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2'-O,4'-C-methylene-bridged ribose

Locked nucleic acid

Gapmers with short high-affinity wings, and mixmers

A locked nucleic acid nucleotide is a ribonucleotide in which a methylene bridge joins the 2'-oxygen to the 4'-carbon of the sugar. The bridge locks the ribose in the C3'-endo conformation of RNA, so the nucleotide is pre-organized for binding: each locked residue raises the melting temperature of the duplex with complementary RNA, per modification, more than either 2'-MOE or 2'-OMe does.

Like the other 2'-modified sugars, a locked residue is not a substrate for RNase H, so a knockdown design is a gapmer with locked wings and a DNA gap. Locked residues also resist nucleases. A design with no gap, in which locked and DNA residues alternate, is a steric blocker, a form used for microRNA inhibition and splice switching.

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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 locked nucleic acid against a targetOrder locked nucleic acid to your sequence

Use

Applications and selection

  • Affinity in a short oligonucleotide

    Where the accessible window on the target is short, or the region is structured, a few locked residues give the affinity that would otherwise need a longer oligonucleotide.

  • A published design, reproduced

    Published gapmers and microRNA inhibitors built on locked nucleic acid are made to the same pattern, position by position.

  • Affinity per modification

    Of the three chemistries sold here, locked nucleic acid raises duplex stability the most per residue, so a design needs the fewest modified positions.

  • What it is not used for

    A knockdown design carrying locked residues at every position: such an oligonucleotide leaves no gap for RNase H.

Design

Design notes

Short wings. Locked wings are kept to a few residues at each end, for two reasons. A locked residue adds so much affinity that a few of them reach the melting temperature the design needs, and a longer wing adds affinity it does not need. That excess is a cost rather than a gain. An oligonucleotide that binds very tightly can hold on to a partially matched sequence elsewhere in the transcriptome, so extra locked residues raise the risk of off-target binding without adding activity the design needs.

The gap. The central run of unmodified deoxynucleotides is what RNase H1 cuts opposite. Keep it DNA and keep it long enough for the enzyme; a locked residue inside the gap blocks cleavage at that position. Write out which positions are locked and which are DNA when you send the sequence.

The backbone. Gapmers are typically made on a phosphorothioate backbone, which resists nucleases and binds proteins, supporting uptake into cells and tissue, and which lowers the affinity of the duplex slightly. At high concentration a phosphorothioate backbone can also raise toxicity.

Mixmers. For steric block and microRNA inhibition, locked residues are spread through the oligonucleotide and alternated with DNA, so there is no gap and no RNase H cleavage. The oligonucleotide occupies its site.

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 locked nucleic acid against a targetOrder locked nucleic acid to your sequence

Related

Beside this chemistry

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