Free energy periodicity in E.coli coding

D. I. Rosnick, D. L. Bitzer, M. A. Vouk, Elebeoba May

Research output: Contribution to journalConference articlepeer-review

5 Scopus citations


Sequences upstream from coding regions in E.coli commonly possess significant complementarity to the exposed part of the 16S rRNA. This region is known as the Shine-Dalgarno sequence. Free energy calculations for binding between homologous sequences suggest that this region is used as a landing site for construction of the ribosome around the mRNA. While strong upstream binding appears to be a condition for translation, it may not be sufficient. Our research suggests that the 16S has a continuing role throughout translation, particularly in ribosomal synchronization with the reading frame. We consider the entire E.coli genome of over 2000 forward coding sequences. Presence of strong upstream binding is confirmed, and a definite three-base periodic signal is observed. The distribution of bases parallels that needed to produce a signal of the type observed.

Original languageEnglish (US)
Pages (from-to)2470-2473
Number of pages4
JournalAnnual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings
StatePublished - Dec 1 2000
Event22nd Annual International Conference of the IEEE Engineering in Medicine and Biology Society - Chicago, IL, United States
Duration: Jul 23 2000Jul 28 2000


  • 16S
  • Free energy
  • Shine-Dalgarno

ASJC Scopus subject areas

  • Signal Processing
  • Biomedical Engineering
  • Computer Vision and Pattern Recognition
  • Health Informatics


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