5AXE

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.125 

wwPDB Validation 3D Report Full Report


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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

  • DOI: 10.1039/c6ob01051b
  • Primary Citation of Related Structures:  

  • 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 oligonucle ...

    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.


    Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan. obika@phs.osaka-u.ac.jp and Discovery Research Laboratory for Innovative Frontier Medicines, Shionogi & Co., Ltd, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*GP*TP*AP*(LSH)P*AP*CP*GP*C)-3')A,B10synthetic construct
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LSH
Query on LSH
A, B
DNA LINKINGC11 H16 N3 O10 P SDT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.125 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 23.685α = 90.00
b = 42.905β = 90.00
c = 45.205γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
MOSFLMdata collection

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-07-20
    Type: Initial release