Custom siRNA Synthesis

Small interfering or short interfering RNAs (siRNAs) are a type of naturally expressed RNA molecules that belong to a member of non-coding RNAs (ncRNAs) family in the cells. They are short, double-stranded nucleic acids and can regulate gene, RNA, and protein functions through the RNA interference (RNAi) pathway. Unlike miRNAs, siRNAs bind sequences with nearly perfect complementarity and lead to cleavage of targets instead of translational suppression.

With a high reputation in the oligonucleotide synthesis field, Creative Biolabs has rich experience in creating a custom siRNA using online design tools and extensive synthesis options for specific applications. Today, our team has built a series of worry-free customizations for siRNA synthesis based on clients' sequences or sequences we have designed as clients' request. The synthesized oligos can meet all demands, including siRNA for different species, specific splice variants, and delivered forms.

Challenges with siRNA-based Therapeutics

RNA-based therapeutics are a relatively new class of drugs based on RNA sequences, including three main categories of RNA therapeutics: siRNA, RNA aptamers, and ribozymes. siRNAs are synthetic mediators of RNAi that are double-stranded RNA (dsRNA) molecules of 21-23 base pairs (bp) in length and have been designed specifically to silence target genes. The oligonucleotides are introduced exogenously into the cell or organism in short form (21-23 bp) or in long form of dsRNA molecules. These dsRNAs are processed by endogenic RNAi machinery after transformed into cells. Despite the potential of siRNA-based therapeutics in cancers, many challenges remain, such as rapid degradation, off-target effects, poor cellular uptake, efficacy, delivery, and immune response and toxicity.

Custom siRNA Synthesis at Creative Biolabs

Figure 1. The process of RNA interference in eukaryotic cells. (Ozcan, 2015)

siRNAs can be used to study single gene function both in vivo and in vitro and are an attractive new tool of therapeutics, especially against undruggable targets for the treatment of cancers and other severe diseases. Though there're many challenges for siRNA manufacture, rational design strategies, chemical modifications, selection algorithms, and nanocarriers offer valuable opportunities to overcome these problems.

At Creative Biolabs, we provide custom siRNA synthesis in multi-scale quantities for clients' silencing purposes. When we receive clients' siRNA sequences, experts will immediately configure these sequences by our design tools. All custom oligonucleotides are synthesized and manufactured under strict ISO standards and undergo quality control (QC) by HPLC and MS, annealed in RNase-free water, and duplex analyzed by gel. Moreover, final siRNAs are shipped in a lyophilized pellet to ensure safety and stability during delivery.

Rational Design of siRNAs

The selection of siRNA backbone is performed by choosing potentially active, nontoxic target inhibitors. This entails chemical synthesis of many different 21-mer siRNAs with 2-nt 3' overhangs. Alternative molecules that enter the RNAi machinery at distinct levels must also be considered. Secondary structures and nucleotide sequences of siRNAs have impacts on efficacy, specificity and off-target profiles. On the basis of the informational analysis of sequences, Creative Biolabs has formulated several rules for the rational design of siRNA.

• 2-nt overhangs at each 3'-end (typically TT or UU) are essential for the recognition of siRNAs.
• GC content of the sequence should ideally be between 30 to 70%, which determines the thermodynamic stability of siRNAs.
• To avoid nucleotide sequences occupied by regulatory proteins and exon-exon junctions, target sequences are usually located at 75-100 bases downstream of the start codon.
• Inclusion or exclusion of specific nucleotides at particular positions (e.g., a G/C at position 1, A/U at positions 10 and 19) is important for the efficacy and specificity of designed siRNAs.

Here, we have free online design tools that can be introduced to global clients, and also support other alternative siRNA designs for customized projects, such as:

Modifications & Labeling

At Creative Biolabs, we customize siRNA with a full range of modifications and fluorescent labels. Currently, our backbone and base modifications contain amino linkers, thio linkers, biotin, dabcyl, phosphate, and many others. For special modifications, please contact our technical specialists.

Meanwhile, our available fluorescent labels include fluorescein, rhodamine, Cyanine3 (Cy3), Cyanine5 (Cy5), Cyanine 570 (Cy570), Cyanine 670 (Cy670), etc. They are superior performance and can be directly substituted for some common dyes. Custom siRNAs might be labeled at either 3' or 5' end of the sense strand, and these labels won't affect the biological activity of siRNAs.

Product Processing Options

• HPLC purified: siRNAs are shipped purified, deprotected, duplexed, and desalted. They are ready for use immediately upon resuspension. In vivo custom synthesized siRNAs present the highest quality available anywhere with a purity of 97%.
• Desalted single strand: siRNAs are shipped deprotected, desalted single strand in a separate tube. And the oligos are ready for use immediately upon resuspension.
• Desalted duplex strands: siRNAs are shipped deprotected and desalted duplex strands in a tube. And the oligos are ready for use immediately upon resuspension.
• siRNA in-vivo-ready: siRNAs are shipped with a minimum of 90% purity. They're delivered with extra processing which includes counter ion (Na⁺) exchange, sterile filtration, dialysis, and endotoxin testing into animals.

The Items Need to Identify

Highlights

• Genome-wide coverage against human, mouse, rat, and other multiple species;
• Various synthesis, purification, modifications, and labelings options for special siRNA;
• Our siRNA products are available in single- or duplex-stranded formats;
• Increased efficacy by optimizing workflow and saving time by leaving construction to our experts.

We also provide ready-to-use high-specificity siRNA products targeting various targets. 2ʹ-O-methyl (2'-OMe), 2ʹ-deoxy-2ʹ-fluoro (2'-F), 2'-O-methoxyethyl (2'-MOE), and locked nucleic acid (LNA) modifications are applicable.

Because siRNA can efficiently silence the expression of target genes in a sequence-specific manner, they became indispensable tools to study the action mechanism of single genes. With proprietary synthesis and purification processes, Creative Biolabs has rapid turn-around time and high-throughput capacity to custom siRNAs that are ready-to-use after undergoing stringent QC. Particularly, our synthesis platforms can produce highly pure siRNA in diverse amounts (nmol) and offer various combinations of sizes, modifications, and purifications for convenient online ordering. If you don't find what you need on this webpage, please don't hesitate to contact us for more information.

Reference

1. Ozcan, G.; et al. (2015). Preclinical and clinical development of siRNA-based therapeutics. Adv Drug Deliv Rev. 87: 108-119.