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Integration of syntactic and semantic properties of the DNA code reveals chromosomes as thermodynamic machines converting energy into information


Understanding genetic regulation is a problem of fundamental importance. Recent studies have made it increasingly evident that, whereas the cellular genetic regulation system embodies multiple disparate elements engaged in numerous interactions, the central issue is the genuine function of the DNA molecule as information carrier. Compelling evidence suggests that the DNA, in addition to the digital information of the linear genetic code (the semantics), encodes equally important continuous, or analog, information that specifies the structural dynamics and configuration (the syntax) of the polymer. These two DNA information types are intrinsically coupled in the primary sequence organisation, and this coupling is directly relevant to regulation of the genetic function. In this review, we emphasise the critical need of holistic integration of the DNA information as a prerequisite for understanding the organisational complexity of the genetic regulation system.

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DNA protection during starvation protein


Functional domain


Factor for inversion stimulation


Histone-like nucleoid-structuring protein


Heat-stable protein from the strain U13


Integration host factor


Leucine responsive protein


Nucleoid-associated protein


Origin of chromosomal replication


RNA polymerase


RNAP vegetative sigma factor (σ70)


RNAP stationary phase sigma factor (σS)


Chromosomal replication terminus


Transcription factor


Target gene


Transcription unit


Transcriptional regulatory network

tyrT :

Tyrosyl transfer RNA gene


Upstream activating sequence


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We thank Rainer Machne and the anonymous reviewers for helpful comments. This work was in part supported by the research grant of the Deutsche Forschungsgemeinschaft (InKoMBio) to G.M.

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Correspondence to Georgi Muskhelishvili.

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Muskhelishvili, G., Travers, A. Integration of syntactic and semantic properties of the DNA code reveals chromosomes as thermodynamic machines converting energy into information. Cell. Mol. Life Sci. 70, 4555–4567 (2013).

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  • Holistic methodology
  • DNA supercoiling
  • Chromosome structure
  • Gene order
  • Transcriptional regulation
  • Nucleoid-associated proteins