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2'-O-methyl ribose

2'-OMe

Steric block, splice switching and microRNA inhibition

In a 2'-OMe nucleotide the 2'-hydroxyl of the ribose carries a methyl group. 2'-O-methylation occurs naturally in ribosomal, transfer and small nuclear RNAs. As a synthetic modification it shifts the sugar toward the C3'-endo pucker of RNA, raises affinity for a complementary RNA relative to DNA, and resists nucleases.

A fully 2'-OMe oligonucleotide is not a knockdown reagent. RNase H1 cleaves the RNA strand of a DNA/RNA duplex, and the duplex a fully 2'-OMe oligonucleotide forms is RNA-like throughout, so the enzyme does not cut it. The oligonucleotide binds its site and stays there. That is what the chemistry is made for, and it is why a knockdown design is a 2'-MOE or locked nucleic acid gapmer instead.

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Designed by AUM against your target, or made to your sequence by quotation.

Delivered yield nmol
  1. 5
  2. 10
  3. 25
  4. 50
  5. 100
  6. 200
  7. 250
  8. 500
  9. 1000
Order 2'-OMe against a targetOrder 2'-OMe to your sequence

Use

Applications and selection

  • Steric block

    The oligonucleotide occupies a site on an RNA so that a protein or another RNA cannot reach it: a translation start site, a regulatory element, a binding site.

  • Splice switching

    Masking a splice site, an enhancer or a silencer on the pre-mRNA makes the spliceosome skip an exon or include one, changing which isoform is made.

  • microRNA inhibition

    The oligonucleotide binds a mature microRNA so that it cannot act on its targets. Fully 2'-OMe antisense oligonucleotides were among the first microRNA inhibitors, and the design is still used.

  • What it is not used for

    Knockdown. A fully 2'-OMe oligonucleotide does not support RNase H cleavage, so a 2'-MOE or locked nucleic acid gapmer is the design for cutting a transcript.

Design

Design notes

Modified at every position. A steric blocker carries the modification at every position, so that no stretch of the oligonucleotide can form the DNA/RNA duplex RNase H1 acts on. The whole length is 2'-OMe: there is no gap and no wing.

Site, not transcript. The oligonucleotide is complementary to the element it must cover, and the outcome is read at that element: a shifted splice product, a change in the protein made, or the loss of a microRNA's effect on its targets. Measure that outcome. A transcript-level assay alone does not show a translation blocker working, because the block is on translation rather than on the abundance of the transcript.

The backbone. A phosphorothioate backbone is the one most often used for stability in cells and in serum; a phosphodiester 2'-OMe oligonucleotide is digested more quickly, though more slowly than unmodified RNA. At high concentration a phosphorothioate backbone can also raise toxicity.

Beside the other two. 2'-OMe raises affinity less per residue than locked nucleic acid and is less resistant to nucleases than 2'-MOE. Published steric blockers and microRNA inhibitors are often built on it, and where such a design exists it can be made exactly as described.

Purification and yields

Purification and study model

Desalt and RPC are sold for cellular studies. HPLC, the grade bought for animal work, is sold for in vivo studies.

Delivered yield nmol
  1. 5
  2. 10
  3. 25
  4. 50
  5. 100
  6. 200
  7. 250
  8. 500
  9. 1000
Purification and study model
PurificationStudy model
desaltin vitro, cellular studies
RPCin vitro, cellular studies
HPLCin vivo, animal studies

Delivered yield is what arrives in the tube, in nmol, not the amount synthesized to produce it. This chemistry is sold at every yield in every tier, so the tier and the yield are chosen independently.

Order 2'-OMe against a targetOrder 2'-OMe to your sequence

Related

Beside this chemistry

For research use only. Not for use in diagnostic or therapeutic procedures.