Ordering is straightforward — just send us the following for each sequence, in any format you prefer (email, Word, or Excel all work great):

Oligo ID / Name: A unique label for each sequence (e.g., "sgRNA-target-1"). This keeps everything organized, especially for multi-sequence orders.

Sequence (5' → 3'): Your RNA sequence in standard single-letter nucleotide code. Please provide it 5' to 3'.

Synthesis Quantity: Let us know how much you need, specified in nanomoles (nmol) or micrograms (µg).

Modifications & Linkages: Note any chemical modifications — backbone chemistries (like phosphorothioate or our proprietary PACE modification), sugar modifications (2'-OMe, 2'-F, LNA), functional labels (biotin, fluorophores), end modifications, or base analogs (pseudouridine, m6A). Our catalogue is at cirena.com/rna-modifications. Don't see what you need? Just ask — we love a good challenge. Send orders or questions to sales@cirena.com and we'll get back to you within 24 hours.

Great question - long RNA is worth protecting carefully, and it's easier than you might think.

Your RNA will be shipped lyophilized; this is the most stable form for long-term storage. Keep it at -20°C in a desiccated environment, and you're looking at a shelf life of up to 36 months. Once resuspended, working aliquots are fine at 4°C for up to a month. Try to avoid repeated freeze-thaw cycles (we recommend no more than five).

A few habits that make a real difference: always use RNase-free tips, tubes, and gloves; store in low-binding polypropylene tubes (like Eppendorf LoBind®); and if your product is fluorescently labeled, keep it away from light.

When you're ready to resuspend, let the sealed tube come to room temperature for ~5 minutes before opening - this prevents condensation from sneaking in.

More questions? We're happy to help.

This is a really important question and not hard to do.

 As mentioned in the storage FAQ - Your RNA will arrive lyophilized as this is the most stable form for shipping and storage.

When you're ready to resuspend your RNA:

• Allow the sealed tube rise to room temperature for ~5 minutes before opening - this prevents condensation from sneaking in

• Use the same buffer you plan to use in your experiment

• Spin the tube for longer than one minute to dissolve all of the material

• Evaluate the concentration prior to use via UV measurement – while manufacturers are very diligent at labeling the tubes, small changes in concentration can have an impact on experimental results

Following these simple steps will help ensure experimental success.

More questions about preparation? Please ask us.

‍ The honest answer is: it depends on length, quantity, purity, and modifications. Here's what to expect for HPLC-purified orders under 30 nmol:

‍ ‍Length Turnaround Time

‍ Up to 150 nt 12–15 business days‍

‍ 151–200 nt 15–20 business days

‍ Over 200 nt 20–25 business days

‍ ‍These times run from order acceptance to shipment, so please add transit time for your location when planning experiments.

A few things worth knowing. Longer sequences require more synthesis cycles and more demanding purification, both take time to do right. Certain modifications can also affect turnaround, so if your order includes anything complex, we'll flag it upfront. For quantities above 30 nmol, timelines vary — just reach out sales@cirena.com and we'll work through the details together.

Cirena orders ship with a Certificate of Analysis that includes the following analytical data:

LC-MS: This confirms sequence identity by measuring the molecular mass of the dominant species. LC-MS verifies that the RNA you receive has the intended sequence and detects any mass shifts that would indicate synthesis errors such as misincorporation, incomplete deprotection, or residual modification.

Analytical HPLC: Provides a purity profile i.e., the relative proportion of full-length product versus truncated sequences and other impurities. The area percent of the full-length peak is reported as the purity value. For most long RNA research applications (CRISPR, prime editing, ncRNA), we recommend a minimum purity of ≥75% full-length.

If you have questions about interpreting the analytical data, or if you would like to discuss what purity is appropriate for your application, our technical team is glad to help.

Modifications give you better control over what your RNA does, and doesn't do, once it's in your experiment, enabling more reliable performance across diverse biological systems.

The most common reason is stability. Unmodified RNA is inherently susceptible to nuclease degradation. Sugar modifications like 2'-OMe and 2'-F help block endonuclease cleavage at specific sites, but the main protection against degradation comes from the backbone. Modifications like phosphorothioate or phosphonoacetate (PACE) alter the linkages between nucleotides directly, extending functional lifetime and improving consistency across replicates and longer workflows, especially in longer or more complex RNA designs.

Modifications also shape how RNA interacts with cellular machinery. Base analogs like pseudouridine or m5C can reduce immunostimulatory responses, which is critical for applications where you want RNA to be functional without triggering an innate immune reaction. Other modifications, like biotin or fluorescent labels, add functional handles for detection, pull-down assays, or imaging.

In short, modifications let you tune the stability, immunogenicity, and functionality of your RNA for your specific application. If you're weighing different options, we're always happy to help you think through what will work best for your experiment.

One of the biggest advantages of chemical synthesis is the sheer range of modifications it can incorporate precisely, and at site-specific positions along the sequence. They fall into a few general families:

Sugar modifications: improve nuclease resistance and binding affinity - examples 2'-O-methyl (2'-OMe), 2'-fluoro (2'-F), and LNA.

Backbone modifications: guard against degradation and can influence how the RNA behaves in biological systems, e.g., phosphorothioate (PS), phosphonoacetate (PACE).

Base modifications and analogs: can reduce immunogenicity or fine-tune base-pairing - examples pseudouridine and 5-methylcytosine.

Terminal modifications: support stability and downstream applications, e.g., 5' caps or specialized 3' end groups,

Functional labels and conjugates: biotin, fluorophores, and amino or thiol linkers add handles for detection, purification, and imaging.

Because each of these can be placed at an exact position, chemical synthesis offers a level of site-specific control that biological methods can't easily match.

We also can help decide what modifications are useful in your applications! Contact rnatechsupport@cirena.com

PACE (phosphonoacetate) is an advanced backbone modification in which the standard phosphodiester linkage is replaced by a phosphonoacetate group. In simpler terms, one of the phosphate's non-bridging oxygens is swapped for a small carboxymethyl arm. It's a subtle change with outsized benefits.

The headline advantage is stability: PACE linkages are highly resistant to nuclease degradation and have been shown to exceed the more familiar phosphorothioate linkage. Unlike some backbone chemistries, PACE preserves the native-like negative charge of natural RNA, and it can improve cellular uptake which provides a meaningful edge for functional work. It also layers cleanly alongside sugar and base modifications.

When should you reach for PACE? It shines where durability matters most, for instance in CRISPR guide RNAs where a few PACE linkages near the 3' end help protect against degradation and can improve editing yields. It's also worth considering whenever your RNA needs to survive a demanding cellular environment.

If you’re interested in seeing data or more applications, navigate over to the “Our Science” section on our website and click “PACE Modification”.

Not quite and the difference comes down to how each method builds the RNA.

In vitro transcription (IVT) uses an RNA polymerase (typically T7) to assemble the strand from nucleotide building blocks. That works beautifully for producing long RNA (thousands of bases), but it also sets limits: the polymerase only accepts certain modified nucleotides, and whatever it does accept is incorporated at every position of that base. So, you can globally swap in analogs like pseudouridine, N1-methylpseudouridine, or 5-methylcytidine (which is how modified mRNA is made) and add features such as 5' caps and poly(A) tails. What you can't do is place a modification at one specific site.

Chemical synthesis works the opposite way, adding one nucleotide at a time and doesn’t proceed until that reaction is finished. This enables site-specific modifications and a much wider chemical toolkit including most sugar and backbone modifications and precise labels that polymerases simply won't incorporate.

So there's some overlap, but chemical synthesis offers far more control. If you would like to learn more about the differences between chemical synthesis and IVT in-depth, we posted an article on our Linkedin:

https://www.linkedin.com/posts/cirena-inc_introducing-ask-an-expert-we-get-a-lot-activity-7485397776105676800-04_M?utm_source=share&utm_medium=member_desktop&rcm=ACoAACxl3ukB2rLnDtoQhj9B7RBpUpI5LXHHf9o

At 100–300 nucleotides, high purity isn't just a single percentage on an HPLC trace, it is the full-length sequence integrity with minimal truncated species, strict removal of immunogenic dsRNA or abortive transcripts, and striving towards zero chemical adducts. This is important to ensure the RNA you receive is functionally homogeneous and ready for cellular or biochemical applications without background noise.