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Adenylated oligonucleotides provide direct substrates for T4 RNA ligase

Product spotlight: Use the adenylation modification for ligation, miRNA library construction, next generation sequencing, 5’ end labeling, and ribosome assembly experiments.

Apr 11, 2012

Revised/updated Nov 1, 2017

Quick facts:

Availability: DNA
Location: 5'
Scales: 100 nmol–10 µmol
Purification: HPLC required IDT
Ordering symbol: /5rApp/

MOD_impA

Figure 1. Adenylated oligonucleotide.

Creating direct substrates for T4 RNA ligase

Two single-stranded nucleic acid fragments can be covalently linked (ligated) by T4 RNA ligase. In the presence of ATP, ligase adenylates the 5’ end of single-stranded nucleic acids, which can then be ligated to the 3’ OH of other single-stranded sequences. However, when ATP is absent, synthetically adenylated oligonucleotides act as direct substrates for T4 RNA ligase, with the pyrophosphate linkage providing the energy required for the reaction and eliminating the need for ATP [1]. IDT custom synthesizes adenylated oligonucleotides using the chemical adenylation method of Unrau and Bartel [2].

Adenylated oiigo applications

Adenylated oligonucleotides can be used in numerous applications. These include miRNA library construction, next generation sequencing, 5’ end labeling, and ribosome assembly experiments.

Ordering adenylated oligos

To add 5’ adenylation to an oligonucleotide order, select 5’ Adenylation from the 5’ mods tab on the oligo entry page. Note that this modification requires HPLC purification, and a 3’ blocking group to prevent oligonucleotide circularization. Preferred blocking groups are C3 Spacer (/3SpC3/) or Dideoxy-C (/3ddC/).

References

  1. England TE, Gumport RI, and Uhlenbeck OC (1977) Dinucleoside pyrophosphate are substrates for T4-induced RNA ligase. Proc Natl Acad Sci USA, 74:4839–4842.
  2. Unrau PJ and Bartel DP (1998) RNA-catalysed nucleotide synthesis. Nature, 395:260–263.

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