Conjugates between a minor groove binding molecule, such as the trimer
of 1,2-dihydro-(3H)-pyrrolo[3,2-e]indole-7-carboxylate (CDPI3), and
an oligonucleotide form unusually stable hybrids with complementary target sequences,
in which the tethered CDPI3 group resides in the minor groove of the
duplex. These conjugates can be used as probes and primers. Due to their unusually
high binding affinity, conjugates as short as 8-mers can be used as amplification
primers with high specificity and efficiency. MGB conjugation also increases the
discriminatory power of short oligonucleotides, providing enhanced detection of
nucleotide sequence mismatches by short oligonucleotides. The MGB-conjugated probes
and primers described herein facilitate various analytic and diagnostic procedures,
such as amplification reactions, PCR, detection of single-nucleotide polymorphisms,
gene hunting, differential display, fluorescence energy transfer, hydrolyzable
probe assays and others; by allowing the use of shorter oligonucleotides, which
have higher specificity and better discriminatory power.
