Pentaphosphorylated magic spot nucleotides: chemoenzymatic synthesis and disassembly-based sensing

Abstract

The magic spot nucleotides (MSNs), (p)ppGpp and (p)ppApp, play central roles in bacterial stress signaling, yet their selective detection and chemical accessibility remain limited. This work presents a scalable chemo-enzymatic synthesis of natural and functionalized pentaphosphorylated MSNs based on a cyclic pyrophosphoryl phosphoramidite (cPyPA) mediated phosphorylation and RNase T2-catalyzed hydrolysis. This approach enables preparative access to defined 3′-monophosphates (ppAp, ppGp) and the pentaphosphorylated products pppApp and pppGpp. In parallel, a metal–ligand disassembly-based fluorescence probe that operates in water was developed for the selective detection of MSNs. Coordination of the alarmone to an Fe(III)-salen complex induces its demetallation and fluorescence activation through salicylaldehyde release, supported by theoretical and spectroscopic studies. The probe displays a two- to threefold selectivity for (p)ppGpp and (p)ppApp over other nucleotides and responds most strongly to MSNs bearing 3′- and 5′-pyrophosphate groups. The probe also detects enzymatically generated ppGpp from Staphylococcus aureus RelP reactions in vitro. This work combines a robust synthesis route for pentaphosphorylated MSNs with a readily accessible fluorescence sensor, thereby laying the foundation for future investigations into bacterial stress signaling.