siRNA for Gene Silencing

siRNA, or small interfering ribonucleic acid, is a type of RNA that is involved in a number of biological processes, most notably RNA interference. RNA interference is a regulatory process that is used to control and limit the expression of specific genes. Regulatory active siRNA consists of annealed, complementary RNA sequences, usually 21-25 nucleotide in length and with symmetric 2 nucleotide 3’ overhangs.

Chemical synthesis enables the incorporation of DNA nucleotides as overhangs thereby rendering the siRNA-duplex more stable against nuclease degradation.

Features and Benefits

High Quality

all siRNAs are MALDI-TOF MS controlled before shipment
Renowned siRNA supplier for top research institutes, pharma/biotech companies

Convenient

Ready to use: siRNA is manufactured as ready to use aqueous solution (40 µM siRNA duplex, 10 mM NaCl, 10 mM TrisHCl, pH 7.5)
Modified siRNAs on request (e.g. GalNAc)
Easy-to-use siRNA design tool on our webshop

Cost Effective

Very competitive pricing for volume as well as repetitive orders
High guaranteed yields; average delivery yield usually significantly higher

Excellent Technical Support

Trained scientists with molecular biology background are happy to support you (from 8 am to 5 pm)

User-friendly Online Ordering System

Easy-to-use online portal, a user-friendly input mask and other helpful tools (e.g. order tracking and history, convenient search and re-order option)

Remark: If you want to design customized siRNA we recommend using our siRNA design tool on the webshop.

Overview

siRNA, or small interfering ribonucleic acid, is a type of RNA that is involved in a number of biological processes, most notably RNA interference. RNA interference is a regulatory process that is used to control and limit the expression of specific genes. While most RNA is single stranded, siRNA is made up of two complementary strands of RNA nucleotides similar to those in DNA. Usually siRNA molecules are 21-25 nucleotide double-stranded RNA (dsRNA) duplexes with symmetric 2 nucleotide 3’ overhangs.

The RNA interference process and the biochemical machinery involved. Double-stranded RNA is cut into short pieces (siRNA) by the endonuclease Dicer. The antisense strand is loaded into the RISC complex and links the complex to the mRNA strand by base-pairing. The RISC complex cuts the mRNA strand, and the mRNA is subsequently degraded.

siRNA Duplexes

Microsynth supplies siRNA duplexes from standard (2x21-mers) to extended length (2x27-mers) at different levels of purity and scales, depending on the intended application:

Desalted siRNA (for screening purposes)
HPLC and PAGE purified siRNA (for screening and for use in cells)
In vivo animal studies (on request)

Product Characteristics:

Synthesis scale¹	Desalted		HPLC		PAGE
Synthesis scale¹	OD260²	[nmol]²	OD260²	[nmol]²	[OD260]²	[nmol]²
Genomics	on request	7	not available		not available
0.04 µmol	9	21	4	8	not available
0.2 µmol	16	35	7	16	2	5
Higher Scales	on request
Classical siRNA duplexes (2x21-mers) have unit prices; if you need longer duplexes, each additional RNA base will be priced accordingly. Modified siRNAs are available upon request.

¹ The synthesis scale represents the initial amount of 3' bases (starting material).

² Yields indicated represent guaranteed yields and apply to a 2x21mer; Calculation: 1 OD = ~2.5 nmol (please note that this calculation is based on sequences with virtually homogenous distribution of the 4 RNA bases)

Control siRNAs

Positive and negative control siRNA are an essential complement to any gene silencing experiment. Positive controls are validated siRNAs known to achieve high levels (>70%) of knockdown. A positive control should be used to optimize transfection and to reconfirm high levels of delivery in each RNAi experiment.

Negative controls are validated siRNAs to show no homology to any known mammalian gene. They are important for distinguishing sequence-specific silencing from non–specific effects in the RNAi experiment. The two most common controls are scrambled and non-targeting controls.
A scrambled control is exactly what it sounds like, it involves taking the siRNA and randomly rearranging its nucleotide sequence.

In the following you will find a selection of siRNA controls that have been validated in numerous scientific publications.

Name	Sense Strand Sequence (5’ -3’)	Sense Strand 3’ Overhang (5’ – 3’)	Anti-Sense Strand 3’ Overhang (5’ – 3’)
Lamin	CUGGACUUCCAGAAGAACA	dTdT	dTdT
GFP	GCAGCACGACUUCUUCAAG	dTdT	dTdT
Luciferase	CGUACGCGGAAUACUUCGA	dTdT	dTdT
Non-targeting negative control	AGGUAGUGUAAUCGCCUUG	dTdT	dTdT
Scrambled negative control	On request

As any specific target siRNA, control siRNAs can be readily ordered in different synthesis scales and purification levels via Microsynth’s webshop.

siRNA Design

To help you designing the most appropriate siRNA, targeting your gene of interest, Microsynth has developed a proprietary software, and made it available on its webshop.

Microsynth’s siRNA design tool is making use of the set of guidelines initially provided by Boese et al [1].
The design results show the best siRNAs according to the Reynolds scores [2]. The best siRNA is most likely the one that shows the highest scores.
The siRNA sequences with the highest scores can be selected and directly be ordered online.
A link to NCBI BLAST is incorporated so you can properly manage the risk of potential off-target effects of the predicted siRNA.

References:
[1] Boese Q, Leake D, Reynolds A, et al. Mechanistic insights aid computational short interfering RNA design. Methods Enzymol. 2005;392:73-96. doi:10.1016/S0076-6879(04)92005-8
[2] Reynolds, A., Leake, D., Boese, Q. et al. Rational siRNA design for RNA interference. Nat Biotechnol 22, 326–330 (2004). https://doi.org/10.1038/nbt936

Figure: Microsynth's siRNA Design Tool
Specify your target sequence and optionally some further parameters such as AA preceding the siRNA core sequence, the number of stretches of identical bases, the G/C content as well as further sequence restrictions (e.g. sequence areas that should be considered or not) to receive your design suggestion (highest scores on top) in a ready-to-order format.

How to Order

Enter our webshop
Click on siRNA in the blue “DNA/RNA Synthesis” domain
Select Normal Entry in order to type or copy/paste the desired sequence information etc. or alternatively select Upload Entry by using our convenient Excel template (can be downloaded during ordering )