DNA base pair stacks with high electric conductance: A systematic structural search

Yuri A. Berlin, Alexander A. Voityuk, Mark A. Ratner*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

19 Scopus citations


We report a computational search for DNA φ-stack structures exhibiting high electric conductance in the hopping regime, based on the INDO/S calculations of electronic coupling and the method of data analysis called k-means clustering. Using homogeneous poly(G)-poly(C) and poly(A)-poly(T) stacks as the simplest structural models, we identify the configurations of neighboring G:C and A:T pairs that allow strong electronic coupling and, therefore, molecular electric conductance much larger than the values reported for the corresponding reference systems in the literature. A computational approach for modeling the impact of thermal fluctuations on the averaged dimer structure was also proposed and applied to the [(G:C),(G:C)] and [(A:T),(A:T)] duplexes. The results of this work may provide guidance for the construction of DNA devices and DNA-based elements of nanoscale molecular circuits. Several factors that cause changes of step parameters favorable to the formation of the predicted stack conformation with high electric conductance of DNA molecules are also discussed; favorable geometries may enhance the conductivity by factors as large as 15.

Original languageEnglish (US)
Pages (from-to)8216-8225
Number of pages10
JournalACS nano
Issue number9
StatePublished - Sep 25 2012


  • DNA
  • electronic coupling
  • molecular conductance
  • step parameters
  • π-stack

ASJC Scopus subject areas

  • General Materials Science
  • General Engineering
  • General Physics and Astronomy


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