Aryl-diyne linkers in bis-triarylborane cations control fluorimetric and Raman sensing of various DNA and RNA

We report four new luminescent tetracationic bis-triarylborane DNA and RNA sensors that show high binding affinities, in several cases even in the nM range. Three of the compounds contain substituted, highly emissive, and structurally flexible bis(2, 6-dimethylphenyl-4- ethynyl)arene linkers (3: arene = 5, 5’-2, 2’-bithiophene ; 4: arene = 1, 4-benzene ; 5: arene = 9, 10-anthracene) between the two boryl moieties and serve as efficient dual Raman and fluorescence chromophores. The shorter analogue 6 employs bis(2, 6- dimethylphenyl)-9, 10-anthracene as the linker and demonstrates the importance of an adequate linker length with a certain level of flexibility by exhibiting generally lower binding affinities than 3-5. Pronounced aggregation - deaggregation processes are observed in fluorimetric titration experiments with DNA for compounds 3 and 5. Molecular modelling of complexes of 5 with AT-DNA, suggest the minor 2 groove as the dominant binding site for monomeric 5, but demonstrate that dimers of 5 can also be accommodated. Strong SERS responses for 3-5 (particularly compound 5) vs. a very weak response for 6 demonstrate the importance of triple bonds for strong Raman activity in molecules of this compound class. The energy of the characteristic stretching vibration of the C≡C bonds is significantly dependent on the aromatic moiety between the triple bonds. The insertion of aromatic moieties between two C≡C bonds thus offers an alternative design for dual Raman and fluorescence chromophores, applicable in multiplex biological Raman imaging.