Directly arylated oligonucleotides as fluorescent molecular rotors for probing DNA single-nucleotide polymorphisms

We developed direct arylated oligonucleotide based molecular rotor (AOMR) to discriminate perfect matched DNA sequence from one base mismatched sequences. Quinolinium salts attached to vinyl aniline would be excellent fluorescent analogs with molecular rotor properties and are suitable for the detection of microenvironment change arising from dynamic motions with match-mismatch DNA base pairs. We applied direct N⁶ arylation of the adenosine located in natural oligonucleotide as a tool to incorporate the molecular rotor (Quinolinium salts attached vinyl aniline) and used it to discriminate perfect matched DNA sequence from one base mismatch sequences. The fluorescence and quantum yield of arylated oligonucleotide based molecular rotor (AOMR), particulary, ^RMA_Qn reveals 28.3 times higher discrimination factor with perfect matched sequence (^RMA_Qn:T) (QY = 0.17) compare to single strand ^RMA_Qn (QY = 0.006) and one base mismatched sequence (^RMA_Qn:G, ^RMA_Qn:A, and ^RMA_Qn:C) at λ_max = 600 nm (orange emission), which would be useful for in vivo application. ^RMA_Qn:T duplex also showed high brightness (6068), 32.9 times higher than single strand ^RMA_Qn (192)_, as a result of restricted rotation of the Quinolinium salts attached vinyl aniline on adenosine moiety with perfect matched sequence compare to the mismatch sequences. Arylated oligonucleotide based molecular rotor (AOMR) proves to be an unprecedented sensitivity in detecting local dynamics of nucleic acids and also would be simple and cost-effective method to prepare SNP probe.