Morin…Ibarra {Nucleic Acids Res 43: 3643}
Maxwell's demon controlling the stepping of a DNA polymerase molecule. In real DNA polymerases, binding of the next correct nucleotide plays the role of Maxwell's demon, by pinning the fluctuating polymerase in the post-translocation state -and the second law of thermodynamics is certainly not violated.
Mechano-chemical kinetics of DNA replication: identification of the translocation step of a replicative DNA polymerase
Morin JA, Cao FJ, Lázaro JM, Arias-Gonzalez JR, Valpuesta JM, Carrascosa JL, Salas M, Ibarra B.
Nucleic Acids Res. 2015 April; 43:3643.
During DNA replication replicative polymerases move in discrete mechanical steps along the DNA template. To address how the chemical cycle is coupled to mechanical motion of the enzyme, here we use optical tweezers to study the translocation mechanism of individual bacteriophage Phi29 DNA polymerases during processive DNA replication. We determine the main kinetic parameters of the nucleotide incorporation cycle and their dependence on external load and nucleotide (dNTP) concentration. The data is inconsistent with power stroke models for translocation, instead supports a loose-coupling mechanism between chemical catalysis and mechanical translocation during DNA replication. According to this mechanism the DNA polymerase works by alternating between a dNTP/PPi-free state, which diffuses thermally between pre- and post-translocated states, and a dNTP/PPi-bound state where dNTP binding stabilizes the post-translocated state. We show how this thermal ratchet mechanism is used by the polymerase to generate work against large opposing loads (∼50 pN).
PubMed: 25800740. Doi: 10.1093/nar/gkv204
