2IDN

NMR structure of a new modified Thrombin Binding Aptamer containing a 5'-5' inversion of polarity site

• PDB DOI: https://doi.org/10.2210/pdb2IDN/pdb
• NAKB: 2IDN

• Classification: DNA
• Mutation(s): No 


• Deposited: 2006-09-15 Released: 2007-01-09 
• Deposition Author(s): Randazzo, A., Martino, L., Virno, A., Mayol, L., Giancola, C.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 20 
• Conformers Submitted: 7 
• Selection Criteria: structures with the lowest energy 

Literature

A new modified thrombin binding aptamer containing a 5'-5' inversion of polarity site.

Martino, L., Virno, A., Randazzo, A., Virgilio, A., Esposito, V., Giancola, C., Bucci, M., Cirino, G., Mayol, L.

(2006) Nucleic Acids Res 34: 6653-6662

• PubMed: 17145716 
• DOI: https://doi.org/10.1093/nar/gkl915
• Primary Citation of Related Structures:  
  2IDN


• PubMed Abstract: 
  

  The solution structure of a new modified thrombin binding aptamer (TBA) containing a 5'-5' inversion of polarity site, namely d(3'GGT5'-5'TGGTGTGGTTGG3'), is reported. NMR and CD spectroscopy, as well as molecular dynamic and mechanic calculations, have been used to characterize the 3D structure. The modified oligonucleotide is characterized by a chair-like structure consisting of two G-tetrads connected by three edge-wise TT, TGT and TT loops. d(3'GGT5'-5'TGGTGTGGTTGG3') is characterized by an unusual folding, being three strands parallel to each other and only one strand oriented in opposite manner. This led to an anti-anti-anti-syn and syn-syn-syn-anti arrangement of the Gs in the two tetrads. The thermal stability of the modified oligonucleotide is 4 degrees C higher than the corresponding unmodified TBA. d(3'GGT5'-5'TGGTGTGGTTGG3') continues to display an anticoagulant activity, even if decreased with respect to the TBA.

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Organizational Affiliation: 

Dipartimento di Chimica, Università degli Studi di Napoli Federico II, via Cintia, I-80126, Napoli, Italy.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 4.74 kDa 
• Atom Count: 315 
• Modelled Residue Count: 15 
• Deposited Residue Count: 15 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
3'-D(P*GP*G*T)-5'-5'-D(P*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3'	A	15	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 20 
• Conformers Submitted: 7 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-01-09 
Deposition Author(s): Randazzo, A., Martino, L., Virno, A., Mayol, L., Giancola, C.

Revision History  

• Version 1.0: 2007-01-09
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-03-09
  Changes: Advisory, Data collection, Database references, Derived calculations