Unexpected Hydration of a Triple Bond During DNA Synthesis: Conjugating 3-(Pyren-1-ylethynyl)indole to DNA for Triplex Studies

Twisted intercalating nucleic acid (TINA) has the ability to stabilize Hoogsteen triplex formation. New oligonucleotides containing 3‐(pyren‐1‐ylethynyl)indole as a DNA linked intercalator backbone have been added to the TINA family and their synthetic route has been devised. The indole ring, under acidic conditions, polarizes the triple bond in the intercalator and this makes hydration of the triple bond possible during the DNA synthesis and an oligonucleotide with 1‐(indol‐3‐yl)‐2‐(pyren‐1‐yl)ethanone as the intercalator is formed. Insertion of the unhydrated and hydrated linker systems gave characteristic UV spectra comparable to its monomeric diols due to π‐conjugated and isolated pyrene systems, respectively. Thermal denaturation profile at pH 6–7.2 showed excellent stabilization of the triplex upon insertion of 3‐(pyren‐1‐ylethynyl)indole when compared to wild‐type triplexes. The investigation includes fluorescence spectroscopic and molecular modeling studies. This work demonstrates a risk for unwanted hydration of a triple bond into the corresponding ketone during DNA synthesis. This is exemplified by the synthesis of 3‐(pyren‐1‐ylethynyl)indole as an intercalator linked to a DNA backbone.