6ADV | pdb_00006adv

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

• PDB DOI: https://doi.org/10.2210/pdb6ADV/pdb
• NAKB: 6ADV

• Classification: DNA
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2018-08-02 Released: 2019-03-27 
• Deposition Author(s): Aoyama, H.A., Habuchi, T.H., Yamaguchi, T.Y., Obika, S.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 
  0.297 (Depositor), 0.309 (DCC) 
• R-Value Work: 
  0.253 (Depositor), 0.256 (DCC) 
• R-Value Observed: 
  0.258 (Depositor) 

Starting Model: experimental

Literature

Hybridization and Mismatch Discrimination Abilities of 2',4'-Bridged Nucleic Acids Bearing 2-Thiothymine or 2-Selenothymine Nucleobase.

Habuchi, T., Yamaguchi, T., Aoyama, H., Horiba, M., Ito, K.R., Obika, S.

(2019) J Org Chem 84: 1430-1439

• PubMed: 30632750 
• DOI: https://doi.org/10.1021/acs.joc.8b02863
• Primary Citation Related Structures: 
  6ADV


• 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-S ² T) or 2-selenothymine (scpBNA-Se ² T) 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-S ² T, 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-S ² T, revealed that the 2-thiocarbonyl moiety plays a crucial role in the destabilization of thymine-guanine mismatched wobble base pairs.

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Organizational Affiliation: 
• Graduate School of Pharmaceutical Sciences , Osaka University , 1-6 Yamadaoka , Suita , Osaka 565-0871 , Japan.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 7.44 kDa 
• Atom Count: 507 
• Modeled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(9V9)P*GP*CP*G)-3'	A, B	12	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free:  0.297 (Depositor), 0.309 (DCC) 
• R-Value Work:  0.253 (Depositor), 0.256 (DCC) 
• R-Value Observed: 0.258 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.49	α = 90
b = 41.13	β = 90
c = 65.42	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-03-27 
Deposition Author(s): Aoyama, H.A., Habuchi, T.H., Yamaguchi, T.Y., Obika, S.O.

Revision History  

• Version 1.0: 2019-03-27
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description