5AXE | pdb_00005axe

Crystal Structure Analysis of DNA Duplexes containing sulfoamide-bridged nucleic acid (SuNA-NH)

• PDB DOI: https://doi.org/10.2210/pdb5AXE/pdb
• NAKB: 5AXE

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


• Deposited: 2015-07-28 Released: 2016-07-20 
• Deposition Author(s): Mitsuoka, Y., Aoyama, H., Kugimiya, A., Fujimura, Y., Yamamoto, T., Waki, R., Wada, F., Tahara, S., Sawamura, M., Noda, M., Hari, Y., Obika, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.95 Å
• R-Value Free: 
  0.144 (Depositor), 0.150 (DCC) 
• R-Value Work: 
  0.125 (Depositor), 0.128 (DCC) 
• R-Value Observed: 
  0.126 (Depositor) 

Starting Model: experimental

Literature

Effect of an N-substituent in sulfonamide-bridged nucleic acid (SuNA) on hybridization ability and duplex structure.

Mitsuoka, Y., Aoyama, H., Kugimiya, A., Fujimura, Y., Yamamoto, T., Waki, R., Wada, F., Tahara, S., Sawamura, M., Noda, M., Hari, Y., Obika, S.

(2016) Org Biomol Chem 14: 6531-6538

• PubMed: 27296230 
• DOI: https://doi.org/10.1039/c6ob01051b
• Primary Citation Related Structures: 
  5AXE, 5AXF


• PubMed Abstract: 
  

  A sulfonamide-bridged nucleic acid without an N-substituent (SuNA[NH]) was successfully synthesized. A comparison of the SuNA[NMe]- and SuNA[NH]-modified oligonucleotides revealed that the duplex-forming abilities of the SuNA[NMe]-modified oligonucleotides with complementary DNA and RNA were higher than those of the SuNA[NH]-modified oligonucleotides. The crystal structures of DNA duplexes containing a SuNA[NR] revealed that the helical structures of the two duplexes and hydration patterns around the bridge moiety were different. These results provide insights into hydration patterns and rationale for the high RNA affinity of SuNA-modified oligonucleotides.

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Organizational Affiliation: 
• Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan. [e-mail] and Discovery Research Laboratory for Innovative Frontier Medicines, Shionogi & Co., Ltd, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan.
Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan. [e-mail].
Discovery Research Laboratory for Innovative Frontier Medicines, Shionogi & Co., Ltd, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan.
Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan. [e-mail] and Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima 770-8514, Japan.

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 6.27 kDa 
• Atom Count: 794 
• Modeled Residue Count: 20 
• Deposited Residue Count: 20 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*GP*TP*AP*(LSH)P*AP*CP*GP*C)-3')	A, B	10	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.95 Å
• R-Value Free:  0.144 (Depositor), 0.150 (DCC) 
• R-Value Work:  0.125 (Depositor), 0.128 (DCC) 
• R-Value Observed: 0.126 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 23.685	α = 90
b = 42.905	β = 90
c = 45.205	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data collection
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-07-20 
Deposition Author(s): Mitsuoka, Y., Aoyama, H., Kugimiya, A., Fujimura, Y., Yamamoto, T., Waki, R., Wada, F., Tahara, S., Sawamura, M., Noda, M., Hari, Y., Obika, S.

Revision History  

• Version 1.0: 2016-07-20
  Type: Initial release
  
• Version 1.1: 2020-02-26
  Changes: Data collection, Derived calculations
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description