The Resolution of nucleic acid‐ligand binding sites by CD first‐neighbor analysis

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Abstract
The first‐neighbor approximation for representation of double‐stranded polynucleotide CD has been used to determine which first‐neighbor units are favorable binding sites for a ligand. Here, we refine the process to yield a more definitive answer. The binding at the first‐neighbor units, ApA:TpT and CpC:GpG, may be unequivocally resolved, and when fewer than six of the remaining eight base‐paired first‐neighbor units are bound by the ligand, they too can be resolved. If this condition is not met, then the binding can be characterized as nonspecific.