1C4L

SOLUTION STRUCTURE OF AN RNA DUPLEX INCLUDING A C-U BASE-PAIR


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 
  • Selection Criteria: SUMMATION OF TOTAL ENERGY (COVALENT GEOMETRY, NON-BOND ENERGY, DISTANCE AND DIHEDRAL ANGLE CONSTRAINTS) 

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This is version 1.2 of the entry. See complete history


Literature

Solution structure of an RNA duplex including a C-U base pair.

Tanaka, Y.Kojima, C.Yamazaki, T.Kodama, T.S.Yasuno, K.Miyashita, S.Ono, A.Ono, A.Kainosho, M.Kyogoku, Y.

(2000) Biochemistry 39: 7074-7080

  • DOI: 10.1021/bi000018m
  • Primary Citation of Related Structures:  
    1C4L

  • PubMed Abstract: 
  • The formation of the C-U base pair in a duplex was observed in solution by means of the temperature profile of (15)N chemical shifts, and the precise geometry of the C-U base pair was also determined by NOE-based structure calculation. From the solution structure of the RNA oligomer, r[CGACUCAGG] ...

    The formation of the C-U base pair in a duplex was observed in solution by means of the temperature profile of (15)N chemical shifts, and the precise geometry of the C-U base pair was also determined by NOE-based structure calculation. From the solution structure of the RNA oligomer, r[CGACUCAGG].r[CCUGCGUCG], it was found that a single C-U mismatch preferred being stacked in the duplex rather than being flipped-out even in solution. Moreover, it adopts an irregular geometry, where the amino nitrogen (N4) of the cytidine and keto-oxygen (O4) of the uridine are within hydrogen-bonding distance, as seen in crystals. To further prove the presence of a hydrogen bond in the C-U pair, we employed a point-labeled cytidine at the exocyclic amino nitrogen of the cytidine in the C-U pair. The temperature profile of its (15)N chemical shift showed a sigmoidal transition curve, indicating the presence of a hydrogen bond in the C-U pair in the duplex.


    Related Citations: 
    • Structure model and physicochemical properties of the C-U mismatch pair in the double stranded RNA in solution
      Tanaka, Y., Kojima, C., Yamazaki, T., Kyogoku, Y., Miyashita, S., Ono, A.S., Kainosho, M.
      (1997) Nucleic Acids Symp Ser 37: 271

    Organizational Affiliation

    Institute for Protein Research, Osaka University, Japan.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*CP*GP*AP*CP*UP*CP*AP*GP*G)-3')A9N/A
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      RNA (5'-R(*CP*CP*UP*GP*CP*GP*UP*CP*G)-3')B9N/A
      Protein Feature View
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      • Reference Sequence
      Experimental Data & Validation

      Experimental Data

      • Method: SOLUTION NMR
      • Conformers Calculated: 50 
      • Conformers Submitted: 
      • Selection Criteria: SUMMATION OF TOTAL ENERGY (COVALENT GEOMETRY, NON-BOND ENERGY, DISTANCE AND DIHEDRAL ANGLE CONSTRAINTS) 
      • OLDERADO: 1C4L Olderado

      Structure Validation

      View Full Validation Report




      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2000-08-09
        Type: Initial release
      • Version 1.1: 2008-04-26
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance