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Abstract
We have performed a comparison of computer-generated random sequences with tRNAs nucleotide sequences present in Bacteria represented as random walks. Nucleotide sequence data of tRNA genes were obtained from the Institute for Genomic Research (TIGR) and the GeneBank library. Random sequence data (white noise) were obtained from the algorithm by Press and Teukolsky. Random walks of nucleotide sequences were obtained by letting the orbit walk a unit step in one of four directions (down, left, right, and up), depending upon the next base (A,C,G, and T) in the sequence, and the distances from the origin calculated. The Visual Basic routines here applied to perform the analysis are presented. Relative Lempel-Ziv complexity. Entropy (sum of the positive Lyapunov indexes) and Hurst indexes of nucleotide sequences and of computer-generated random data were evaluated over the distances of their random walk. Our data show that the values of nonlinear parameters obtained from the bacteria are lower than the values of randomly generated sequences (p<0.01, p<0.05, p<0.01), meaning that the tRNA sequence is more ordered than a pure destructured random data and it owns a “memory”. The observed deviation from pure randomness should be arisen from some constraints like the secondary structure of this biologic macromolecule and/or from the peculiar origin of this macromolecule by repeated subunits. These data indicate that evolution earlier chose nonrandom “alphabets”: order together randomness were present at the dawn of life. Our method, here presented and described, provides an efficient tool to assess the amount of order/disorder in the primary structure of nucleic acid sequences.
Highlights
Billions years ago, according to the exon theory of genes [1] small RNAs translated into peptides of 15-20 amino acids: minigenes of pre-the primitive informational polymers (tRNAs) codifying RNA hairpin structures
We have performed a comparison of computer-generated random sequences with tRNAs nucleotide sequences present in Bacteria represented as random walks
In order to test the hypothesis that the nucleotide sequences of the primitive informational polymers might not be chosen randomly, we introduce the comparison of computer-generated random sequences with tRNAs nucleotide sequences present in the bacterial genomes based on the description of nucleic acid sequences as random walks and their analysis by nonlinear approaches over the distances from the origin
Summary
Billions years ago, according to the exon theory of genes [1] small RNAs translated into peptides of 15-20 amino acids: minigenes of pre-tRNAs codifying RNA hairpin structures. The dimerization of two equal RNA hairpin structures may have lead to the formation of the cruciform structure of the tRNA molecule: tRNA reflects the primordial genes of that era. In order to test the hypothesis that the nucleotide sequences of the primitive informational polymers (tRNAs) might not be chosen randomly, we introduce the comparison of computer-generated random sequences with tRNAs nucleotide sequences present in the bacterial genomes based on the description of nucleic acid sequences as random walks and their analysis by nonlinear approaches over the distances from the origin
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