Minor groove binder phosphoramidites and methods of use

Abstract

Minor groove binder phosphoramidites having the formula M-L-PA, wherein M is a minor groove binder comprising a protected heteroaromatic amine, L is a linker, and PA is a phosphoramidite group, have been synthesized. Preferred methods of synthesis include synthesizing a minor groove binder intermediate containing a transiently protected hydroxyl group, protecting heteroaromatic amines of the corresponding minor groove binder intermediate as carbamate intermediates, reacting the carbamate intermediate to remove the transient protecting group to yield carbamate-protected minor groove binder agent as an intermediate with a free hydroxyl group, and converting the intermediate with a free hydroxyl group to the desired minor groove binder phosphoramidite. These minor groove binder phosphoramidites are useful in the preparation of oligonucleotide conjugates, particularly those for use as probes and primers. In preferred methods, an oligonucleotide sequence is synthesized using nucleoside phosphoramidites and the minor groove binder phosphoramidite is incorporated into the oligonucleotide sequence to form a protected oligonucleotide-minor groove binder conjugate. Then, deprotection produces the oligonucleotide-minor groove binder.