Position Dependence of 2-Aminopurine Spectra in Adenosine Pentadeoxynucleotides

The fluorescent probe/base, 2-aminopurine (2AP), has been incorporated into DNA pentamers that otherwise contain only adenine, the base that has been shown to stack strongly with itself and with the adenine mimic, 2AP. The probe base has been placed in each of the five positions in single strands. Optical spectral shifts, energy-transfer efficiencies, and their respective temperature dependencies behave simply as a function of 2AP position: those quantities approximately double when 2AP is placed between two adenines, compared to 2AP at either end of the chain. Transfer efficiencies of 80% (at 5°C) are measured for APAAA and AAPAA, 68% for AAAPA, while PAAAA and AAAAP efficiencies are 52% and 46%, respectively (P = 2AP). The spectroscopic parameters are therefore reliable measures of local DNA conformation that can be interpreted in a straightforward manner in terms of interbase electronic interactions. Interactions of 2AP with nonadenine bases have previously been shown to mostly be much weaker.