RNA polymerase is a unique Maxwell’s demon that converts its transcribing genetic information to free energy for its movement

Abstract

RNA polymerase (RNAP) catalyzes RNA synthesis from template DNA via translocation on the DNA. The experimental value of the free energy change required for RNAP translocation exhibits an unexplainable discrepancy. To address this, we propose a transcription system model based on information thermodynamics. The state function of RNAP was defined from its position on the template DNA (m), its migration direction (d), and the deoxyribonucleotide (dNTP) that it transcribes (N). Based on the state function, the free energy change in the RNAP translocation was defined as the sum of ΔGd in the movement fluctuation or the mutual entropy term kB TlogP(N) from the appearance probability P(N) of N to be transcribed by RNAP. In conclusion, a discrepancy in free energy change values is due to either ΔGd or kB TlogP(N) involvement. The discrepancy highlights that RNAP is a unique information-work converter or Maxwell’s demon that can feed back the obtained dNTP-type information into its self-movement along the DNA.