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Protein complexation with DNA phosphates as a cause for DNA duplex destabilization: A thermodynamic model
Author(s) -
Van Genderen Marcel H. P.,
Buck Henk M.
Publication year - 1989
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.360281002
Subject(s) - chemistry , duplex (building) , dna , transcription bubble , phosphate , rna , helicase , coding strand , crystallography , biophysics , polymerase , stereochemistry , biochemistry , gene , biology , rna dependent rna polymerase
Complexation of positively charged sites in a protein with the negative DNA phosphate groups shields the phosphate charges. This diminishes inter strand electrostatic repulsions, which stabilizes the duplex. When phosphate shidlding is present in one DNA strand only, the conformation of this strand changes due to a decrease of intra strand phosphate–phosphate repulsions. This destabilizes the duplex since then the strands differ in conformation. A thermodynamic model is formulated to describe this stabilization/destabilization effect in terms of changed enthalpies and entropies of hybridization. It is found that protein complexation with one DNA strand can indeed lower the T M value of a duplex. The model is applied to the action of helicases (replication), RNA polymerases (transcription), and restriction endonucleases. Mechanisms with unilateral charge shielding are proposed for their duplex‐destabilizing properties.