The fluorescent analogue 2-aminopurine (2AP) of the canonical nucleobase adenine (6 aminopurine) base-pairs with thymine (T) without disrupting the helical structure of the DNA. It therefore finds frequent use in molecular biology for probing DNA and RNA structure and conformational dynamics. However, detailed understanding of the processes responsible for fluorescence quenching remains largely elusive on a fundamental level. While attempts have been made to ascribe decreased excited-state lifetimes to intra-strand charge transfer and stacking interactions, possible influences from dynamic inter-strand H-bonding have been widely ignored. Here, we investigate the electronic relaxation of UV-excited 2AP-T in Watson-Crick (WC) and Hoogsteen (HS) conformations. While the WC conformation features slowed-down, monomer-like electronic relaxation inτ ~ 1.6 ns towards ground-state recovery and triplet formation, the dynamics associated with 2AP-T in the HS motif exhibit faster deactivation inτ ~ 70 ps. As recent research has revealed abundant transient inter-strand H-bonding in the Hoogsteen motif for duplex DNA, the established model for dynamic fluorescence quenching may need to be revised in the light of our results. The underlying supramolecular photophysical mechanisms are discussed in terms of a proposed excited-state double proton transfer as an efficient deactivation channel for recovery of the HS species in the electronic ground state.