Table 1.

RNA fragments monitored by MALDI-TOF MS, masses of product overhangs, and proposed mechanisms of formation

terminal overhanga	Δ mass (amu) b	proposed mechanisms of formation
3’-OH	0.00	hydrolysis,c MALDI d
2’,3’-cPO4	61.96	endonucleolysis,e MALDI d
3’-PO4	79.98	1’-H, 2’-H, 3’-H, 4’-H, or 5’-H abstraction,f hydrolysis,c MALDI d
3’-PG	138.02	4’-H abstraction f
3’-a-B	176.06	MALDI d
5’-z	−18.02	MALDI d
5’-OH	0.00	endonucleolysis,e hydrolysis,c MALDI d
5’-PO4	79.98	1’-H, 2’-H, 3’-H, 4’-H, or 5’-H abstraction,f hydrolysis,cMALDI d

^aSee Figure 2.

^bRelative to the nascent terminal hydroxyl group.

^cThe 3’-OH and 5’-PO₄ overhangs are expected as minor hydrolysis products, while hydrolysis is expected to give primarily 3’-PO₄ (or 2’-PO₄) and 5’-OH overhangs.

^dFragmentation of RNA during MALDI-TOF MS.^35–38

^eFrom 2’-OH-mediated transesterification.

^fReported for the analogous oxidative scission of DNA.²¹