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 

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This is version 1.2 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:  
    2KP3, 2KP4

  • 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 calculations on a fully modified 10-mer hybrid duplex ...

    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

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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*(GFL)P*(CFL)P*(TAF)P*(A5L)P*(TAF)P*(A5L)P*(A5L)P*(TAF)P*(GFL)P*(GFL))-3')A 10N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
RNA (5'-R(*CP*CP*AP*UP*UP*AP*UP*AP*GP*C)-3')B 10N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 10 
  • Conformers Submitted: 10 
  • Selection Criteria: all calculated structures submitted 
  • OLDERADO: 2KP4 Olderado

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-02-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2022-03-16
    Changes: Data collection, Database references, Derived calculations