The dinucleotide AppppA (5',5'''-P1, P4-diadenosine tetraphosphate) is rapidly synthesized in cells exposed to heat stress or oxidative stress. Stress-induced AppppA accumulation has been observed in all cell types studied to date. In order to study the function(s) of AppppA, we created a mutation in the Escherichia coli gene that encodes the sole AppppN hydrolase (apaH). High levels of AppppA have subsequently been shown to affect many cellular processes, including expression of catabolite repressible genes and the ability to survive starvation, oxidative stress and near-UV irradiation. Nevertheless, the precise role of AppppA remains undefined. In order to better understand the mechanism by which AppppA exerts its effects, we attempted to determine which proteins bind to AppppA by synthesizing (alpha'-32P) 8-N3AppppA for use in photocrosslinking experiments with extract derived from cells with different genetic backgrounds and exposed to various stress conditions. We report here that several E. coli proteins bind AppppA, including the heat shock and oxidative stress proteins DnaK, GroEL, E89, C45 and C40. In addition, we show that apaH mutants, which have high basal levels of AppppA, are hypersensitive to killing by heat.