DNA Binding Interactions
Polymerases interact with the phosphate backbone and the minor groove of the DNA, so their interactions do not depend on the specific nucleotide sequence. The binding is largely mediated by electrostatic interactions between the DNA and the "thumb" and "palm" domains of the metaphorically hand-shaped DNA polymerase molecule. When the polymerase advances along the DNA sequence after adding a nucleotide, the interactions with the minor groove dissociate but those with the phosphate backbone remain more stable, allowing rapid re-binding to the minor groove at the next nucleotide.
Interactions with the DNA are also facilitated by DNA clamp proteins, which are multimeric proteins that completely encircle the DNA, with which they associate at replication forks. Their central pore is sufficiently large to admit the DNA strands and some surrounding water molecules, which allows the clamp to slide along the DNA without dissociating from it and without loosening the protein-protein interactions that maintain the toroid shape. When associated with a DNA clamp, DNA polymerase is dramatically more processive; without the clamp most polymerases have a processivity of only about 100 nucleotides. The interactions between the polymerase and the clamp are more persistent than those between the polymerase and the DNA. Thus, when the polymerase dissociates from the DNA, it is still bound to the clamp and can rapidly reassociate with the DNA. An example of such a DNA clamp is PCNA (proliferating cell nuclear antigen) found in S. cervesiae.
Read more about this topic: Processivity
Famous quotes containing the words dna, binding and/or interactions:
“Here [in London, history] ... seemed the very fabric of things, as if the city were a single growth of stone and brick, uncounted strata of message and meaning, age upon age, generated over the centuries to the dictates of some now all-but-unreadable DNA of commerce and empire.”
—William Gibson (b. 1948)
“What is lawful is not binding only on some and not binding on others. Lawfulness extends everywhere, through the wide-ruling air and the boundless light of the sky.”
—Empedocles 484–424 B.C., Greek philosopher. The Presocratics, p. 142, ed. Philip Wheelwright, The Bobbs-Merrill Co., Inc. (1960)
“In our interactions with people, a benevolent hypocrisy is frequently required—acting as though we do not see through the motives of their actions.”
—Friedrich Nietzsche (1844–1900)