Figure 1.
(A) Variables, , parameters,
, and sequence position
are represented together with 5′ and 3′ ends on both template and replicated strands. (B) Polymerase (green) replicating a template DNA strand. Emphasis is placed on the linearity and directionality of the process.
is the number of nucleotides that this nanomachine covers when it is bound to the DNA. (C) Polymerase replicating DNA. Emphasis is placed on the recognition of errors based on the sequence-induced secondary structure of the DNA: the structure of DNA polymerase (a ‘palm’, [7]) and dsDNA (a double helix) are evolutionarly adapted to optimally fit each other when Watson-Crick base-pairs are formed. A complete turn of the double helix in B-form is
base-pairs.
Figure 2.
Entropy of replication in equilibrium.
Each panel shows the entropy per nucleotide in the absence (solid line) and presence of nearest neighbor influence for an Ising mechanism (dashed lines) and for a Turing mechanism (dotted lines). (A) Monotonous template sequences: black lines, polydA; red lines, polydC; green lines, polydG; and blue lines, polydT. (B) Black lines, periodic template sequence: ACGTACGTACGTA…; red lines, random template sequence TCCGAGTAGATCT …
Figure 3.
Internal Energy of replication in equilibrium.
Each panel shows the mean energy per nucleotide in the absence (solid line) and presence of nearest neighbor influence for an Ising mechanism (dashed lines) and for a Turing mechanism (dotted lines). (A) Monotonous template sequences: black lines, polydA; red lines, polydC; green lines, polydG; and blue lines, polydT. (B) Black lines, periodic template sequence: ACGTACGTACGTA…; red lines, random template sequence TCCGAGTAGATCT …
Figure 4.
Helmholtz Free Energy of replication in equilibrium.
Each panel shows the free energy per nucleotide in the absence (solid line) and presence of nearest neighbor influence for an Ising mechanism (dashed lines) and for a Turing mechanism (dotted lines). (A) Monotonous template sequences: black lines, polydA; red lines, polydC; green lines, polydG; and blue lines, polydT. (B) Black lines, periodic template sequence: ACGTACGTACGTA…; red lines, random template sequence TCCGAGTAGATCT …