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PDBsum entry 2chk

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Nucleic acid PDB id
2chk
Jmol
Contents
DNA/RNA
PDB id:
2chk
Name: Nucleic acid
Title: Nmr structure of tllllt quadruplex
Structure: 5'-d( T lcg lcg lcg lcgp Tp)-3'. Chain: a, b, c, d. Other_details: telomeric sequence from o. Nova
Source: Synthetic: yes
NMR struc: 20 models
Authors: J.T.Nielsen,M.Petersen
Key ref: J.T.Nielsen et al. (2006). NMR solution structures of LNA (locked nucleic acid) modified quadruplexes. Nucleic Acids Res, 34, 2006-2014. PubMed id: 16614450
Date:
15-Mar-06     Release date:   19-Apr-06    
 Headers
 References

 

 
Nucleic Acids Res 34:2006-2014 (2006)
PubMed id: 16614450  
 
 
NMR solution structures of LNA (locked nucleic acid) modified quadruplexes.
J.T.Nielsen, K.Arar, M.Petersen.
 
  ABSTRACT  
 
We have determined the NMR solution structures of the quadruplexes formed by d(TGLGLT) and d(TL4T), where L denotes LNA (locked nucleic acid) modified G-residues. Both structures are tetrameric, parallel and right-handed and the native global fold of the corresponding DNA quadruplex is retained upon introduction of the LNA nucleotides. However, local structural alterations are observed owing to the locked LNA sugars. In particular, a distinct change in the sugar-phosphate backbone is observed at the G2pL3 and L2pL3 base steps and sequence dependent changes in the twist between tetrads are also seen. Both the LNA modified quadruplexes have raised thermostability as compared to the DNA quadruplex. The quadruplex-forming capability of d(TGLGLT) is of particular interest as it expands the design flexibility for stable parallel LNA quadruplexes and shows that LNA nucleotides can be mixed with DNA or other modified nucleic acids. As such, LNA-based quadruplexes can be decorated by a variety of chemical modifications. Such LNA quadruplex scaffolds might find applications in the developing field of nanobiotechnology.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21062811 E.B.Pedersen, J.T.Nielsen, C.Nielsen, and V.V.Filichev (2011).
Enhanced anti-HIV-1 activity of G-quadruplexes comprising locked nucleic acids and intercalating nucleic acids.
  Nucleic Acids Res, 39, 2470-2481.  
19603111 R.N.Veedu, and J.Wengel (2009).
Locked nucleic acid nucleoside triphosphates and polymerases: on the way towards evolution of LNA aptamers.
  Mol Biosyst, 5, 787-792.  
18414740 A.Galeone, L.Mayol, A.Virgilio, A.Virno, and A.Randazzo (2008).
A further contribution to the extreme variability of quadruplex structures from oligodeoxyribonucleotides containing inversion of polarity sites in the G-tract.
  Mol Biosyst, 4, 426-430.  
18236491 T.M.Ou, Y.J.Lu, J.H.Tan, Z.S.Huang, K.Y.Wong, and L.Q.Gu (2008).
G-quadruplexes: targets in anticancer drug design.
  ChemMedChem, 3, 690-713.  
17768146 I.Lebars, T.Richard, C.Di Primo, and J.J.Toulmé (2007).
NMR structure of a kissing complex formed between the TAR RNA element of HIV-1 and a LNA-modified aptamer.
  Nucleic Acids Res, 35, 6103-6114.
PDB codes: 2oom 2pn9
16944520 L.Petraccone, E.Erra, A.Randazzo, and C.Giancola (2006).
Energetic aspects of locked nucleic acids quadruplex association and dissociation.
  Biopolymers, 83, 584-594.  
17012276 S.Burge, G.N.Parkinson, P.Hazel, A.K.Todd, and S.Neidle (2006).
Quadruplex DNA: sequence, topology and structure.
  Nucleic Acids Res, 34, 5402-5415.  
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 codes are shown on the right.