Title

Authors

Affiliation

Facultad de Medicina, UAEM, Calle Ixtaccihuatl Esq Leñeros, Col. Los Volcanes C.P. 62350, Cuernavaca, Morelos, Mexico

Email

joaquin.sanchez@microbio.gu.se; *Corresponding authors

Article Type

Hypothesis

Date

Received May 16, 2013; Accepted May 19, 2013; Published June 08, 2013

The use of sequences encoding identical peptides (SEIP) for the in silico analysis of coding DNA from different species has not been reported; the study of such sequences could directly reveal properties of coding DNA that are independent of peptide sequences. For practical purposes SEIP might also be manipulated for e.g. heterologous protein expression. We extracted 1,551 SEIP from human and E. coli and 2,631 SEIP from human and D. melanogaster. We then analyzed codon usage and intercodon dinucleotide tendencies and found differences in both, with more conspicuous disparities between human and E. coli than between human and D. melanogaster. We also briefly manipulated SEIP to find out if they could be used to create new coding sequences. We hence attempted replacement of human by E. coli codons via dicodon exchange but found that full replacement was not possible, this indicated robust species-specific dicodon tendencies. To test another form of codon replacement we isolated SEIP from human and the jellyfish green fluorescent protein (GFP) and we then re-constructed the GFP coding DNA with human tetra-peptide-coding sequences. Results provide proof-of-principle that SEIP may be used to reveal differences in the properties of coding DNA and to reconstruct in pieces a protein coding DNA with sequences from a different organism, the latter might be exploited in heterologous protein expression.

Keywords

synonymous codons, intercodon dinucleotides, codon pairs, codon allocation tendencies, green fluorescent protein, heterologous protein expression.

Citation

Sánchez,    Bioinformation 9(10): 511-517 (2013)

Edited by

P Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.