6GPI

Tc-DNA/DNA duplex


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation 3D Report Full Report


This is version 2.1 of the entry. See complete history

Literature

NMR solution structure of tricyclo-DNA containing duplexes: insight into enhanced thermal stability and nuclease resistance.

Istrate, A.Johannsen, S.Istrate, A.Sigel, R.K.O.Leumann, C.J.

(2019) Nucleic Acids Res. 47: 4872-4882

  • DOI: 10.1093/nar/gkz197
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Tc-DNA is a conformationally constrained oligonucleotide analogue which shows significant increase in thermal stability when hybridized with RNA, DNA or tc-DNA. Remarkably, recent studies revealed that tc-DNA antisense oligonucleotides (AO) hold grea ...

    Tc-DNA is a conformationally constrained oligonucleotide analogue which shows significant increase in thermal stability when hybridized with RNA, DNA or tc-DNA. Remarkably, recent studies revealed that tc-DNA antisense oligonucleotides (AO) hold great promise for the treatment of Duchenne muscular dystrophy and spinal muscular atrophy. To date, no high-resolution structural data is available for fully modified tc-DNA duplexes and little is known about the origins of their enhanced thermal stability. Here, we report the structures of a fully modified tc-DNA oligonucleotide paired with either complementary RNA, DNA or tc-DNA. All three investigated duplexes maintain a right-handed helical structure with Watson-Crick base pairing and overall geometry intermediate between A- and B-type, but closer to A-type structures. All sugars of the tc-DNA and RNA residues adopt a North conformation whereas the DNA deoxyribose are found in a South-East-North conformation equilibrium. The conformation of the tc-DNA strand in the three determined structures is nearly identical and despite the different nature and local geometry of the complementary strand, the overall structures of the examined duplexes are very similar suggesting that the tc-DNA strand dominates the duplex structure.


    Organizational Affiliation

    Department of Chemistry, Winterthurerstrasse 190, University of Zürich, Zürich CH-8057, Switzerland.,Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern CH-3012, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
tc-DNA (5'-D(*(TCJ)P*(TTK)P*(TCJ)P*(TCS)P*(TCS)P*(TCJ)P*(TTK)P*(TTK)P*(TCY)P*(TCJ))-3')A10Homo sapiens
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*TP*AP*AP*GP*CP*CP*GP*AP*G)-3')B10Homo sapiens
Small Molecules
Modified Residues  5 Unique
IDChainsTypeFormula2D DiagramParent
F7H
Query on F7H
A
DNA linkingC13 H17 N3 O4DC
EAN
Query on EAN
A
DNA linkingC13 H17 N2 O8 PDT
TCY
Query on TCY
A
DNA linkingC13 H16 N5 O6 PDA
F4Q
Query on F4Q
A
DNA linkingC13 H16 N5 O7 PDG
TCJ
Query on TCJ
A
DNA linkingC13 H18 N3 O7 PDC
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the least restraint violations 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland--

Revision History 

  • Version 1.0: 2018-06-13
    Type: Initial release
  • Version 1.1: 2019-04-03
    Type: Data collection, Database references
  • Version 1.2: 2019-05-08
    Type: Data collection
  • Version 2.0: 2019-05-15
    Type: Data collection, Polymer sequence
  • Version 2.1: 2019-05-22
    Type: Data collection, Database references