The interactions of bacteriophage T4 regA protein, a unique translatio
nal regulator, with RNAs of various size and sequence were studied usi
ng electrospray ionization-Fourier transform ion cyclotron resonance-m
ass spectrometry. Using very gentle interface conditions, regA/RNA com
plexes with a 1:1 binding stoichiometry were observed for all four tar
get RNAs studied, consistent with solution binding studies. Competitiv
e binding of target RNAs and their degradation products with regA demo
nstrated that the loss of a single nucleotide resulted in a dramatic c
hange in binding affinity in some cases. Competitive binding of regA w
ith four target RNAs revealed similar relative binding affinity order
to that suggested by previous in vitro repression experiments. The use
of sustained off-resonance irradiation for collisionally induced diss
ociation of a regA/RNA complex suggested the potential for directly ob
taining information regarding the regA binding domain. (C) 1998 Academ
ic Press.