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From Proteopedia
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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 <scene name='75/751165/Positive_interaction/1'>DNA Binding Surface</scene>. 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 <scene name='75/751165/Aromatic_regions/1'>aromatic</scene> and planar regions on the SSB. These different methods allow the binding to be nonspecific to the order of nucleic acids. | 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 <scene name='75/751165/Positive_interaction/1'>DNA Binding Surface</scene>. 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 <scene name='75/751165/Aromatic_regions/1'>aromatic</scene> and planar regions on the SSB. These different methods allow the binding to be nonspecific to the order of nucleic acids. | ||
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| + | An important structure in the binding of single stranded proteins is the OB fold. This structure is made up of a five-stranded antiparallel beta barrel that ends in an alpha helix. This structure provides a small area where the protein can interact with 2-5 nucleotides. The beta barrels are tightly twisted which enhances the ability of the amino acid side chains to interact with the DNA. | ||
Revision as of 20:56, 8 February 2017
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
During the initial stages of DNA replication, one of the enzymes associated with this process, DNA Helicase, breaks the hydrogen bonds between the complementary nucleotides of the two antiparallel strands. After this occurs, DNA, like any large macromolecule, is susceptible to forming secondary and more complex structures due to the varying properties of its constituent components.
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 . 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 and planar regions on the SSB. These different methods allow the binding to be nonspecific to the order of nucleic acids.
An important structure in the binding of single stranded proteins is the OB fold. This structure is made up of a five-stranded antiparallel beta barrel that ends in an alpha helix. This structure provides a small area where the protein can interact with 2-5 nucleotides. The beta barrels are tightly twisted which enhances the ability of the amino acid side chains to interact with the DNA.
