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RNA oligonucleotides

RNA Oligonucleotides

RNA oligonucleotides are mainly used to study the involvement of RNA in gene regulation. Synthetic siRNA duplexes are introduced into cells to cause RNA interference and inhibit the expression of a specific messenger RNA (mRNA). In contrast miRNAs are able to regulate the expression of several mRNAs. They can be inhibited by synthetic single stranded RNAs acting as miRNA antagonists. On the other hand synthetic miRNAs or miRNA mimics can be used in order to induce the degradation of the mRNA and consequently induce the gene silencing effect.

RNA oligonucleotides specifications

  • Length*: From 5 to 139 bases
  • Synthesis scale: 10 nmol • 40 nmol • 200 nmol • 1000 nmol*
  • Backbone: RNA, LNA®, 2’O-Me RNA, 2'O-MOE RNA and all linkages
  • Modifications:
    • 5’:Phosphate, 6-FAM, CyR3, Cy5R, TET, HEX,...
    • 3’: DABCYL, TEG-Cholesteryl, TAMRA...
  • Purification: SePOP Desalting or IEX-RP/HPLC
  • Quality Control: MALDI-TOF MS
  • Format: Dried
  • Packaging: 2 mL tube
  • Documentation: Technical data sheet
  • siRNA Design: Free and guaranteed
  • Shipping: At room temperature


RNA Interference

Custom and control siRNA
siRNA design assistance
miRNA Inhibitors and Mimics

RNA backbones

RNA
LNA®
2’O-Me RNA
2’O-MOE
Phosphorothioate Linkages

Improve the efficiency of your RNA oligo

Three factors can improve the efficiency of your antisense oligonucleotides:

  • The resistance to nuclease before and during residence in cells,
  • The ability to cross the cellular membrane with some level of efficiency,
  • The binding affinity and specificity for the target sequence.

Resistance to nucleases

Choosing a backbone slightly different of the classical RNA structure may improve stability and resistance of your oligos against nucleases without modifying its function.

  • LNA® (Locked Nucleic Acid) is a bicyclic nucleic acid with a structure locked into a rigid C3'-endo position, which favours RNA A-type helix duplex geometry. This exceptional structure confers a very strong thermal stability towards complementary DNA and RNA template suitable for hybridisation assays requiring high specificity and/or reproducibility.
  • 2’O-Me RNA are partially resistant to a variety of ribo- and deoxyribonucleases. They form more stable hybrids with complementary RNA strands than equivalent DNA/RNA sequences. They are ideal for antisense probes.
  • 2’-O-(2-Methoxyethyl)- oligoribonucleotides or 2’-O-MOE have an analogue chemical structure to RNA excepted that a methoxyethyl residue is attached at the 2’-O-position. The chemical group at this position confers to the oligo backbone a highest nuclease resistance and a better binding affinity compared to the classical RNA molecule making it a useful tool for antisense applications.
  • Phosphorothioate bonds possess an increased resistance against nucleases due to the substitution of a non-bridging oxygen by sulphur.

In addition, using a 3’-terminal cap limit the degradation by nucleases (e.g., 3’-aminopropyl modification or by using a 3’-3’ terminal linkage)

Ability to cross the cellular membrane

Improved transport through the cellular membrane can be achieved by oligonucleotides modifications:

  • The use of a carrier molecule linked to the oligonucleotide (e.g., cholesterol),
  • Backbone modification to more lipophilic linkages (methylphosphonate),
  • The incorporation of modified monomers (5-(1-propynyl)-2’-deoxy-Uridine (pdU) and 5-(1-propynyl)-2’-deoxyCytidine (pdC).

Binding affinity

To increase the affinity and specificity of an RNA oligonucleotide, recommended modifications are:

*Larger synthesis scales are available on request.

 

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