| Summary: | It is well established that gene regulation can be achieved through activator and repressor proteins that bind to DNA and switch particular genes on or off, and that complex metabolic networks deter- mine the levels of transcription of a given gene at a given time. Using three complementary computa- tional techniques to study the sequence-dependence of DNA denaturation within DNA minicircles, we have observed that whenever the ends of the DNA are con- strained, information can be transferred over long distances directly by the transmission of mechanical stress through the DNA itself, without any require- ment for external signalling factors. Our models com- bine atomistic molecular dynamics (MD) with coarse- grained simulations and statistical mechanical calcu- lations to span three distinct spatial resolutions and timescale regimes. While they give a consensus view of the non-locality of sequence-dependent denatura- tion in highly bent and supercoiled DNA loops, each also reveals a unique aspect of long-range informa- tional transfer that occurs as a result of restraining the DNA within the closed loop of the minicircles.
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