2KP4

Structure of 2'F-ANA/RNA hybrid duplex


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 10 
  • Conformers Submitted: 10 
  • Selection Criteria: all calculated structures submitted 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Differential stability of 2'F-ANA*RNA and ANA*RNA hybrid duplexes: roles of structure, pseudohydrogen bonding, hydration, ion uptake and flexibility.

Watts, J.K.Martin-Pintado, N.Gomez-Pinto, I.Schwartzentruber, J.Portella, G.Orozco, M.Gonzalez, C.Damha, M.J.

(2010) Nucleic Acids Res. 38: 2498-2511

  • DOI: 10.1093/nar/gkp1225
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Hybrids of RNA with arabinonucleic acids 2'F-ANA and ANA have very similar structures but strikingly different thermal stabilities. We now present a thorough study combining NMR and other biophysical methods together with state-of-the-art theoretical ...

    Hybrids of RNA with arabinonucleic acids 2'F-ANA and ANA have very similar structures but strikingly different thermal stabilities. We now present a thorough study combining NMR and other biophysical methods together with state-of-the-art theoretical calculations on a fully modified 10-mer hybrid duplex. Comparison between the solution structure of 2'F-ANA*RNA and ANA*RNA hybrids indicates that the increased binding affinity of 2'F-ANA is related to several subtle differences, most importantly a favorable pseudohydrogen bond (2'F-purine H8) which contrasts with unfavorable 2'-OH-nucleobase steric interactions in the case of ANA. While both 2'F-ANA and ANA strands maintained conformations in the southern/eastern sugar pucker range, the 2'F-ANA strand's structure was more compatible with the A-like structure of a hybrid duplex. No dramatic differences are found in terms of relative hydration for the two hybrids, but the ANA*RNA duplex showed lower uptake of counterions than its 2'F-ANA*RNA counterpart. Finally, while the two hybrid duplexes are of similar rigidities, 2'F-ANA single strands may be more suitably preorganized for duplex formation. Thus the dramatically increased stability of 2'F-ANA*RNA and ANA*RNA duplexes is caused by differences in at least four areas, of which structure and pseudohydrogen bonding are the most important.


    Organizational Affiliation

    Department of Chemistry, McGill University, Montreal, QC H3A 2K6, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*(GFL)P*(CFL)P*(TAF)P*(A5L)P*(TAF)P*(A5L)P*(A5L)P*(TAF)P*(GFL)P*(GFL))-3')A10N/A
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*CP*CP*AP*UP*UP*AP*UP*AP*GP*C)-3')B10N/A
Small Molecules
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
GFL
Query on GFL
A
DNA LINKINGC10 H13 F N5 O7 PDG
CFL
Query on CFL
A
DNA LINKINGC9 H13 F N3 O7 PDC
TAF
Query on TAF
A
DNA LINKINGC10 H14 F N2 O8 PDT
A5L
Query on A5L
A
DNA LINKINGC10 H13 F N5 O6 PDA
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 10 
  • Conformers Submitted: 10 
  • Selection Criteria: all calculated structures submitted 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-02-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance