AccuTarget™ Predesigned siRNA

AccuTarget ™ Genome-wide Predesigned siRNAs are designed for Human, Mouse and Rat genomes. You can order from our homepage by searching their symbol, gene No, Refseq accession No, and description then selecting the type of purification and Guarantee yield (nmole).

All siRNA synthesis are delivered within 2~4 days after the date of order confirmation. If additional modifications are requested, the duration time will vary according to the composite schedule.

The maximum strands for synthesis are 85 mers for single stranded RNA and 30 mers for siRNA.

If you need us to syntheize siRNA more than 30 mer, please contact us at sirna@bioneer.co.kr.

Genome-wide predesigned siRNA, validation siRNA, siRNA Library, and control siRNA are synthesized by purifying the same concentration of sense and antisense and checking with MALDI-TOF mass spectrometer. Then, annealing process is done and dried in duplex form for delivery. The sent sample are shipped with DEPC D.W. for it to be used immediately by dissolving at the desired concentration (recommended at 100 μM).
When custom siRNA is ordered along with the annealing service, the same process is done. However, if you did not request the service, you can use the annealing buffer (1X) to anneal according to the protocol sent with the sample.

10 nmole scale siRNA at 100nM is sufficient to transfection into 100 wells in 6-well plate. Generally, Bio-RP purification can be used to get good results for simple cell experiments. 

Yes, we use dA, dC, dG, and dT bases to synthesize the chimeric RNA of desired sequence mixed with DNA and RNA. Synthesis of 2'-O-Methyl type RNA and 2'-F (rA, rC, rG, rUrU, rC) RNA is also available. Please follow the order guide on the web when ordering those kinds from our homepage.

For genome-wide predesigned siRNA produced by Bioneer, only 3 types of candidates can be provided. If you want to order more than 4 candidates, Custom siRNA service must be used. Sequences can only be checked after ordering the siRNA. If you want to compare them with the sequences in the thesis or change the design condition, please contact us by email at sirna@bioneer.co.kr.

Try checking the siRNA with PAGE to see whether it was degraded. If not, we recommend looking at the transfection efficiency. We provide free two siRNA if two out of three purchased pre-designed siRNA show less than 80% of knockdown efficiency. Please send us following data for validation. 

1. siRNA knockdown efficiency data - NC: AccuTarget Negative Control, siRNA concentration: 100 nM
2. Transfection efficiency data - PC : AccuTarget ™ GAPDH/GFP/Luciferase siRNA

(We also accept siRNA knockdown data gained from laboratory protocols as a positive control. However, the cell line and transfection methods should be performed in the same way.)

Unless there are no specifications stated in the order form, all the ordered siRNA will be marked with -OH on 5' and 3' ends.For 5-phosphate-loaded siRNAs, you must order 5 'phosphorylation-modified siRNAs.

Modification of siRNA is crucial for its wide application. The simplest method is using phosphoramidite to label the siRNA with its synthesizer.

If modification is needed on the 5’ position, labeling of phosphoramidite is carried out by binding after synthesizing the siRNA with the requested sequences.

3’-Modification is more complicated than 5’-modification. In this case, a solid support attached with the label is used during the siRNA synthesis process, allowing it to be labeled as it is made.

By using phosphoramidite with the label attached to the 5’ position of the deoxyuridine base, the label can be implanted on the desired position of the sequence resulting in synthesis of internal modified siRNA.

The following shows the examples of siRNA modification provided by our company.

• 5' Amine - 3' amine modification

• 5' Phosphorylation & 3' phosphorylation

• 5' Thiol - 3' Thiol Modification

• 5' Biotin - Internal Biotin-dT Modification

• 5' Fluorescein - 3' Fluorescein modification

• 3' TAMRA modification

We are also capable of providing about 100 types of modification including the ones shown above. For the full list, please check our homepage.

All the siRNA synthesis are generally done in a clean room. Those product are delivered in their most stable lyophilized form and can be stored more than a year at -20℃. When the aerosol particles containing RNase are introduced, the siRNA dissolved in DEPC-DW may be decomposed during freezing and thawing process. Therefore, upon its receipt, it is highly recommended to immediately divide the sample in RNase-free tubes to store the aliquots and use only the amount of siRNA needed for your protocol without thawing the whole. Also, note that special care must be taken for RNAs during their storage as their phosphodiester bonds may be broken at pH of 11 or higher.

siRNA can be stored in the form of solution for longer storage period by using DEPC D.W. solvent shipped with your order. 

Their fluorescence may decrease in the presence of light, so it is recommended to store in a dark container and keep in a place with no light. In case of orders with cyanine 3 and 5, avoid storage in basic conditions as those will be degraded at pH 9 or higher.

As the amounts of synthesized siRNAs are very small, it is difficult to directly quantify by their mass. Therefore, we use an indirect method to estimate their quantity by measuring the amount of absorbed light by siRNAs and express it in form of O.D. (optical density).

siRNA synthesis is normally fulfilled with guarantee nmole unit. Results are also reported in the same unit. However, if you must use in ng or μg, you must first convert the mole into g. As the molecular weight is shown in the report, you can easily do the conversion by using the following formula.

Molecular weight (g) x number of mole (nmole) = Amount of siRNA (ng)

The “volume for 100 pmole/µl’ written on the siRNA synthesis kit represents the volume of DEPC D.W. needed to achieve the concentration of 100 pmole/µl. For instance, if your report shows the values for two siRNA are 100 and 200, you can make concentration of 100 pmole/µl of DEPC D.W. by adding 100 µl and 200 µl in respective oligomer tubes.

In other words, each tube contains following amount of siRNA:

100 μl x 100 pmole/μl = 10,000 pmole = 10 nmole
200 μl x 100 pmole/μl = 20,000 pmole = 20 nmole 

Although its final use will dictate the concentration of siRNA, our company provides the value for making 100 pmole/µl of siRNA, which is the most convenient concentration to be used in general cases.

First, as designing the siRNA with high efficiency is made by estimating the sequences optimized with various physical and biochemical factors, it is recommended to try at least three different siRNA samples to find the best one for your protocols.

Second, to check the knockdown effect of siRNA at the protein level, treat the target mRNA with the siRNA and measure the mRNA level through real-time PCR, then use either ELISA or Western blot to inspect the inhibition of protein expression.

Third, it is highly important to minimize the RNase contamination. Not only the enzyme is present in unsterilized containers and skins, but also in air or aerosols. Extra care must be taken to prevent the RNase degradation of siRNA.

Fourth, cells should be kept healthy, maintaining a proper number and using a transfection reagent. Having excessive cells may reduce the transfection efficiency.

Finally, keep in mind that setting the control group is cruical for interpreting the results. Using positive controls, negative controls, and fluorescently labeled siRNA allow identifying errors in experimental design and process. 

If this is your first time using siRNA, it is important to adjust additional experimental conditions such as concentration of siRNA, the number of cells cultured, and the exclusion of antibiotics.

Furthermore, as having positive control, negative control, and fluorescent labeled siRNA will help interpreting your results, when using cell lines with uncertain transfection efficiency, use NC-FITC, fluorescent labeled scrambled siRNA, for checking the intracellular delivery efficiency of siRNA.

Easily monitor the siRNA delivery using the positive control or NC-FITC by using our products.

* Positive control : AccuTarget ™ Positive Control siRNAs (Human GAPDH,GFP,Luciferase)

* Negative control : AccuTarget ™ Negative Control siRNAs (Human, Mouse, Rat)

* NC-FITC : AccuTarget ™ Fluorescein-labeled Negative Control siRNA

About 60-70% cell density is appropriate for transfection of siRNA. (HeLa cell, 6-well plate standard : 1.5 x 10⁵ cells/well , However, adjustment may require according to user's condition.)

Its starting concentration will be100 nM, but the optimization process will be required to meet the cell conditions by gradually reducing the concentration. (100 pmol/well)

This is probably the most confusing part for the majority of people. When transfecting 100nM siRNA into a well of 6-well plate, where the volume of transfection solution is 1 ml, you will need 100 pmole of siRNA to treat it at the concentration of 100 nM (100 pmole/ml). Adding 2 μl of 50 μM(50 pmole/μl) siRNA stock will allow to transfect 100 pmoles of siRNA. If you were to order 10 nmole, it will be sufficient to transfection 100 wells at 100 nM (100 pmole/ml).

It is recommended to use a suitable transfection reagent depending on the cell conditions to be tested.

As each cell line has different transfection efficiency, please refer to the technical data of each manufacturer.  

The transfection efficiency can be checked by fluorescence microscopy after transfecting NC-FITC. Furthermore, before this experiment, cell conditions and transfection conditions such as the concentration of siRNA and transfection agent can be tested by using NC-FITC as the test reagent.

AccuTarget ™ Negative control siRNA, compatible with human, mouse, and rat, is a non-targeting siRNA having a low homology sequence to all known genes in the those. Therefore, it can be used as a negative control for knockdown experiments of all genes.

AccuTarget ™ Positive control siRNA have high knockdown efficiency on target genes. Also, it provides an efficient siRNA for GAPDH, a house-keeping gene expressed in all cells, to indirectly check transfection efficiency. In addition, siRNAs that show high-efficiency knock-down effects on GFP and Luciferase, which are commonly used as reporter genes, are also avaliable.

While qRT-PCR and Northern blot can be used to confirm the mRNA degradation, Western blot can be used to confirm the reduction of the protein. Generally, the most widely used assay method is qRT-PCR for measuring the expression inhibition efficiency compared to negative control siRNA.

AccuTarget ™ Genome-wide predesigned siRNAs is a predesigned siRNA using Turbo si-Designer, an efficient siRNA design algorithm jointly developed by Korea Research Institute of BIoscience and Biotechnology(KRIBB) and BIONEER. Using this technology, we provide a qualified AccuTarget ™ Genome-wide predesigned siRNA database with high knockdown efficiency.

Currently, BIONEER's website allows you to purchase predesigned siRNAs for Human (18,048 genes), Mouse (17,117 genes), and Rat (9,392 genes) within 2-3 days of ordering. 

AccuTarget™ siRNA is designed by the highly efficient Turbo si-Designer algorithm developed by Korea Research Institute of BIoscience and Biotechnology(KRIBB) and BIONEER.
This product can be ordered as a set with Real-Time PCR primers. More than 10 siRNAs can be also  ordered in flexible siRNA Library format as a plate type.

You can order siRNA candidates from the BIONEER ordering site by entering the gene name or gene accession number you want. If you have ordered through Custom siRNA service, not Predesigned siRNAs for your desired genes, you can order via the Turbo si-Designer algorithm by email (sirna@bioneer.co.kr). However, this only applies orders having to 3 or more candidate for the same gene.

Generally, all siRNA and miRNA are provided with RNA duplex of 20-23 mer. Thus, almost all the miRNA can be used similarly with siRNA. For other miRNA-only applications, please see below.

You can find it on the MirBase (http://www.mirbase.org) 22Version. For newly discovered miRNAs that have not been updated, please order them via Custom siRNA service.

There are some controversies regarding this topic. While some reports state that miRNA function varies depending on the cell types, others claim that miRNAs work similarly. For more information, please refer to the related documents. (Reference : 1-4)

As miRNAs inhibit protein expression of target mRNA, either conduct a luciferase assay using a luciferase vector containing the miRNA binding site of the 3’UTR of the target mRNA or a Western blot. To view both protocols, please refer to related literatures. (Reference : 5)

Moreover, since  miRNAs are also known to cause the degradation of some mRNAs, qPCR can be also used.

As with siRNA, fluorescent labeling can be used with miRNA for checking the transfection efficiency. You can order fluorescence-labeled miRNAs with custom siRNA. Requesting to attach the fluorescence on the strand having miRNA activity may cause loss of its function. Thus, it is recommended to fluoresce the opposite strand if possible.

AccuTarget ™ Human miRNA is a chemically synthesized mature miRNA based on miRBase sequence information, purified to high purity and sold on a regular basis. If you would like to order miRNA individually, you can do so using our custom RNA synthesis service.

We recommend using the miRNA Negative Control (Cat.No.SN-1001-CFG).

miRNA mimic is a chemical synthesis of mature miRNA with a double strand oligonucleotide designed to act as a miRNA in vivo. miRNA inhibitors are complementary synthetic oligos that strongly hybridize to miRNAs to act as their inhibitors.