6ADV

Crystal Structure Analysis of the duplex containing the S2T(2',4'-BNA/LNA)G mismatch pairs

Summary for 6ADV

• Entry DOI: 10.2210/pdb6adv/pdb
• Descriptor: 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(9V9)P*GP*CP*G)-3' (2 entities in total)
• Functional Keywords: dna, lna, 2', 4'-bna, mismatched base pairs
• Biological source: synthetic construct
• Total number of polymer chains: 2
• Total formula weight: 7444.96

Authors

Aoyama, H.A.,Habuchi, T.H.,Yamaguchi, T.Y.,Obika, S.O. (deposition date: 2018-08-02, release date: 2019-03-27, Last modification date: 2023-11-22)

Primary citation

Habuchi, T.,Yamaguchi, T.,Aoyama, H.,Horiba, M.,Ito, K.R.,Obika, S.
Hybridization and Mismatch Discrimination Abilities of 2',4'-Bridged Nucleic Acids Bearing 2-Thiothymine or 2-Selenothymine Nucleobase.
J. Org. Chem., 84:1430-1439, 2019

PubMed Abstract: Oligonucleotides modified with 2'- O,4'- C-spirocyclopropylene-bridged nucleic acid (scpBNA) exhibit excellent duplex-forming ability with their complementary single-stranded RNA (ssRNA). Here, we demonstrate that scpBNA bearing a 2-thiothymine (scpBNA-ST) or 2-selenothymine (scpBNA-SeT) nucleobase provides robust mismatch discrimination capabilities to oligonucleotides without compromising their high binding affinities toward the full complementary ssRNA. X-ray crystallographic analysis of a self-assembling oligonucleotide featuring 2',4'-BNA/LNA-2-thiothymine (2',4'-BNA/LNA-ST, where 2',4'-BNA and LNA stand for "2'- O,4'- C-methylene-bridged nucleic acid" and "locked nucleic acid", respectively), a prototype of scpBNA-ST, revealed that the 2-thiocarbonyl moiety plays a crucial role in the destabilization of thymine-guanine mismatched wobble base pairs.

PubMed: 30632750
DOI: 10.1021/acs.joc.8b02863

Experimental method

X-RAY DIFFRACTION (1.96 Å)