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PDBsum entry 105d

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dna_rna links
DNA PDB id
105d
Jmol
Contents
DNA/RNA
PDB id:
105d
Name: DNA
Title: Solution structures of the i-motif tetramers of d(tcc), d(5mcct) and d(t5mcc). Novel noe connections between amino protons and sugar protons
Structure: DNA (5'-d( Tp Cp C)-3'). Chain: a, b, c, d. Engineered: yes
Source: Synthetic: yes
NMR struc: 8 models
Authors: J.-L.Leroy,M.Gueron
Key ref:
J.L.Leroy and M.Guéron (1995). Solution structures of the i-motif tetramers of d(TCC), d(5methylCCT) and d(T5methylCC): novel NOE connections between amino protons and sugar protons. Structure, 3, 101-120. PubMed id: 7743125 DOI: 10.1016/S0969-2126(01)00138-1
Date:
22-Dec-94     Release date:   07-Feb-95    
 Headers
 References

 

 
DOI no: 10.1016/S0969-2126(01)00138-1 Structure 3:101-120 (1995)
PubMed id: 7743125  
 
 
Solution structures of the i-motif tetramers of d(TCC), d(5methylCCT) and d(T5methylCC): novel NOE connections between amino protons and sugar protons.
J.L.Leroy, M.Guéron.
 
  ABSTRACT  
 
BACKGROUND: At slightly acid or even neutral pH, oligodeoxynucleotides that include a stretch of cytidines form a tetramer structure in which two parallel-stranded duplexes have their hemi-protonated C.C+ base pairs face-to-face and fully intercalated, in a so-called i-motif, first observed serendipitously in [d(TC5)]4. RESULTS: A high-definition structure of [d(TCC)]4 was computed on the basis of inter-residue distances corresponding to 21 NOESY cross-peaks measured at short mixing times. A similarly defined structure of [d(5mCCT)]4 was also obtained. A small number of very characteristic (amino proton)-(sugar proton) cross-peaks entails the intercalation topology. The structure is generally similar to that of [d(TC5)]4. The sequence d(T5mCC) forms two tetramers in comparable proportions. The intercalation topologies are read off the two patterns of (amino proton)-(sugar proton) cross-peaks: one is the same as in the d(TCC) tetramer, the other has the intercalated strands shifted by one base, which avoids the steric hindrance between the methyl groups of the 5mC pairs of the two duplexes. CONCLUSIONS: The structures obtained in this work and the procedures introduced to characterize them and to solve the problems linked to the symmetry of the structure provide tools for further exploring the conditions required for formation of the i-motif.
 
  Selected figure(s)  
 
Figure 10.
Figure 10. Stereoview, normal to the wide groove, of the lowest-energy conformer of [d(TCC)][4] . T1, green; C2, red; C3 yellow. Figure 10. Stereoview, normal to the wide groove, of the lowest-energy conformer of [d(TCC)][4] . T1, green; C2, red; C3 yellow.
Figure 11.
Figure 11. Views of the eight lowest-energy conformers of the d(TCC) tetramer. (a) View of the wide groove. (b) View of the narrow groove. Colour coding as in Figure 10. Figure 11. Views of the eight lowest-energy conformers of the d(TCC) tetramer. (a) View of the wide groove. (b) View of the narrow groove. Colour coding as in [3]Figure 10.
 
  The above figures are reprinted by permission from Cell Press: Structure (1995, 3, 101-120) copyright 1995.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20355286 A.I.Holm, L.M.Nielsen, B.Kohler, S.V.Hoffmann, and S.Brøndsted Nielsen (2010).
Electronic coupling between cytosine bases in DNA single strands and i-motifs revealed from synchrotron radiation circular dichroism experiments.
  Phys Chem Chem Phys, 12, 3426-3430.  
20657837 J.Dai, E.Hatzakis, L.H.Hurley, and D.Yang (2010).
I-motif structures formed in the human c-MYC promoter are highly dynamic--insights into sequence redundancy and I-motif stability.
  PLoS One, 5, e11647.  
19780129 M.Kaushik, M.Prasad, S.Kaushik, A.Singh, and S.Kukreti (2010).
Structural transition from dimeric to tetrameric i-motif, caused by the presence of TAA at the 3'-end of human telomeric C-rich sequence.
  Biopolymers, 93, 150-160.  
19433505 J.L.Leroy (2009).
The formation pathway of i-motif tetramers.
  Nucleic Acids Res, 37, 4127-4134.  
18045788 C.Bardin, and J.L.Leroy (2008).
The formation pathway of tetramolecular G-quadruplexes.
  Nucleic Acids Res, 36, 477-488.  
17330895 J.Völker, H.H.Klump, and K.J.Breslauer (2007).
The energetics of i-DNA tetraplex structures formed intermolecularly by d(TC5) and intramolecularly by d[(C5T3)3C5].
  Biopolymers, 86, 136-147.  
16936319 S.Modi, A.H.Wani, and Y.Krishnan (2006).
The PNA-DNA hybrid I-motif: implications for sugar-sugar contacts in i-motif tetramerization.
  Nucleic Acids Res, 34, 4354-4363.  
15869382 J.Völker, and K.J.Breslauer (2005).
Communication between noncontacting macromolecules.
  Annu Rev Biophys Biomol Struct, 34, 21-42.  
16204453 M.Canalia, and J.L.Leroy (2005).
Structure, internal motions and association-dissociation kinetics of the i-motif dimer of d(5mCCTCACTCC).
  Nucleic Acids Res, 33, 5471-5481.
PDB code: 2awv
15647504 N.Esmaili, and J.L.Leroy (2005).
i-motif solution structure and dynamics of the d(AACCCC) and d(CCCCAA) tetrahymena telomeric repeats.
  Nucleic Acids Res, 33, 213-224.
PDB codes: 1ybl 1ybn 1ybr
16010354 V.V.Jolad, F.K.Murad, J.R.Arnold, and J.Fisher (2005).
Solution conformation of d(C(4)ACAC(4)TGT)(2); an intramolecularly folded i-motif from the insulin minisatellite.
  Org Biomol Chem, 3, 2234-2236.  
16206324 Y.Zhao, Z.X.Zeng, Z.Y.Kan, Y.H.Hao, and Z.Tan (2005).
The folding and unfolding kinetics of the i-motif structure formed by the C-rich strand of human telomere DNA.
  Chembiochem, 6, 1957-1960.  
12770889 T.E.Malliavin, J.Gau, K.Snoussi, and J.L.Leroy (2003).
Stability of the I-motif structure is related to the interactions between phosphodiester backbones.
  Biophys J, 84, 3838-3847.  
11438725 J.Völker, H.H.Klump, and K.J.Breslauer (2001).
Communication between noncontacting macromolecules.
  Proc Natl Acad Sci U S A, 98, 7694-7699.  
11160907 K.Kanaori, N.Shibayama, K.Gohda, K.Tajima, and K.Makino (2001).
Multiple four-stranded conformations of human telomere sequence d(CCCTAA) in solution.
  Nucleic Acids Res, 29, 831-840.  
11027145 F.Geinguenaud, J.Liquier, M.G.Brevnov, O.V.Petrauskene, Y.I.Alexeev, E.S.Gromova, and E.Taillandier (2000).
Parallel self-associated structures formed by T,C-rich sequences at acidic pH.
  Biochemistry, 39, 12650-12658.  
10851195 M.Guéron, and J.L.Leroy (2000).
The i-motif in nucleic acids.
  Curr Opin Struct Biol, 10, 326-331.  
9737878 K.Kanaori, A.Maeda, H.Kanehara, K.Tajima, and K.Makino (1998).
1H nuclear magnetic resonance study on equilibrium between two four-stranded solution conformations of short d(CnT).
  Biochemistry, 37, 12979-12986.  
9687367 W.Shepard, W.B.Cruse, R.Fourme, E.de la Fortelle, and T.Prangé (1998).
A zipper-like duplex in DNA: the crystal structure of d(GCGAAAGCT) at 2.1 A resolution.
  Structure, 6, 849-861.
PDB code: 376d
9282112 R.J.Wellinger, and D.Sen (1997).
The DNA structures at the ends of eukaryotic chromosomes.
  Eur J Cancer, 33, 735-749.  
9331414 S.Nonin, A.T.Phan, and J.L.Leroy (1997).
Solution structure and base pair opening kinetics of the i-motif dimer of d(5mCCTTTACC): a noncanonical structure with possible roles in chromosome stability.
  Structure, 5, 1231-1246.
PDB code: 1bae
8901542 I.Berger, M.Egli, and A.Rich (1996).
Inter-strand C-H...O hydrogen bonds stabilizing four-stranded intercalated molecules: stereoelectronic effects of O4' in cytosine-rich DNA.
  Proc Natl Acad Sci U S A, 93, 12116-12121.  
8639535 J.M.Benevides, C.Kang, and G.J.Thomas (1996).
Raman signature of the four-stranded intercalated cytosine motif in crystal and solution structures of DNA deoxycytidylates d(CCCT) and d(C8).
  Biochemistry, 35, 5747-5755.  
8679634 L.Lacroix, J.L.Mergny, J.L.Leroy, and C.Hélène (1996).
Inability of RNA to form the i-motif: implications for triplex formation.
  Biochemistry, 35, 8715-8722.  
8953261 R.Wu, and T.Wu (1996).
A novel intact circular dsDNA supercoil.
  Bull Math Biol, 58, 1171-1185.  
8946802 Y.Guan, and G.J.Thomas (1996).
Vibrational analysis of nucleic acids. IV. Normal modes of the DNA phosphodiester structure modeled by diethyl phosphate.
  Biopolymers, 39, 813-835.  
7583631 M.Kochoyan, and J.L.Leroy (1995).
Hydration and solution structure of nucleic acids.
  Curr Opin Struct Biol, 5, 329-333.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.