2KD4

Solution structure and thermodynamics of 2',5' RNA intercalation


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 10 
  • Conformers Submitted: 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Solution structure and thermodynamics of 2',5' RNA intercalation.

Horowitz, E.D.Lilavivat, S.Holladay, B.W.Germann, M.W.Hud, N.V.

(2009) J Am Chem Soc 131: 5831-5838

  • DOI: 10.1021/ja810068e
  • Primary Citation of Related Structures:  
    2KD4

  • PubMed Abstract: 
  • As a means to explore the influence of the nucleic acid backbone on the intercalative binding of ligands to DNA and RNA, we have determined the solution structure of a proflavine-bound 2',5'-linked octamer duplex with the sequence GCCGCGGC. This stru ...

    As a means to explore the influence of the nucleic acid backbone on the intercalative binding of ligands to DNA and RNA, we have determined the solution structure of a proflavine-bound 2',5'-linked octamer duplex with the sequence GCCGCGGC. This structure represents the first NMR structure of an intercalated RNA duplex, of either backbone structural isomer. By comparison with X-ray crystal structures, we have identified similarities and differences between intercalated 3',5' and 2',5'-linked RNA duplexes. First, the two forms of RNA have different sugar pucker geometries at the intercalated nucleotide steps, yet have the same interphosphate distances. Second, as in intercalated 3',5' RNA, the phosphate backbone angle zeta at the 2',5' RNA intercalation site prefers to be in the trans conformation, whereas unintercalated 2',5' and 3',5' RNA prefer the -gauche conformation. These observations provide new insights regarding the transitions required for intercalation of a phosphodiester-ribose backbone and suggest a possible contribution of the backbone to the origin of the nearest-neighbor exclusion principle. Thermodynamic studies presented for intercalation of both structural RNA isomers also reveal a surprising sensitivity of intercalator binding enthalpy and entropy to the details of RNA backbone structure.


    Organizational Affiliation

    Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, School of Chemistry and Biochemistry, Atlanta, Georgia 30332-0400, USA.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-R(*GP*CP*CP*GP*CP*GP*GP*C)-2'A, B8N/A
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    PRL
    Query on PRL

    Download CCD File 
    A, B
    PROFLAVIN
    C13 H11 N3
    WDVSHHCDHLJJJR-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: SOLUTION NMR
    • Conformers Calculated: 10 
    • Conformers Submitted: 
    • Selection Criteria: structures with the lowest energy 
    • OLDERADO: 2KD4 Olderado

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2009-04-07
      Type: Initial release
    • Version 1.1: 2011-07-13
      Changes: Version format compliance