective support silencing in vitro and in vivo. Unit Structure: Unit Molecular Weight: 307.17 References: Chiu, Y. L. and Rana, T. M. siRNA function in RNAi: a chemical modification analysis. RNA, 9, 1034-1048 (2003).	2'-F-C	$40.80	$43.86	$58.14	$66.30	$102.00
2'-Fluoro-guanosine 2'-Fluoro-guanosine Modification Code: 2'-F-G Description: 2'-Fluoro-nucleosides adopt an RNA-type sugar conformation, presumably due to the high electronegativity of fluorine. Fluorine substitution (2'-F) slightly stabilizes dsRNA duplex (~1 °C in Tm per modification). 2'-F substitution is among the best tolerated modification types and therefore allows the creation of highly modified, active siRNAs, both strands tolerate 2'-F modifications at most positions and substitution of all siRNA pyrimidines was reported to greatly enhance serum stability and to effective support silencing in vitro and in vivo. Unit Structure: Unit Molecular Weight: 347.20 References: Chiu, Y. L. and Rana, T. M. siRNA function in RNAi: a chemical modification analysis. RNA, 9, 1034-1048 (2003).	2'-F-G	$59.16	$61.20	$86.70	$88.74	$163.20
2'-Fluoro-uridine 2'-Fluoro-uridine Modification Code: 2'-F-U Description: 2'-Fluoro-nucleosides adopt an RNA-type sugar conformation, presumably due to the high electronegativity of fluorine. Fluorine substitution (2'-F) slightly stabilizes dsRNA duplex (~1 °C in Tm per modification). 2'-F substitution is among the best tolerated modification types and therefore allows the creation of highly modified, active siRNAs, both strands tolerate 2'-F modifications at most positions and substitution of all siRNA pyrimidines was reported to greatly enhance serum stability and to effective support silencing in vitro and in vivo. Unit Structure: Unit Molecular Weight: 308.16 References: Chiu, Y. L. and Rana, T. M. siRNA function in RNAi: a chemical modification analysis. RNA, 9, 1034-1048 (2003).	2'-F-U	$40.80	$43.86	$58.14	$66.30	$102.00
2'-OMe-inosine 2'-OMe-inosine Modification Code: mI Description: The naturally occurring 2'-O-methyl (2'-OMe) modification is the first and most extensively tested 2'-substitutions; 2'-OMe slightly enhances the binding affinity toward RNA (Tm increase of 0.5-0.7 °C per modification). 2'-OMe modification has been extensively used to generate fully functional siRNAs with higher nuclease resistance, reduced siRNA immunogenicity, and less off-targeting. Inosine serves as a more-or-less universal base, as it is capable of pairing with all four natural nucleotides, though not with equal affinity (I-C >I-A>I-T~I-G>I-I). Unit Structure: Unit Molecular Weight: 344.22 References: Soutschek, J. et al. Therapeutic silencing of an endogenous gene by systemic administration of modified siRNAs. Nature, 432, 173-178 (2004). Allerson, C. R. et al. Fully 2'-modified oligonucleotide duplexes with improved in vitro potency and stability compared to unmodified small interfering RNA. J. Med. Chem, 48, 901-904 (2005).	mI	$74.46	$81.60	$91.80	$117.30	$204.00
Amino Modifiers	Short Code	0.05 µmol	0.2 µmol	0.4 µmol	1.0 µmol	2.0 µmol
3'-Amino modifier C12 3'-Amino modifier C12 Modification Code: N12-3' Description: Amine linkers are commonly used for derivatizing RNA oligonucleotides via NHS activated esters, isothiocyanate, or sulfonyl chloride derivatives of various ligands, such as fluorescent dyes. The C12 long linker is provided as the deprotected and reactive free amine. Unit Structure: Unit Molecular Weight: 264.33	N12-3'	$102.00	$132.60	$147.90	$183.60	$326.40
3'-Amino modifier C6 3'-Amino modifier C6 Modification Code: N6-3' Description: Amine linkers are commonly used for derivatizing RNA oligonucleotides via NHS activated esters, isothiocyanate, or sulfonyl chloride derivatives of various ligands, such as fluorescent dyes. The C6 linker is provided as the deprotected and reactive free amine. Unit Structure: Unit Molecular Weight: 180.16	N6-3'	$102.00	$132.60	$147.90	$183.60	$326.40
5'-Amino modifier C12 5'-Amino modifier C12 Modification Code: N12 Description: Amine linkers are commonly used for derivatizing RNA oligonucleotides via NHS activated esters, isothiocyanate, or sulfonyl chloride derivatives of various ligands, such as fluorescent dyes. This long linker is provided as the deprotected and reactive free amine. Unit Structure: Unit Molecular Weight: 263.32	N12	$76.50	$94.86	$107.10	$132.60	$234.60
5'-Amino modifier C3 5'-Amino modifier C3 Modification Code: N3 Description: Amine linkers are commonly used for derivatizing RNA oligonucleotides via NHS activated esters, isothiocyanate, or sulfonyl chloride derivatives of various ligands, such as fluorescent dyes. The C3 linker is provided as the deprotected and reactive free amine. Unit Structure: Unit Molecular Weight: 138.08	N3	$74.46	$81.60	$91.80	$117.30	$204.00
5'-Amino modifier C5 5'-Amino modifier C5 Modification Code: N5 Description: Amine linkers are commonly used for derivatizing RNA oligonucleotides via NHS activated esters, isothiocyanate, or sulfonyl chloride derivatives of various ligands, such as fluorescent dyes. The C5 linker is provided as the deprotected and reactive free amine. Unit Structure: Unit Molecular Weight: 166.14	N5	$74.46	$81.60	$91.80	$117.30	$204.00
5'-Amino modifier C6 5'-Amino modifier C6 Modification Code: N6 Description: Amine linkers are commonly used for derivatizing RNA oligonucleotides via NHS activated esters, isothiocyanate, or sulfonyl chloride derivatives of various ligands, such as fluorescent dyes. The C6 linker is provided as the deprotected and reactive free amine. Unit Structure: Unit Molecular Weight: 180.16	N6	$74.46	$81.60	$91.80	$117.30	$204.00
5-Aminohexylacrylamino-uridine 5-Aminohexylacrylamino-uridine Modification Code: 5-LC-N-U Description: Amine-modified oligonucleotides react with active succinimidyl ester, isothiocyanate, or sulfonyl chloride derivatives of various ligands, such as fluorescent dyes. 5-Aminohexylacrylamino-U is designed in the way that its long linker arm projects into the major groove of double-stranded DNA/RNA. After conjugation, large molecules (i.e. fluorescent dyes) placed cannot interact with the double stranded oligonucleotide thus no disruption of hybridization. Unit Structure: Unit Molecular Weight: 474.41 References: Ruth, J. L. Oligodeoxynucleotides with reporter groups attached to the base., in Olignucleotides and analogues: a practical approach (Eckstein, F. ed.), Oxford University Press, Oxford, pp. 255-282 (1991).	5-LC-N-U	$102.00	$132.60	$147.90	$183.60	$326.40
Thiol Modifiers	Short Code	0.05 µmol	0.2 µmol	0.4 µmol	1.0 µmol	2.0 µmol
3'-Disulfide thiol-modifier 3'-Disulfide thiol-modifier Modification Code: S-S-3' Description: The disulfide thiol-modifier may be used for introducing 5'- or 3'-thiol (-SH) linkages. SH-modified oligonucleotide can be used to form reversible disulfide bonds (ligand-S-S-oligo) or irreversible bonds with a variety of activated accepting groups. Maleimide, bormide, iodide, or sulphonyl derivatives are suitable for tagging thiol-linked oligos with a variety of groups such as fluorescent dyes, biotin, and enzymes. Thiol-modified siRNA and RNA oligonucleotides with the thiol group in a protected or oxidized form prevent the formation of dimers. Prior to use, the disulfide (S-S) group on the thiol-modified oligonucleotide can be deprotected or reduced to -SH for conjugation. Unit Structure: Unit Molecular Weight: 622.69	S-S-3'	$102.00	$132.60	$147.90	$183.60	$326.40
5'-Disulfide thiol-modifier 5'-Disulfide thiol-modifier Modification Code: S-S Description: The disulfide thiol-modifier may be used for introducing 5'- or 3'-thiol (-SH) linkages. SH-modified oligonucleotide can be used to form reversible disulfide bonds (ligand-S-S-oligo) or irreversible bonds with a variety of activated accepting groups. Maleimide, bormide, iodide, or sulphonyl derivatives are suitable for tagging thiol-linked oligos with a variety of groups such as fluorescent dyes, biotin, and enzymes. Thiol-modified siRNA and RNA oligonucleotides with the thiol group in a protected or oxidized form prevent the formation of dimers. Prior to use, the disulfide (S-S) group on the thiol-modified oligonucleotide can be deprotected or reduced to -SH for conjugation. Unit Structure: Unit Molecular Weight: 329.43	S-S	$102.00	$132.60	$147.90	$183.60	$326.40
Spacer Modifiers	Short Code	0.05 µmol	0.2 µmol	0.4 µmol	1.0 µmol	2.0 µmol
C18 Spacer C18 spacer Modification Code: 18S Description: The spacer C3, C9, and 18 are used to insert a spacer arm in an oligonucleotide. Spacers are used for investigating duplex formation, creating distance between an oligonucleotide and a conjugated Modification. 3'-Spacer may also act as a blocker of exonuclease and polymerase activity at the 3'-terminus. The spacers may be added in multiple additions when a longer spacer is required. Deoxy-abasic spacer or ribo-abasic spacer is used to introduce a stable abasic site within an oligonucleotide. Unit Structure: Unit Molecular Weight: 344.30 References: Durand, M. et al. Circular dichroism studies of an oligodeoxyribonucleotide containing a hairpin loop made of a hexaethylene glycol chain: conformation and stability. Nucleic Acid Res. 18, 6353-6359 (1990).	18S	$30.60	$32.64	$42.84	$59.16	$102.00
C3 Spacer C3 spacer Modification Code: C3 Description: The spacer C3, C9, and 18 are used to insert a spacer arm in an oligonucleotide. Spacers are used for investigating duplex formation, creating distance between an oligonucleotide and a conjugated Modification. 3'-Spacer may also act as a blocker of exonuclease and polymerase activity at the 3'-terminus. The spacers may be added in multiple additions when a longer spacer is required. Deoxy-abasic spacer or ribo-abasic spacer is used to introduce a stable abasic site within an oligonucleotide. Unit Structure: Unit Molecular Weight: 138.06 References: Wang Y. et al. C3-Spacer-containing circular oligonucleotides as inhibitors of human topoisomerase I. Bioorg. Med. Chem. Lett. 18, 3597-3602 (2008).	C3	$30.60	$32.64	$42.84	$59.16	$102.00
C9 Spacer C9 spacer Modification Code: 9S Description: The spacer C3, C9, and 18 are used to insert a spacer arm in an oligonucleotide. Spacers are used for investigating duplex formation, creating distance between an oligonucleotide and a conjugated Modification. 3'-Spacer may also act as a blocker of exonuclease and polymerase activity at the 3'-terminus. The spacers may be added in multiple additions when a longer spacer is required. Deoxy-abasic spacer or ribo-abasic spacer is used to introduce a stable abasic site within an oligonucleotide. Unit Structure: Unit Molecular Weight: 212.14 References: Durand, M. et al. Circular dichroism studies f an oligodeoxyribonucleotide containing a hairpin loop made of a hexaethylene glycol chain: conformation and stability. Nucleic Acid Res. 18, 6353-6359 (1990).	9S	$30.60	$32.64	$42.84	$59.16	$102.00
dSpacer dSpacer Modification Code: dab Description: The spacer C3, C9, and 18 are used to insert a spacer arm in an oligonucleotide. Spacers are used for investigating duplex formation, creating distance between an oligonucleotide and a conjugated Modification. 3'-Spacer may also act as a blocker of exonuclease and polymerase activity at the 3'-terminus. The spacers may be added in multiple additions when a longer spacer is required. Deoxy-abasic spacer or ribo-abasic spacer is used to introduce a stable abasic site within an oligonucleotide. Unit Structure: Unit Molecular Weight: 180.10 References: Vesnaver, G. et al. Influence of abasic and anucleosidic sites on the stability, conformation, and melting behavior of a DNA duplex: correlations of thermodynamic and structure data. Proc. Natl. Acad. Sci. USA 86, 3614-3618 (1989). Taniho, K. et al. Synthesis and biological properties of chemically modified siRNAs bearing 1-deoxy-D-ribofuranose in their 3'-overhang region. Bioorg. Med. Chem. Lett. 22, 2518-2521 (2012).	dab	$76.50	$94.86	$107.10	$132.60	$234.60
rSpacer rSpacer Modification Code: rab Description: The spacer C3, C9, and 18 are used to insert a spacer arm in an oligonucleotide. Spacers are used for investigating duplex formation, creating distance between an oligonucleotide and a conjugated Modification. 3'-Spacer may also act as a blocker of exonuclease and polymerase activity at the 3'-terminus. The spacers may be added in multiple additions when a longer spacer is required. Deoxy-abasic spacer or ribo-abasic spacer is used to introduce a stable abasic site within an oligonucleotide. Unit Structure: Unit Molecular Weight: 196.09 References: Vesnaver, G. et al. Influence of abasic and anucleosidic sites on the stability, conformation, and melting behavior of a DNA duplex: correlations of thermodynamic and structure data. Proc. Natl. Acad. Sci. USA 86, 3614-3618 (1989). Taniho, K. et al. Synthesis and biological properties of chemically modified siRNAs bearing 1-deoxy-D-ribofuranose in their 3'-overhang region. Bioorg. Med. Chem. Lett. 22, 2518-2521 (2012).	rab	$229.50	$284.58	$321.30	$397.80	$703.80
Chain Terminators	Short Code	0.05 µmol	0.2 µmol	0.4 µmol	1.0 µmol	2.0 µmol
3' Inverted abasic 3' Inverted abasic Modification Code: b Unit Structure: Unit Molecular Weight: 181.10	b	$45.90	$53.04	$64.26	$79.56	$135.70
3' Inverted deoxy-thymidine 3' Inverted deoxy-thymidine Modification Code: idT-3' Description: Inverted thymidine (5'- and/or 3'-inverted T) modification is introduced at 5'- and/or 3'-end to make the oligonucleotides resistant to nucleases. Unit Structure: Unit Molecular Weight: 305.20 References: Takei, Y. et al. 5'-,3'-Inverted thymidine-modified antisense oligodeoxynucleotide targeting midkine. Its design and application in cancer therapy. J. Biol. Chem. 277, 23800-23806 (2002).	idT-3'	$45.90	$53.04	$64.26	$79.56	$135.70
3'-Terminal 3'-Deoxy-Guanosine 3'-Terminal 3'-deoxy-guanosine Modification Code: 3'dG Unit Structure: Unit Molecular Weight: 330.22	3'dG	$56.10	$81.60	$91.80	$122.40	$183.60
3'-Terminal dideoxy-cytidine 3'-Terminal dideoxy-cytidine Modification Code: ddC Unit Structure: Unit Molecular Weight: 274.19	ddC	$76.50	$94.86	$107.10	$132.60	$234.60
5' Inverted deoxy-thymidine 5' Inverted deoxy-thymidine Modification Code: idT Description: Inverted thymidine (5'- and/or 3'-inverted T) modification is introduced at the 5'- and/or 3'-end to make the oligonucleotides resistant to nucleases. Unit Structure: Unit Molecular Weight: 305.20 References: Takei, Y. et al. 5'-,3'-Inverted thymidine-modified antisense oligodeoxynucleotide targeting midkine. Its design and application in cancer therapy. J. Biol. Chem. 277, 23800-23806 (2002).	idT	$30.60	$32.64	$42.84	$59.16	$102.00
5' Terminal 5'-deoxy-ribo-adenosine 5' Terminal 5'-deoxy-ribo-adenosine Modification Code: 5'dA Unit Structure: Unit Molecular Weight: 314.22	5'dA	$30.60	$32.64	$42.84	$59.16	$102.00
5' Terminal 5'-deoxy-ribo-cytidine 5' Terminal 5'-deoxy-ribo-cytidine Modification Code: 5'dC Unit Structure: Unit Molecular Weight: 290.19	5'dC	$30.60	$32.64	$42.84	$59.16	$102.00
5' Terminal 5'-deoxy-ribo-guanosine 5' Terminal 5'-deoxy-ribo-guanosine Modification Code: 5'dG Unit Structure: Unit Molecular Weight: 330.22	5'dG	$30.60	$32.64	$42.84	$59.16	$102.00
5' Terminal 5'-deoxy-ribo-uridine 5' Terminal 5'-deoxy-ribo-uridine Modification Code: 5'dU Unit Structure: Unit Molecular Weight: 291.18	5'dU	$30.60	$32.64	$42.84	$59.16	$102.00
Labeling	Short Code	0.05 µmol	0.2 µmol	0.4 µmol	1.0 µmol	2.0 µmol
3-Biotin 3-Biotin Modification Code: 3-Bi Description: Biotin is widely used throughout biological research to conjugate proteins and nucleic acids for biochemical assays. Because both streptavidin and avidin bind biotin with high affinity (Kd of 10 ^-14 mol/l to 10^-15 mol/l) and specifically, biotinylated proteins or nucleic acids of interest can be isolated from a sample by exploiting this highly stable interaction. Unit Structure: Unit Molecular Weight: 653.70	3'-Bi	$76.50	$96.90	$107.10	$132.60	$193.80
3'-Cholesterol 3'-Cholesterol Modification Code: 3'-Chl Description: Potential therapeutic oligonucleotides must permeate the cell membrane for optimal activity. The addition of lipophilic groups such as cholesterol to a siRNA enhances gene silencing in vivo. Efficient and selective uptake of cholesterol siRNA conjugates depends on interactions with lipoprotein particles, lipoprotein receptors and transmembrane proteins. High-density lipoprotein (HDL) directs siRNA delivery into liver, gut, kidney and steroidogenic organs, whereas low-density lipoprotein (LDL) targets siRNA primarily to the liver. Unit Structure: Unit Molecular Weight: 705.94 References: Mackellar, C. et al. Synthesis and physical properties of anti-HIV antisense oligonucleotides bearing terminal lipophilic groups. Nucleic Acid Res. 20, 3411-3417 (1992). Wolfrum, C. et al. Mechanisms and optimization of in vivo delivery of lipophilic siRNAs. Nature Biotechnology 25, 1149-1157 (2007).	3'-Chl	$112.20	$147.90	$168.30	$214.20	$372.30
3' TEG-Cholesterol 3' TEG-Cholesterol Modification Code: TEG-Chl-3' Description: Cholesterol TEG Modification is a lipophilic modification aiding in cellular delivery. The TEG liker arm facilitates solubility issues of the oligio making it soluble in aqueous buffers. It has been used as a transfection aid for antisense oligos and siRNAs, both in vitro and in vivo. Cholesterol is a very hydrophobic modification that is best purified using RP-HPLC. Unit Structure: Chemical Formula: C₄₀H₇₁NO₁₁P Unit Molecular Weight: 755.97 g/mol References: M. Manoharan, Antisense Nucleic Acid Drug Dev, 2002, 12, 103-20	TEG-Chl-3'	$112.20	$147.90	$168.30	$214.20	$372.30
3'-Cy3 3'-Cy3 Modification Code: Cy3-3' Description: Cy3 and Cy5 are the most popular cyanine dyes used in life sciences, typically combined for two color detection. Cy3 dyes fluoresce orange (547 nm excitationand 563 nm emission), while Cy5 is fluorescent in the red region (662 nm) but absorbs in the orange region (646 nm). Cy3- or Cy5-labeled siRNA remain fully functional and can be used to understand siRNA distribution and metabolism by tracking siRNA movements after transfection. Unit Structure: Unit Molecular Weight: 800.85 Cy3 Extinction Coefficient: 136,000 Excitation/Emission Max: 547 nm/563 nm References: Mishra, A. et al. Cyanines during the 1990s: A review. Chem. Rev. 100, 1973-2011 (2000).	Cy3-3'	$86.70	$107.10	$127.50	$147.90	$275.40
3'-Cy5 3'-Cy5 Modification Code: Cy5-3' Description: Cy3 and Cy5 are the most popular cyanine dyes used in life sciences, typically combined for two color detection. Cy3 dyes fluoresce orange (547 nm excitationand 563 nm emission), while Cy5 is fluorescent in the red region (662 nm) but absorbs in the orange region (646 nm). Cy3- or Cy5-labeled siRNA remain fully functional and can be used to understand siRNA distribution and metabolism by tracking siRNA movements after transfection. Unit Structure: Unit Molecular Weight: 826.88 Cy5 Extinction Coefficient: 250,000 Excitation/Emission Max: 646 nm/662 nm References: Mishra, A. et al. Cyanines during the 1990s: A review. Chem. Rev. 100, 1973-2011 (2000).	Cy5-3'	$86.70	$107.10	$127.50	$147.90	$275.40
3'-Cy5.5 3'-Cy5.5 Modification Code: Cy5^5-3' Description: Cyanine dyes are the most popular fluorescent dyes used in life sciences for labeling nucleic acids and proteins. Cy5.5 is a far-red (and near-infrared) emitting dye which is ideal for fluorescence measurements where background fluorescence is a concern. It is also suitable for in vivo NIR imaging experiments. Cy5.5-labeled siRNA remain fully functional and can be used to understand siRNA distribution and metabolism by tracking siRNA movements after transfection. Unit Structure: Unit Molecular Weight: 927.00 Cy5.5 Extinction Coefficient: 209,000 Excitation/Emission Max: 688 nm/707 nm References: Mishra, A. et al. Cyanines during the 1990s: A review. Chem. Rev. 100, 1973-2011 (2000). Lee, S.-Y. et al. Stability and cellular uptake of polymerized siRNA (poly-siRNA)/polyethylenimine (PEI) complexes for efficient gene silencing. J. Controlled Release 141, 339-346 (2010).	Cy5^5-3'	$86.70	$107.10	$127.50	$147.90	$275.40
3’ Black Hole Quencher 1 3’ Black Hole Quencher 1	BHQ-1-3’	$112.20	$147.90	$168.30	$214.20	$372.30
3’ Black Hole Quencher 2 3’ Black Hole Quencher 2	BHQ-2-3’	$112.20	$147.90	$168.30	$214.20	$372.30
3'-Fluorescein 3'-Fluorescein Modification Code: 3'-Fl 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. Fluorescein-labeled siRNAs can be used to visualize cellular uptake of siRNA and to quantify siRNA transfection/delivery efficiency. Unit Structure: Unit Molecular Weight: 609.50 Extinction Coefficient: 75,000 Excitation/Emission Max: 494 nm/520 nm	3'-Fl	$76.50	$94.86	$107.10	$132.60	$234.60
3'-Biotin LC 3'-Biotin LC Modification Code: 3'-LCBi Description: Biotin is widely used throughout biological research to conjugate proteins and nucleic acids for biochemical assays. Because both streptavidin and avidin bind biotin with high affinity (Kd of 10 ^-14 mol/l to 10^-15 mol/l) and specifically, biotinylated proteins or nucleic acids of interest can be isolated from a sample by exploiting this highly stable interaction. Unit Structure: Unit Molecular Weight: 519.62	3'-LCBi	$112.20	$147.90	$168.30	$214.20	$372.30
3'-Biotin LC LC 3'-Biotin LC LC Modification Code: 3'-2LCBi Description: Biotin is widely used throughout biological research to conjugate proteins and nucleic acids for biochemical assays. Because both streptavidin and avidin bind biotin with high affinity (Kd of 10 ^-14 mol/l to 10^-15 mol/l) and specifically, biotinylated proteins or nucleic acids of interest can be isolated from a sample by exploiting this highly stable interaction. Unit Structure: Unit Molecular Weight: 632.78	3'-2LCBi	$112.20	$147.90	$168.30	$214.20	$372.30
3'-Puromycin 3'-Puromycin Modification Code: Pmn Description: One of the most challenging requirements associated with combinatorial chemistry is the recovery of sequence information of the oligonucleotide or peptide selected by the screening assay. A method has been developed to generate a fusion product between mRNA and the polypeptide it encodes using in vitro translation of synthetic RNAs 3'-labeled with puromycin, an antibiotic that mimics transfer RNA. Puromycin binds in the ribosome's A site, forms a peptide bond with the growing peptide chain, and blocks further peptide elongation. By linking puromycin to mRNA, a peptide-RNA fusion product results from the translation of the message linking the encoding mRNA with its peptide product. Unit Structure: Unit Molecular Weight: 534.49 References: Roberts, R. W. and Szostak, J. W. RNA-peptide fusions for the in vitro selection of peptides and proteins. Proc. Natl. Acad. Sci. USA 94, 12297-12302 (1997).	Pmn	$45.90	$53.04	$64.26	$79.56	$137.70
3'-TAMRA 3'-TAMRA Modification Code: 3'-TAM Description: Carboxytetramethylrhodamine (TAMRA) is a fluorescent dye that is a derivative of rhodamine, and is used to label oligonucleotides at the 5'- or 3'-ends, or internally. TAMRA-modified oligonucleotides play a particularly important role in both fluorescence resonance energy transfer (FRET) and real-time PCR applications. Unit Structure: Unit Molecular Weight: 869.82 Extinction Coefficient: 90,000 Excitation/Emission Max: 550 nm/570 nm	3'-TAM	$242.76	$285.60	$336.60	$387.60	$673.20
5'-Biotin 5'-Biotin Modification Code: Bi Description: Biotin is widely used throughout biological research to conjugate proteins and nucleic acids for biochemical assays. Because both streptavidin and avidin bind biotin with high affinity (Kd of 10 ^-14 mol/l to 10^-15 mol/l) and specifically, biotinylated proteins or nucleic acids of interest can be isolated from a sample by exploiting this highly stable interaction. Unit Structure: Unit Molecular Weight: 406.46	Bi	$91.80	$96.90	$107.10	$158.10	$275.40
5'-Cholesterol 5'-Cholesterol Modification Code: Chl Description: Potential therapeutic oligonucleotides must permeate the cell membrane for optimal activity. The addition of lipophilic groups such as cholesterol to a siRNA enhances gene silencing in vivo. Efficient and selective uptake of cholesterol siRNA conjugates depends on interactions with lipoprotein particles, lipoprotein receptors and transmembrane proteins. High-density lipoprotein (HDL) directs siRNA delivery into liver, gut, kidney and steroidogenic organs, whereas low-density lipoprotein (LDL) targets siRNA primarily to the liver. Unit Structure: Unit Molecular Weight: 624.00 References: Mackellar, C. et al. Synthesis and physical properties of anti-HIV antisense oligonucleotides bearing terminal lipophilic groups. Nucleic Acid Res. 20, 3411-3417 (1992). Wolfrum, C. et al. Mechanisms and optimization of in vivo delivery of lipophilic siRNAs. Nature Biotechnology 25, 1149-1157 (2007).	Chl	$112.20	$147.90	$168.30	$214.20	$372.30
5' Cholesterol-TEG 5' Cholesterol-TEG Modification Code: Chl-TEG Description: Cholesterol TEG Modification is a lipophilic modification aiding in cellular delivery. The TEG liker arm facilitates solubility issues of the oligio making it soluble in aqueous buffers. It has been used as a transfection aid for antisense oligos and siRNAs, both in vitro and in vivo. Cholesterol is a very hydrophobic modification that is best purified using RP-HPLC. Unit Structure: Chemical Formula: C₄₀H₇₁NO₁₁P Unit Molecular Weight: 755.97 g/mol References: M. Manoharan, Antisense Nucleic Acid Drug Dev, 2002, 12, 103-28.	Chl-TEG	$336.60	$443.70	$504.90	$664.60	$1116.90
5'-Cy3 5'-Cy3 Modification Code: Cy3 Description: Cy3 and Cy5 are the most popular cyanine dyes used in life sciences, typically combined for two color detection. Cy3 dyes fluoresce orange (547 nm excitationand 563 nm emission), while Cy5 is fluorescent in the red region (662 nm) but absorbs in the orange region (646 nm). Cy3- or Cy5-labeled siRNA remain fully functional and can be used to understand siRNA distribution and metabolism by tracking siRNA movements after transfection. Unit Structure: Unit Molecular Weight: 507.59 Cy3 Extinction Coefficient: 136,000 Excitation/Emission Max: 547 nm/563 nm	Cy3	$76.50	$96.90	$117.30	$137.70	$255.00
5'-Cy5 5'-Cy5 Modification Code: Cy5 Description: Cy3 and Cy5 are the most popular cyanine dyes used in life sciences, typically combined for two color detection. Cy3 dyes fluoresce orange (547 nm excitationand 563 nm emission), while Cy5 is fluorescent in the red region (662 nm) but absorbs in the orange region (646 nm). Cy3- or Cy5-labeled siRNA remain fully functional and can be used to understand siRNA distribution and metabolism by tracking siRNA movements after transfection. Unit Structure: Unit Molecular Weight: 533.63 Cy5 Extinction Coefficient: 250,000 Excitation/Emission Max: 646 nm/662 nm References: Mishra, A. et al. Cyanines during the 1990s: A review. Chem. Rev. 100, 1973-2011 (2000).	Cy5	$76.50	$96.90	$117.30	$137.70	$255.00
5'-Cy5.5 5'-Cy5.5 Modification Code: Cy5^5 Description: Cyanine dyes are the most popular fluorescent dyes used in life sciences for labeling nucleic acids and proteins. Cy5.5 is a far-red (and near-infrared) emitting dye which is ideal for fluorescence measurements where background fluorescence is a concern. It is also suitable for in vivo NIR imaging experiments. Cy5.5-labeled siRNA remain fully functional and can be used to understand siRNA distribution and metabolism by tracking siRNA movements after transfection. Unit Structure: Unit Molecular Weight: 633.75 Cy5.5 Extinction Coefficient: 209,000 Excitation/Emission Max: 688 nm/707 nm References: Mishra, A. et al. Cyanines during the 1990s: A review. Chem. Rev. 100, 1973-2011 (2000). Lee, S.-Y. et al. Stability and cellular uptake of polymerized siRNA (poly-siRNA)/polyethylenimine (PEI) complexes for efficient gene silencing. J. Controlled Release 141, 339-346 (2010).	Cy5^5	$150.96	$178.50	$209.10	$255.00	$459.00
5’ Black Hole Quencher 1 5’ Black Hole Quencher 1	BHQ-1	-	$650.76	$740.52	$943.50	$1641.48
5’ Black Hole Quencher 2 5’ Black Hole Quencher 2	BHQ-2	-	$650.76	$740.52	$943.50	$1641.48
5'-Dabcyl 5'-Dabcyl Modification Code: Dabcyl Description: The dabcyl moiety is fairly unique in its ability to quench the fluorescence of virtually any fluorescent tag in its immediate vicinity, making it the preferred quencher for molecular beacon probes. Unit Structure: Unit Molecular Weight: 430.18 References: Tyagi, S. and Kramer, F.R. Molecular beacons: probes that fluoresce upon hybridization. Nature Biotechnology, 4, 303-308 (1996).	Dabcyl	$102.00	$132.60	$147.90	$183.60	$326.40
5'-Fluorescein 5'-Fluorescein Modification Code: Fl 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. Fluorescein-labeled siRNAs can be used to visualize cellular uptake of siRNA and to quantify siRNA transfection/delivery efficiency. Unit Structure: Unit Molecular Weight: 538.47 Extinction Coefficient: 75,000 Excitation/Emission Max: 494 nm/525 nm	Fl	$91.80	$96.90	$107.10	$137.70	$234.60
5'-Pyrene 5'-Pyrene Modification Code: 5'-Pyr Description: Pyrene is a polycyclic aromatic hydrocarbon (PAH) consisting of four fused benzene rings. Because pyrene can be chemically modified in various ways and its fluorescence quantum efficiencies are high in both monomers and excimer emissions, pyrene-modified olignucleotides have been exploited as fluorescent probes of DNA and RNA in hybridization assays. In addition, pyrene fluorescence is largely affected by environmental factors, such as solvent and nearby nucleotide bases, which has led to its development as a potential probe for nucleic acid structures. Unit Structure: Unit Molecular Weight: 450.49 Pyrene Extinction Coefficient: 54,000 Excitation/Emission Max: 335 nm/381 nm References: Nakamura, M. et al. Pyrene is highly emissive when attached to the RNA duplex but not to the DNA duplex: the structural bases of this difference. Nucleic Acids Res. 33, 5887-5895 (2005). Du, H. et al. PhotochemCAD: A computer-aided design and research tools in photochemistry. Photochem. Photobiol. 68, 141-142 (1998).	5'-Pyr	$117.30	$158.10	$193.80	$244.80	$469.20
5'-TAMRA 5'-TAMRA Modification Code: TAM Description: Carboxytetramethylrhodamine (TAMRA) is a fluorescent dye that is a derivative of rhodamine, and is used to label oligonucleotides at the 5'- or 3'-ends, or internally. TAMRA-modified oligonucleotides play a particularly important role in both fluorescence resonance energy transfer (FRET) and real-time PCR applications. Unit Structure: Unit Molecular Weight: 576.57 Extinction Coefficient: 89,000 Excitation/Emission Max: 556 nm/580 nm	TAM	$242.76	$285.60	$336.60	$387.60	$673.20
5'-TET 5'-TET Modification Code: TET Description: Tetrachloro fluorescein (TET) is tetra-chloro derivative of fluorescein that is used to fluorescently label oligonucleotides. TET plays a role in real-time PCR applications, being used as a reporter moiety in probes and primers. For dual-label probes, TET is most commonly paired with the dark quencher BHQ-1, as the two have excellent spectral overlap. TET can be used to label DNA/RNA oligos for use as hybridization probes in a variety of in vivo and in vitro research or diagnostic applications, as well as for structure-function studies of DNA, RNA, and protein-oligonucleotide complexes. Unit Structure: Unit Molecular Weight: 676.24 Extinction Coefficient: 86,000 Excitation/Emission Max: 519 nm/539 nm	TET	$76.50	$94.86	$107.10	$132.60	$234.60
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 Modification Code: dN Description: Mixed 2'-deoxyribonucleoside bases in the same ratio (dA:dC:dG:dT=25%:25%:25%:25%). Unit Structure: Unit Molecular Weight: 308.95 (average of dA, dC, dG, and dT)	dN	$45.90	$53.04	$64.26	$79.56	$137.70
dS dS Modification Code: dS Description: Mixed 2'-deoxycytidine and 2'-deoxyguanosine bases in the same ratio (dC:dG=50%:50%). Unit Structure: Unit Molecular Weight: 309.20 (average of dC and dG)	dS	$45.90	$53.04	$64.26	$79.56	$137.70
dW dW Modification Code: dW Description: Mixed 2'-deoxyadenosine and 2'-deoxythymidine bases in the same ratio (dA:dT=50%:50%). Unit Structure: Unit Molecular Weight: 308.70 (average of dA and dT)	dW	$45.90	$53.04	$64.26	$79.56	$137.70
mN mN Modification Code: mN Description: Mixed 2'-O-methyl-nucleoside bases in the same ratio (mA:mC:mG:mU=25%:25%:25%:25%). Unit Structure: Unit Molecular Weight: 335.47 (average of mA, mC, mG, and mU)	mN	$45.90	$53.04	$64.26	$79.56	$137.70
rN rN Modification Code: rN Description: Mixed ribonucleoside bases in the same ratio (rA:rG:rC:rU=25%:25%:25%:25%). Unit Structure: Unit Molecular Weight: 321.44 (average of rA, rG, rC, and rU)	rN	$45.90	$53.04	$64.26	$79.56	$137.70
rS rS Modification Code: rS Description: Mixed guanosine and cytidine bases in the same ratio (rG:rC=50%:50%). Unit Structure: Unit Molecular Weight: 325.20 (average of rG and rC)	rS	$45.90	$53.04	$64.26	$79.56	$137.70
rW rW Modification Code: rW Description: Mixed adenosine and uridine bases in the same ratio (rA:rU=50%:50%). Unit Structure: Unit Molecular Weight: 317.69 (average of rA and rU)	rW	$45.90	$53.04	$64.26	$79.56	$137.70

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	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.

Dharmacon Custom RNA synthesis

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Additional Resources

Dharmacon RNA synthesis capabilities are well beyond the industry standard

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

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:

Protected RNA must be deprotected prior to use. You have two options for deprotecting your RNA oligos:

Fluorescent dyes available online:

5'-Fluorescein

5'-TAMRA-hexyl linker

Modification Name: 5’-Cy3

Modification Name: 3’-Cy3

Modification Name: 5’-Cy5

Modification Name: 3’-Cy5

Modification Name: 5’-Cy5.5

Modification Name: 3’-Cy5.5

Showing modifications available for:

Standard RNA Bases (A, C, G, U)

2'-OMe RNA Bases (A, C, G, U)

2'-Deoxy Bases (A, C, G, T)

1-Methyl-guanosine

2,6-Diaminopurine

2-Methyl-adenosine

2-Aminopurine

4-Thio-uridine

5-Bromo-uridine

5-Fluoro-cytidine

5-Fluoro-uridine

5-Iodo-uridine

5-Methyl-cytidine

5-Methyl-deoxycytidine

5-Methyl-uridine

Inosine

N3-Methyl-uridine

N6,N6-Dimethyl-adenosine

N6-Methyl-adenosine

Pseudouridine

Purine ribonucleoside

Pyrrolo-cytidine

Ribavirin

Phosphorothioate

5'-Phosphate

2'-Amino-butyryl-pyrene-uridine

2'-Amino-cytidine

2'-Amino-uridine

2'-Deoxy-uridine

2'-Fluoro-adenosine

2'-Fluoro-cytidine

2'-Fluoro-guanosine

2'-Fluoro-uridine

2'-OMe-inosine

3'-Amino modifier C12

3'-Amino modifier C6

5'-Amino modifier C12

5'-Amino modifier C3

5'-Amino modifier C5

5'-Amino modifier C6

5-Aminohexylacrylamino-uridine

3'-Disulfide thiol-modifier

5'-Disulfide thiol-modifier

C18 spacer

C3 spacer

C9 spacer

dSpacer

rSpacer

3' Inverted abasic

3' Inverted deoxy-thymidine

3'-Terminal 3'-deoxy-guanosine

3'-Terminal dideoxy-cytidine