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Finding needles in DNA stacks

Locating the 104 damaged nucleotides in a cell's DNA poses a significant challenge to DNA repair enzymes on a daily basis (1). Base excision repair (BER) glycosylases are responsible for finding subtle atomic-level changes in a base amidst a sea of undamaged bases, and they must do so before replication leads to improper nucleotide insertion causing a mutation (2). Many years ago it was recognized that random on-off binding of proteins to duplex DNA was an inefficient way to locate the sites of damage, leading to proposals of protein sliding on the duplex in addition to short hopping or longer-range jumping to different sections of the genome (3). In a recent issue of PNAS, new data from Boal et al. (4) provided evidence of an alternative mechanism in which the bacterial BER enzymes EndoIII and MutY communicate over a long segment of base-paired DNA by tapping into the ability of a perfectly complementary duplex to transport charge along the helix. Such a mechanism would greatly exceed the rate of 1D scanning by procession of a macromolecule along the DNA duplex.