1BW7

SOLUTION STRUCTURE OF A DNA DUPLEX CONTAINING A REPLICABLE DIFLUOROTOLUENE-ADENINE PAIR

• PDB DOI: https://doi.org/10.2210/pdb1BW7/pdb
• NAKB: 1BW7

• Classification: DNA
• Mutation(s): No 


• Deposited: 1998-09-30 Released: 1998-10-07 
• Deposition Author(s): Guckian, K.M., Krugh, T.R., Kool, E.T.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 1 

Literature

Solution structure of a DNA duplex containing a replicable difluorotoluene-adenine pair.

Guckian, K.M., Krugh, T.R., Kool, E.T.

(1998) Nat Struct Biol 5: 954-959

• PubMed: 9808039 
• DOI: https://doi.org/10.1038/2930
• Primary Citation of Related Structures:  
  1BW7


• PubMed Abstract: 
  

  A nonpolar aromatic nucleoside derivative based on 2,4-difluorotoluene (F), a non-hydrogen bonding shape analog of thymidine, was recently shown to be replicated against adenine with high efficiency and fidelity. This led to the suggestion that geometric matching, potentially even in the absence of hydrogen bonding between bases in a pair, may be sufficient to direct nucleotide selection during replication. We have examined the solution structure of the F-A pair in the context of a 12 base pair DNA duplex. We find that, despite the destabilization caused by this analog, the F-A pair very closely resembles that of a T x A pair in the same context. This lends support to the importance of shape matching in replication.

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Organizational Affiliation: 

Department of Chemistry, University of Rochester, New York 14627, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 7.33 kDa 
• Atom Count: 486 
• Modelled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*CP*AP*TP*(DFT)P*GP*TP*TP*AP*CP*C)-3')	A	12	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*GP*TP*AP*AP*CP*AP*AP*TP*GP*CP*G)-3')	B	12	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 1 

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-10-07 
Deposition Author(s): Guckian, K.M., Krugh, T.R., Kool, E.T.

Revision History  

• Version 1.0: 1998-10-07
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-12-28
  Changes: Advisory
• Version 1.4: 2024-04-10
  Changes: Data collection, Database references, Derived calculations