Abstract:
: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 determine the levels of transcription of a given gene at a given time. Using three complementary computational techniques to study the sequence-dependence of DNA denaturation within DNA minicircles, we have observed that whenever the ends of the DNA are constrained, information can be transferred over long distances directly by the transmission of mechanical stress through the DNA itself, without any requirement for external signalling factors. Our models combine atomistic molecular dynamics (MD) with coarse-grained simulations and statistical mechanical calculations to span three distinct spatial resolutions and timescale regimes. While they give a consensus view of the non-locality of sequence-dependent denaturation in highly bent and supercoiled DNA loops, each also reveals a unique aspect of long-range informational transfer that occurs as a result of restraining the DNA within the closed loop of the minicircles.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Sutthibutpong T,Matek C,Benham C,Slade GG,Noy A,Laughton C,K Doye JP,Louis AA,Harris SAdoi
10.1093/nar/gkw815subject
Has Abstractpub_date
2016-11-02 00:00:00pages
9121-9130issue
19eissn
0305-1048issn
1362-4962pii
gkw815journal_volume
44pub_type
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