ISDA

Entry Detail

PDB ID:

7OZZ

Keywords:

DNA-RNA HYBRID

Title:

The crystal structure of a DNA:RNA hybrid duplex sequence CTTTTCTTTG with LNA-amide modification

Biological Source:

Source Organism:

synthetic construct

Host Organism:

synthetic construct

PDB Version:

Deposition Date:

2021-06-29

Release Date:

2022-08-03

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.70 Å

R-Value Free:

0.23

R-Value Work:

0.20

R-Value Observed:

0.20

Space Group:

P 61

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Macromolecular Entities

Polymer Type:polyribonucleotide
Description:RNA (5'-R(*CP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3')
Chain IDs:A
Chain Length:10
Number of Molecules:1
Biological Source:synthetic construct

Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(*CP*TP*(05H)P*TP*CP*TP*TP*TP*G)-3')
Chain IDs:B
Chain Length:9
Number of Molecules:1
Biological Source:synthetic construct

Ligand Molecules

Primary Citation

An LNA-amide modification that enhances the cell uptake and activity of phosphorothioate exon-skipping oligonucleotides.

Baker, Y.R, Thorpe, C, Chen, J, Poller, L.M, Cox, L, Kumar, P, Lim, W.F, Lie, L, McClorey, G, Epple, S, Singleton, D, McDonough, M.A, Hardwick, J.S, Christensen, K.E, Wood, M.J.A, Hall, J.P, El-Sagheer, A.H, Brown, T.Show

Nat Commun 13 4036 4036 (2022)

PMID: 35821218 DOI: 10.1038/s41467-022-31636-2

Abstact

Oligonucleotides that target mRNA have great promise as therapeutic agents for life-threatening conditions but suffer from poor bioavailability, hence high cost. As currently untreatable diseases come within the reach of oligonucleotide therapies, new analogues are urgently needed to address this. With this in mind we describe reduced-charge oligonucleotides containing artificial LNA-amide linkages with improved gymnotic cell uptake, RNA affinity, stability and potency. To construct such oligonucleotides, five LNA-amide monomers (A, T, C, 5mC and G), where the 3'-OH is replaced by an ethanoic acid group, are synthesised in good yield and used in solid-phase oligonucleotide synthesis to form amide linkages with high efficiency. The artificial backbone causes minimal structural deviation to the DNA:RNA duplex. These studies indicate that splice-switching oligonucleotides containing LNA-amide linkages and phosphorothioates display improved activity relative to oligonucleotides lacking amides, highlighting the therapeutic potential of this technology.

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Primary Citation of related structures