8I50 image
Deposition Date 2023-01-21
Release Date 2023-08-09
Last Version Date 2023-09-06
Entry Detail
PDB ID:
8I50
Keywords:
Title:
Crystal structure of DNA octamer containing GuNA[Me,Me]
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
0.95 Å
R-Value Free:
0.19
R-Value Work:
0.16
R-Value Observed:
0.17
Space Group:
P 61 2 2
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*GP*(OIQ)P*GP*(BRU)P*AP*CP*AP*C)-3')
Chain IDs:A
Chain Length:8
Number of Molecules:1
Biological Source:synthetic construct
Primary Citation
Mechanism of the extremely high duplex-forming ability of oligonucleotides modified with N-tert-butylguanidine- or N-tert-butyl-N'- methylguanidine-bridged nucleic acids.
Nucleic Acids Res. 51 7749 7761 (2023)
PMID: 37462081 DOI: 10.1093/nar/gkad608

Abstact

Antisense oligonucleotides (ASOs) are becoming a promising class of drugs for treating various diseases. Over the past few decades, many modified nucleic acids have been developed for application to ASOs, aiming to enhance their duplex-forming ability toward cognate mRNA and improve their stability against enzymatic degradations. Modulating the sugar conformation of nucleic acids by substituting an electron-withdrawing group at the 2'-position or incorporating a 2',4'-bridging structure is a common approach for enhancing duplex-forming ability. Here, we report on incorporating an N-tert-butylguanidinium group at the 2',4'-bridging structure, which greatly enhances duplex-forming ability because of its interactions with the minor groove. Our results indicated that hydrophobic substituents fitting the grooves of duplexes also have great potential to increase duplex-forming ability.

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Primary Citation of related structures