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From Proteopedia
DNA Single Strand Binding Proteins
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IMPORTANT INFORMATION ssDNA-binding proteins commonly take advantage of this electronegative character and line their DNA-binding surfaces with the electropositive amino acid residues lysine and arginine
Function
Interactions
During the DNA replication process SSB's interact with single strand DNA. Single stranded DNA occurs during cellular respiration. It consists of the same base, sugar, and phosphate of double stranded DNA, but has lost the hydrogen bonds with the other strand. Single stranded DNA has a negative electronegativity due to the negative charge on the non-bridging oxygens in the phosphodiester bond.
The main interactions between the single stranded binding protein and the single stranded DNA occur through electrostatic interactions, hydrogen bonding, and stacking interactions. The single strand DNA has a slightly negative charge due to a negative charge on one of the oxygens that make up the phosphodiester bond. Therefore, the SSB often has amino acids that have a positive charge, like lysine and arginine, on the surface of the DNA binding surface. Amino acid side chains, amines, and carbonyl groups can also create hydrogen bonds with the backbone and bases of the DNA. All DNA nucleic acids have aromatic ring structures. These structures are rather flat. The SSBs use this common structure to make stacking interactions between the nucleic acid and the aromatic and planar regions on the SSB. These different methods allow the binding to be nonspecific to the order of nucleic acids.
