Major Groove Recognition of DNA by Carbohydrates

Because of the number of distinguishable interactions within the DNA major groove, there is considerable interest in discovering the governing factors involved in DNA recognition. Carbohydrates represent a class of DNAinteractive agents capable of binding the major groove due to their size and intricate distribution of hydrophobic and hydrophilic interactions within their molecular structure. To date a limited number of carbohydrates have been found to interact within the DNA major groove; the majority have been shown to bind within the minor groove. Representative carbohydrates that bind within the major groove include neocarzinostatin, nogalamycin, and a few aminoglycoside (neomycin) conjugates developed in our labs. An overview of the various DNA groove-binding carbohydrates is presented, with particular emphasis on novel aminoglycoside-based approaches in probing the molecular environment and requirements therein associated with the DNA major groove.