Main > NUCLEIC ACID > DNA > Alkylation Agents. > Quinone Methide Deriv. > Org.: USA. U (Technique) > NPLS Contents
team has discovered a new way to alkylate single-stranded DNAs in a sequence-specific manner. To design the alkylating agent Authors simply added a group for generating a quinone methide to a single-stranded DNA ligand.
A quinone methide is a highly reactive functionality capable of alkylating nearby structures, but with an even stronger tendency to react intramolecularly to form a self-adduct. In the self-adduct form, the quinone methide is inactive. However, the intramolecular reaction is reversible, so the reagent always remains ready to revert to its highly reactive form.
The DNA ligand to which the quinone methide is attached is capable of binding sequence-specifically to a DNA target strand. Binding is incomplete because the presence of the self-adduct makes some bases on the DNA ligand inaccessible to complementary bases on the DNA target.
After partial binding of the two strands occurs, the self-adduct equilibrates back to its reactive quinone methide form. When the quinone methide re-forms, conformational restrictions that initially inhibited complete interstrand base pairing are lifted, full binding of the two DNA strands occurs, and the reactive quinone methide can then alkylate a base on the complementary target strand.
The approach complements two current strategies used to alkylate DNA or other target structures selectively. Right now, one can use an affinity reagent with
an attached reactive alkylating group to bring the reactive group to a target, or, if the target happens to be an enzyme, one can use a mechanism-based inhibitor to alkylate it. A mechanism-based inhibitor is a substrate analog that binds at an enzyme s active site. The reactivity of a latent reactive group on the inhibitor is triggered specifically when the enzyme tries to process
the analog as if it were a regular substrate.
The problem with affinity reagents is that they have tended to exhibit insufficient specificity or they have been plagued by too many competitive interactions when people have tried to get them to work in vivo. And the problem with mechanism-based inhibitors is that they can only be used for targets with catalytic activity--making them largely inapplicable to DNA, for example, which rarely acts as a catalyst. THE TARGET-PROMOTED alkylation system designed by AUTHORS could sidestep some of these problems and could be useful for specific types of applications, such as experiments in which one would like to alkylate and thereby disable or label a specific gene sequence.
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