Efficient discrimination of single nucleotide polymorphisms (SNPs) using oligonucleotides modified with C5-pyrene-functionalized DNA and flanking Locked Nucleic Acid (LNA) monomers.

Oligodeoxyribonucleotides modified with 5-[3-(1-pyrenecarboxamido) propynyl]-2'-deoxyuridine monomer X and proximal LNA monomers display higher affinity for complementary DNA, more pronounced increases in fluorescence emission upon DNA binding, and improved discrimination of SNPs at non-stringent conditions, relative to the corresponding LNA-free probes across a range of sequence contexts. The results reported herein suggest that the introduction of LNA monomers influences the position of nearby fluorophores via indirect conformational restriction, a characteristic that can be utilized to develop optimized fluorophore-labeled probes for SNP-discrimination studies.