DNA Information: Laws of Perception

Muskhelishvili, Georgi

doi:10.1007/978-3-319-17425-9

Cited by 1 publication

(3 citation statements)

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“…The regulatory sequence organization requirement of having an AT-rich terminus region and GC-rich origin is achieved by the selective usage of either synonymous codons or amino acids [ 9 ]. For example, the amino acid serine is encoded by AGT, TCA, TCT, AGC, TCC, and TCG.…”

Section: Resultsmentioning

confidence: 99%

“…The observed gradient of Gibbs entropy from the origin to the terminus in both replichores is partly due to the GC content based selective usage of synonymous codons. The gradient of thermodynamic stability has been previously related to the process of replication and the demand to utilize the anabolic and catabolic genes at different stages of the growth cycle, facilitated by their location on the opposite chromosomal ends [ 1 , 3 , 4 , 9 ]. Another core finding is the relation between the genomic distribution of anabolic and catabolic genes and the Gibbs entropy.…”

Section: Discussionmentioning

confidence: 99%

“…Preferred direction for bending (anisotropy), stiffness, thermodynamic stability, and supercoiling are among the properties that are essentially dependent on the DNA sequence organization [ 3 , 6 , 7 ]. Previous studies provided compelling arguments concerning the peculiar relationship of interdependence between the two types of DNA information [ 1 – 4 , 8 , 9 ].…”

Section: Introductionmentioning

confidence: 99%

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Relationship between digital information and thermodynamic stability in bacterial genomes

Nigatu

Henkel

Sobetzko

et al. 2016

J Bioinform Sys Biology

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Ever since the introduction of the Watson-Crick model, numerous efforts have been made to fully characterize the digital information content of the DNA. However, it became increasingly evident that variations of DNA configuration also provide an “analog” type of information related to the physicochemical properties of the DNA, such as thermodynamic stability and supercoiling. Hence, the parallel investigation of the digital information contained in the base sequence with associated analog parameters is very important for understanding the coding capacity of the DNA. In this paper, we represented analog information by its thermodynamic stability and compare it with digital information using Shannon and Gibbs entropy measures on the complete genome sequences of several bacteria, including Escherichia coli (E. coli), Bacillus subtilis (B. subtilis), Streptomyces coelicolor (S. coelicolor), and Salmonella typhimurium (S. typhimurium). Furthermore, the link to the broader classes of functional gene groups (anabolic and catabolic) is examined. Obtained results demonstrate the couplings between thermodynamic stability and digital sequence organization in the bacterial genomes. In addition, our data suggest a determinative role of the genome-wide distribution of DNA thermodynamic stability in the spatial organization of functional gene groups.

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Section: Resultsmentioning

confidence: 99%