Custom RNA

Short Summary

• Insert "r" before the base (rA, rU, rC, rG) for RNA bases.
• To enter 2’-O-Methyl RNA bases, enter [2OMeX] with X being the RNA base, for example [2OMeU] or [2OMeG].
• To enter chimeric DNA/RNA, use parenthesis to designate the RNA bases, such as AC(AU)N(C)TUC(CU).

Detailed Directions for the RNA order page

Use this order editor to order only single stranded RNA (ssRNA). To order siRNA, use the siMAX siRNA order editor.

You can provide the details of the RNA sequence using any of the three formats - 1) Manual Entry, 2) Upload file, and 3) Copy and Paste. Entering information using either of the three formats will take you to step 2, where you can choose additional synthesis scale and purification options.

To order an RNA oligo using this editor, simply enter the desired sequence in the order editor. The RNA bases allowed include C, U, G, and A. For eg., to order the Myotonic Dystrophy-associated RNA fragment containing CUG repeats, rC rU rG rC rU rG rC rU rG simply enter CUGCUGCUG in this order editor. To include modifications in the internal positions or in the termini, choose the available modifications from the dropdown list or type in the appropriate designator at the appropriate position. Please note that for standard RNA sequences, you can replace the sequence with its complementary sequence by clicking on the appropriate icon on the left. Once all the details of the required oligo are entered, add the oligo to the cart and check out.

Detailed Directions for DNA/RNA Chimeric order page

Use this order editor to order Chimeric Oligonucleotides, i.e., oligonucleotides that contain both ribo- and deoxyribo- nucleotides. To order are only sequences that contain only deoxyribonucleotides or ribonucleotides use the custom DNA or ssRNA order editors. The Chimeric ordering page should be used for ordering only mixed DNA/RNA sequences.

You can order the chimeric oligos either 1) manually or by 2) uploading an excel file after filling the details of the chimeric oligos.

Please use the following format to enter the various segments of the sequence:

• ACGT = DNA bases,
• (ACGU) = RNA bases,
• A*C*(G*U) = PTO '*' linker between the DNA and RNA bases,
• I = 2'-deoxyInosine,
• U = 2'-deoxyUridine
• Standard IUB/IUPAC codes for the degenerate bases.

For example, to place an order for the chimeric dA dC rA rU dN rC dT dU dC*rC rU,enter the following AC(AU)N(C)TUC*(CU) in the chimeric order editor. Please note that all chimeric oligos are delivered after HPLC purification.

Modifications are found here. When these modifications are included in the sequence, the synthesized oligos are only offered with HPLC purification. Please note that to order 2’-O-Methyl substituted ribonucleotides, use the designators [2OMeA], [2OMeC], [2OMeG], and [2OMeU] in the sequence. To order deoxyInosine or deoxyUridine simply use the single letter codes I or U, respectively, in the sequence of the oligonucleotide.

Fluors

Fluorophore	Designator	5'	Int	3'	Max Abs (nm)	Max Em (nm)	Extinction coefficient (M–1cm–1)	QY††
Cyanine5 dye	[Cy5]	✓			646	662	250,000	0.3
5-FAM	[5FAM]	✓			492	518
6-FAM	[FAM]	✓			495	521	75,000	0.9
HEX	[HEX]	✓			537	556	96,000	0.7
TET	[TET]	✓			519	539	86,000	0.9
†† QY (quantum yield) is a calculated ratio between the number of photons emitted and the number of photons absorbed. The most desireable QY for DLP purposes approaches 1.

Mixed Bases

MIXED BASES	Designator	5'	Int	3'	Composition
N (any base)	[N]	✓	✓	✓	N = (A, 25%; C, 25%; G, 25%; T, 25%)
B (not A)	[B]	✓	✓	✓	B = (C, 33.3%; G, 33.3%; T, 33.3%)
D (not C)	[D]	✓	✓	✓	D = (A, 33.3%; G, 33.3%; T, 33.3%)
H (not G)	[H]	✓	✓	✓	H = (A, 33.3%; C, 33.3%; T, 33.3%)
V (not T)	[V]	✓	✓	✓	V = (A, 33.3%; C, 33.3%; G, 33.3%)
K (G and T)	[K]	✓	✓	✓	K = (G, 50%; T, 50%)
M (A and C)	[M]	✓	✓	✓	M = (A, 50%; C, 50%)
R (purines)	[R]	✓	✓	✓	R = (A, 50%; G, 50%)
S (strong bonds)	[S]	✓	✓	✓	S = (C, 50%; G, 50%)
W (weak bonds)	[W]	✓	✓	✓	W = (A, 50%; T, 50%)
Y (pyrimidines)	[Y]	✓	✓	✓	Y = (C, 50%; T, 50%)

Attachment Mods

Attachment Mods	Designator	5'	Int	3'	Structure
Amino Modifier C6	[AmC6]	✓			link
Amino Modifier C6-dT	[AmC6dT]		✓		link
Amino Modifier C7	[AmC7]			✓	link
Phosphate	[PHO]	✓		✓	link

Non-flour labels

Non-flour labels	Designator	5'	Int	3'	Structure
Biotin-ON	[BioON]	✓	✓		link
Biotin-TEG (5' or 3')	[BIOTEG]	✓		✓	link
Biotin-TEG (internal)	[BIOTEGi]		✓		link
Cholesteryl-TEG (5' or Int)	[CholTEG]	✓	✓		link

Modified Bases, Spacers, Misc

Modified Bases, Spacers, Misc	Designator	5'	Int	3'	Structure
2'-O-Methyl-A	[2OMeA]	✓	✓	✓	link
2'-O-Methyl-C	[2OMeC]	✓	✓	✓	link
2'-O-Methyl-G	[2OMeG]	✓	✓	✓	link
2'-O-Methyl-U	[2OMeU]	✓	✓	✓	link
2'-Fluoro-A	[2FA]	✓	✓	✓
2'-Fluoro-C	[2FG]	✓	✓	✓
2'-Fluoro-G	[2FG]	✓	✓	✓	link
2'-Fluoro-U	[2FU]	✓	✓	✓
I	[I]	✓	✓	✓	link
U	[U]	✓	✓		link

Chimeric oligonucleotides are oligos that have both DNA or RNA bases in the sequence, including the modified RNA bases or linkers, such as 2’-O-methyl-Ribonucleotides and phosphorothioate bonds. The use of chimerics is recommended in applications where the stability of the RNA is critical for the success of the project. The use of DNA bases or 2’-O-methylated bases at nuclease sensitive portions of the oligo increase its resistance to digestion by nucleases. Use the dedicated order editor to order your nuclease-resistant chimerics. When you order Chimerics from Eurofins Genomics, you get:

• Dedicated online order editor
• Chimeric oligos from 6 to 80 bases
• Wide range of modifications
• All chimeric oligos are purified using HPLC
• Quality control by OD measurement and MALDI-TOF MS

Our experience over the decades has shown that HPLC purification is critical for the success in applications with chimeric oligos. We also recommend that you perform Na⁺ salt exchange using commercially available desalting column (e.g., NAP or MicroSpin columns) before use in cells or live animals.

Eurofins Genomics US is FDA compliant for cGMP manufacturing. If you require GMP and/or OEM services, please contact us.

Learn more about cGMP oligo manufacturing at Eurofins Genomics.