Distribution of pyrimidine oligonucleotides in complementary strand fractions of Escherichia coli deoxyribonucleic acid

Rudner, Rivka; Ledoux, Mary

doi:10.1021/bi00698a019

Cited by 7 publications

(1 citation statement)

References 7 publications

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“…They were first reported for the chemical composition of Bacillus subtilis DNA Karkas et al 1968). Similar results were obtained for Escherichia coli, B. megaterium, B. stearothermophilus, Proteus vulgaris, Salmonella typhimurium, Serratia marcescens, and E. coli phage T4 (Rudner et al 1969;Karkas et al 1970;Rudner and LeDoux 1974). When long DNA sequences became available, PR2 was also found to hold for the eukaryotic SV40, polyoma, and Bk viruses (Nussinov 1982); for Homo sapiens (Fickett et al 1992); and for many other species (Prabhu 1993;Lobry 1995).…”

Section: Introductionsupporting

confidence: 68%

Relationships Between Genomic G+C Content, RNA Secondary Structures, and Optimal Growth Temperature in Prokaryotes

1997

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G:C pairs are more stable than A:T pairs because they have an additional hydrogen bond. This has led to many studies on the correlation between the guanine+cytosine (G+C) content of nucleic acids and temperature over the last 20 years. We collected the optimal growth temperatures (Topt) and the G+C contents of genomic DNA; 23S, 16S, and 5S ribosomal RNAs; and transfer RNAs for 764 prokaryotic species. No correlation was found between genomic G+C content and Topt, but there were striking correlations between the G+C content of ribosomal and transfer RNA stems and Topt. Two explanations have been proposed-neutral evolution and selection pressure-for the approximate equalities of G and C (respectively, A and T) contents within each strand of DNA molecules. Our results do not support the notion that selection pressure induces complementary oligonucleotides in close proximity and therefore numerous secondary structures in prokaryotic DNA, as the genomic G+C content does not behave in the same way as that of folded RNA with respect to optimal growth temperature.

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Section: Introductionsupporting

confidence: 68%

Relationships Between Genomic G+C Content, RNA Secondary Structures, and Optimal Growth Temperature in Prokaryotes

1997

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Evolution of DNA structure: Direction, mechanism, rate

Mazin

1976

J Mol Evol

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On the basis of the results of an analysis of frequencies of pyrimidine oligonucleotides, the degree of pyrimidine clustering of DNA in species from different taxa has been determined. A tendency for an increase in the index of clustering of DNA was revealed in the sequence: invertebrates, fishes, amphibians, reptiles, birds, mammals. A mechanism is postulated, according to which the increase in the degree of clustering of DNA d-ring the evolution may be associated with the accumulation of mutations, Purine equalibrium Pyrimidine transversions, resulting in a selective enrichment of one of the chains of DNA with pyrimidines and the other- with purines, i.e. in an increase in the degree of purine-pyrimidine imbalance (asymmetry) of DNA complementary chains. This mechanism of DNA evolution is supported by the presence of positive correlation between the degree of clustering and the degree of the chain asymmetry of natural DNAs, as well as the character of the amino acid substitutions in cytochromes c in different species. The progressive evolution of different groups of organisms on the whole may have been accompanied by an acceleration of the rates of evolution of the DNA structure. On the basis of the amino acid sequence of cytochromes c in different species the degree of clustering and the degree of the chain asymmetry of the corresponding structural genes of DNA was found to have a general tendency towards an increase in the following order: invertebrates, fishes, amphibians, reptiles, birds, mammals. Thus, evolution of cytochrome c cistron is a vector process based on a selection of mutations which, on the one hand, are neurtral to protein, and, on the other hand, result in the sense chain of DNA being enriched with pyrimidines and the nonsense one (and the corresponding mRNA)- with purines. Hence, it is the polynucleotide template rather than protein, that must have been the "object of selection". The frequency of substitutions in cytochromes c cistron for vertebrates is 1.56x13(-9) per nucleotide per year. It is believed that the evolutionary modification of the DNA structure may be associated with an increase in the interference resistance of the translation, i.e. with selection for codons of highest readout stability.

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Absence of long pyrimidine tracts in cytosine-rich repeating units present in Escherichia coli DNA

Lin

1975

Biochimica et Biophysica Acta (BBA) - Nucleic Acids and Protein

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Distribution of pyrimidine oligonucleotides in complementary strand fractions of Escherichia coli deoxyribonucleic acid

Cited by 7 publications

References 7 publications

Relationships Between Genomic G+C Content, RNA Secondary Structures, and Optimal Growth Temperature in Prokaryotes

Relationships Between Genomic G+C Content, RNA Secondary Structures, and Optimal Growth Temperature in Prokaryotes

Evolution of DNA structure: Direction, mechanism, rate

Absence of long pyrimidine tracts in cytosine-rich repeating units present in Escherichia coli DNA

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