Binding to Lattices of Sites
Charles P. Woodbury · 2007
A number of important biopolymer and synthetic polymer systems form what are essentially one-dimensional arrays of binding sites. The polymer chain can be idealized as a linear array or lattice of monomeric units that are potential binding sites for ligands such as drugs, protons, and proteins. A familiar example of such a linear lattice would be a polynucleotide, whose bases or base pairs serve as the points of contact to bind polyamines, dye molecules, proteins, etc. Many other linear biopolymers (proteins, polysaccharides, etc.) of course might be idealized as linear lattices of sites, too. The exact definition of a site, however, will depend on the nature of the ligand as well as on the composition and sequence of the monomeric units in the polymer. For example, with double-stranded polynucleotides it may be expedient in some cases to think of the phosphates of the phosphodiester backbone as forming the lattice of sites, especially when the ligand-polynucleotide interaction is primarily through ionic attraction. In other cases, in which hydrogen bonding to particular base sequences is involved, for example, it may be better to view as the binding sites the bases or base pair units that offer such points for interaction. And yet again, when considering the intercalation of planar aromatic ligands, such as ethidium, into double-stranded DNA, one can think of the site as being formed by adjacent base pairs, as they unstack and unwind the helix to form a pocket for the planar ligand. An interesting complication here is the potential for overlap between binding sites for ligands that cover or interact with two or more adjacent monomeric units in the macromolecule.