1RME

DNA (5'-D(MCYP*CP*TP*CP*C)-3') tetramer, NMR, 1 structure


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 24 
  • Conformers Submitted: 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure and conversion kinetics of a bi-stable DNA i-motif: broken symmetry in the [d(5mCCTCC)]4 tetramer.

Nonin, S.Leroy, J.L.

(1996) J Mol Biol 261: 399-414

  • DOI: 10.1006/jmbi.1996.0472
  • Primary Citation of Related Structures:  
    1RME

  • PubMed Abstract: 
  • At slightly acidic pH, protonation of C-rich oligomers results in the formation of a four-stranded structure composed of two parallel duplexes in a head to tail orientation with their hemi-protonated C.C+ pairs intercalated in a so-called i-motif. In all cases reported previously the duplexes are identical ...

    At slightly acidic pH, protonation of C-rich oligomers results in the formation of a four-stranded structure composed of two parallel duplexes in a head to tail orientation with their hemi-protonated C.C+ pairs intercalated in a so-called i-motif. In all cases reported previously the duplexes are identical. The tetramer formed by the d(5mCCTCC) oligomer is different. The structure is computed on the basis of 55 inter-residue distances derived from NOESY cross-peaks measured at short mixing times. It consists of two intercalated non-equivalent symmetrical duplexes. The base stacking order is C5* C1 C4* C2 (T3*) T3 C2* C4 C1* C5, but the thymidine bases (T3*) of one duplex are looped out and lie in the wide grooves of the tetramer. The thymidine bases T3 stack as a symmetrical T.T pair between the sequentially adjacent C2.C2+ pair and the C2*.C2*+ pair of the other duplex. Numerous exchange cross-peaks provide evidence for duplex interconversion. The interconversion rate is 1.4 s-1 at 0 degree C and the activation energy is 94 kJ/mol. The opening of the T3.T3 pair, the closing of the T3*.T3 pair, and the opening of the C2*.C2*+ pair occur simultaneously with the duplex interconversion. This suggests that the concerted opening and closing of the thymidine bases drive the duplex interconversion. Opening of the C4.C4+ and C4*.C4*+ pairs, and dissociation of the tetramer are not part of the interconversion since they occur at much slower rates. Duplex interconversion within the [d(5mCCTCC)]4 tetramer provides the first structural and kinetics characterization of broken symmetry in a biopolymer. The tetramer formed by d(5mCCUCC) adopts a similar structure, but the rate of duplex interconversion is faster: 40 s-1 at 0 degree C. At 32 degrees C, interconversion is fast on the NMR time scale.


    Related Citations: 
    • Solution Structures of the I-Motif Tetramers of D(Tcc), D(5Methylcct) and D(T5Methylcc): Novel Noe Connections between Amino Protons and Sugar Protons
      Leroy, J.L., Gueron, M.
      (1995) Structure 3: 101

    Organizational Affiliation

    Groupe de Biophysique de l'Ecole Polytechnique et de 1'URA D1254 du CNRS, Palaiseau, France.



Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*(MCY)P*CP*TP*CP*C)-3')A, B, C, D5synthetic construct
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 24 
  • Conformers Submitted: 
  • Selection Criteria: structures with the least restraint violations 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-01-11
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-03-14
    Changes: Data collection, Derived calculations, Experimental preparation, Other, Source and taxonomy