Title :
Free energy periodicity in E. coli coding
Author :
Rosnick, D.I. ; Bitzer, D.L. ; Vouk, M.A. ; May, E.E.
Author_Institution :
Dept. of Comput. Sci., North Carolina State Univ., Raleigh, NC, USA
Abstract :
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. The authors´ research suggests that the 16S has a continuing role throughout translation, particularly in ribosomal synchronization with the reading frame. The authors 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
Keywords :
free energy; genetics; microorganisms; 16S rRNA; E. coli coding; Shine-Dalgarno sequence; bases distribution; binding between homologous sequences; free energy periodicity; mRNA; ribosomal synchronization; ribosome construction; strong upstream binding; three-base periodic signal; Bioinformatics; Computer science; DNA; Displays; Genomics; Noise level; Phase detection; Region 5; Sequences; USA Councils;
Conference_Titel :
Engineering in Medicine and Biology Society, 2000. Proceedings of the 22nd Annual International Conference of the IEEE
Conference_Location :
Chicago, IL
Print_ISBN :
0-7803-6465-1
DOI :
10.1109/IEMBS.2000.901311
