Photo‐cidnp Study of Adenylyl‐containing Deoxy‐dinucleotides. Pair Substitution Effects Due to Intramolecular Cation Radical Deprotonation

Abstract— 360 MHz 1H photo‐CIDNP spectra of several adenylyl containing deoxy dinucleotides show that fast deprotonation at the 6‐amino group of the adenylyl radical cation can occur via two intramolecular routes. One is mediated by the 5′‐phosphomonoester group and only occurs for the pdA moiety at the 3′ end of the dinucleotide, e.g. in pdTpdA and pdApdA; molecular model building studies reveal that fluctuations away from the B‐DNA like conformation are involved. In the second route the deprotonation is catalyzed by N‐l located on an adjacent adenine ring, like in dApdA and pdApdA; it probably occurs for both adenylyl units in a stacked conformation. This fast deprotonation leads to the observation of negative polarization for the adenineH–8 as was observed in the case of adenosine 5‐monophosphate in the presence of added phosphate.