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  • Research Article
  • Open Access

Analysis of Free Energy Signals Arising from Nucleotide Hybridization Between rRNA and mRNA Sequences during Translation in Eubacteria

  • 1Email author,
  • 2,
  • 3 and
  • 3
EURASIP Journal on Bioinformatics and Systems Biology20062006:23613

  • Received: 14 April 2006
  • Accepted: 3 October 2006
  • Published:


A decoding algorithm is tested that mechanistically models the progressive alignments that arise as the mRNA moves past the rRNA tail during translation elongation. Each of these alignments provides an opportunity for hybridization between the single-stranded, -terminal nucleotides of the 16S rRNA and the spatially accessible window of mRNA sequence, from which a free energy value can be calculated. Using this algorithm we show that a periodic, energetic pattern of frequency 1/3 is revealed. This periodic signal exists in the majority of coding regions of eubacterial genes, but not in the non-coding regions encoding the 16S and 23S rRNAs. Signal analysis reveals that the population of coding regions of each bacterial species has a mean phase that is correlated in a statistically significant way with species ( ) content. These results suggest that the periodic signal could function as a synchronization signal for the maintenance of reading frame and that codon usage provides a mechanism for manipulation of signal phase.


  • Nucleotide
  • Codon
  • Free Energy
  • Bacterial Species
  • Signal Analysis

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Authors’ Affiliations

Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, NC 27695, USA
Department of Forestry, North Carolina State University, Raleigh, NC 27695, USA
Department of Computer Science, North Carolina State University, Raleigh, NC 27695, USA


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© Lalit Ponnala et al. 2006

This article is published under license to BioMed Central Ltd. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.