Symmetry observations in long nucleotide sequences: a commentary on the Discovery Note of Qi and Cuticchia

  title={Symmetry observations in long nucleotide sequences: a commentary on the Discovery Note of Qi and Cuticchia},
  author={Donald R. Forsdyke},
  volume={18 1},
The relative quantities of bases in DNA were determined chemically many years before sequencing technologies permitted direct counting of bases. Apparently unaware of the rich literature on the topic, bioinformaticists are today rediscovering the 'wheels' of Chargaff, Wyatt and other biochemists. It follows from Chargaff's second parity rule (%A = %T, %G = %C for single stranded DNA) that the symmetries observed for the two pairs of complementary mononucleotide bases, should also apply to the… 

Purine loading, stem-loops and Chargaff’s second parity rule: a discussion of the application of elementary principles to early chemical observations

Arguments that purine loading is specific for the loops of RNA-synonymous strands of genes whose transcripts function by virtue of their secondary structure need to take into account, as controls, the loop regions of mRNA- synonymous strands.

Distribution of words with a predefined range of mismatches to a DNA probe in bacterial genomes

The ratio of k-neighbor match counts in two distinct genomes for a given probe is a measure of its specificity, and examination of the extreme values of these ratios indicates that probes with a high discriminative power exist for each tested pair.

How is the biological information arranged in genome

The structural features for the biologically active genomic DNA were observed all living cells including the organelle- and the viralgenome, the potentiality of a new analytical method of the genome structure based on the appearance frequency, Sequence Spectrum Method (SSM) could be analyzed DNA, RNA and protein on genome and the structural features of genome might be related the biological complexity.

The rules of long DNA-sequences and tetra-groups of oligonucleotides

The article represents a new class of hidden symmetries in long sequences of oligonucleotides of single stranded DNA from their representative set that are associated with the common ability of all living organisms to grow and develop on the basis of incorporation into their body of new and new molecules of nutrients becoming new quantum-mechanic subsystems of the united quantum- mechanic organism.

Structural features of the nucleotide sequences of virus and organelle genomes

The base sequences of the genomic DNA including the genomic-RNA might be universal in all genomes, and the relationship between the structural features of the genome and the biological complexity was discussed.

Nucleotide tetramers TCGA and CTAG: viral DNA and the genetic code (hypothesis)

  • F. Filatov
  • Biology
    Journal of microbiology, epidemiology and immunobiology
  • 2022
A comparative analysis of CTAG and TCGA tetra-nucleotide FPs in viral DNAs suggests that these tetramers may have participated in the origin of the universal genetic code.

Limited contribution of stem-loop potential to symmetry of single-stranded genomic DNA

It is concluded that the contribution of the widespread stem-loop potential of single-stranded genomic DNA to the formation and maintenance of strand symmetry would be very limited, at least for higher-order oligonucleotides.

Neutralism versus selectionism: Chargaff's second parity rule, revisited

F Forsdyke's results were consistent with his PR2 hypothesis, appeared to resolve some root problems in biology and provided a theoretical underpinning for alignment-free taxonomic analyses using relative oligonucleotide frequencies (k-mer analysis), consistent with Chargaff's cluster rule.

Optimum growth temperature and the base composition of open reading frames in prokaryotes

The previously observed positive correlation between (G+C)% and optimum growth temperature, which applies to RNA species whose structure is of major importance for their function (ribosomal and transfer RNAs) does not apply to mRNAs, and hence is unlikely to apply generally to genomic DNA.



Relative roles of primary sequence and (G + C)% in determining the hierarchy of frequencies of complementary trinucleotide pairs in DNAs of different species

It is proposed that Chargaff's rule applies to single-stranded DNA because there has been an evolutionary selection pressure favoring mutations that generate complementary oligonucleotides in close proximity, thus creating a potential to form stem-loops and impair interspecies recombination by interfering with stem-loop interactions.

Accounting units in DNA.

It is proposed that Chargaff's second parity rule reflects the evolution of genome-wide stem-loop potential as part of short- and long-range accounting processes which work together to sustain the integrity of various levels of information in DNA.

Deviations from Chargaff's second parity rule correlate with direction of transcription.

It is suggested that the disposition of genes in nucleic acid sequences arises from their having to adapt to a preexisting mosaic of genomic regions, each distinguished by its potential to extrude single-strand loops enriched for a particular base (or two non-Watson-Crick pairing bases).

Compositional symmetries in complete genomes

This paper analyzes the compositional correlations in the complete genomes and finds correlations between A = T and G = C equimolar frequencies and higher order oligonucleotides.

Concordant evolution of coding and noncoding regions of DNA made possible by the universal rule of TA/CG deficiency-TG/CT excess.

  • T. YomoS. Ohno
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 1989
The universal rule of TA/CG deficiency-TG/CT excess previously proposed as the construction principle of coding sequences applies to noncoding regions of the gene as well, and it would appear that the universal rule as an intrinsic force has been exerting far greater influence than natural selection in the evolution of genes.

Analysis of the codon bias in E. coli sequences.

There is a high correlation between the level of codon bias, the tRNA population and the abundance of protein product, indicating biased patterns are exploited by the cell for the production of widely different levels of gene product.

Symmetry observations in long nucleotide sequences.

  • V. Prabhu
  • Computer Science
    Nucleic acids research
  • 1993
A study of all sequences longer than 50 000 nucleotides currently in GenBank reveals a simple symmetry principle that extends to sets of n-tuples of higher order n with increase in the length of the sequence.

Chargaff's legacy.


  • G. R. Wyatt
  • Biology, Chemistry
    The Journal of general physiology
  • 1952
Purine and pyrimidine bases have been estimated from the desoxyribonucleic acids of eleven insect viruses, and no general parallelism is evident between DNA composition and biological relationship.