Probe	Chemical Structure (Adduct Red, Leaving Group Blue). Letters refer to Box_l_ProbeStructures.	Primary Modification Sites	Half-Life	Reference
	N-methyl-isatoic anhydride (NMIA)	a	2’ OH, all nts	430 s	Merino et al., 2005
	1-methyl-7-nitroisatoic anhydride (1M7)	b	2’ OH, all nts	14 s	Mortimer and Weeks, 2007
	1-methyl-6-nitroisatoic anhydride (1M6)	c	2’ OH, all nts	31 s	Steen et al., 2012
SHAPE	Benzoyl cyanide (BzCN)	d	2’ OH, all nts	0.25 s	Mortimer and Weeks, 2008
	2-methylnicotinic acid imidazolide (NAI)	e	2’ OH, all nts	33 min	Spitale et al., 2013
	2-methyl-3-furoic acid imidazolide (FAI)	f	2’ OH, all nts	73 min	Spitale et al., 2013
	2-methylnicotinic acid imidazolide azide (NAI-N3)	g	2’ OH, all nts	33 min	Spitale et al., 2015
	Dimethyl sulfate (DMS)	h	G N7, A N1, C N3	N/A	Peattie and Gilbert, 1980; Tijerina et al., 2007
Base Specific	N-cyclohexyl-N’-(2-morpholinoethyl)carbodiimide metho-p-toluenesulfonate	i	G N1, U N3	N/A	Gilham, 1962; Ho and Gilham 1967
	Kethoxal, other 1,2-dicarbonyl compounds	j	G N1 and N4	N/A	Litt and Hancock, 1967; Mitchell et al., 2018
Solvent Accessibility	Hydroxyl Radical	k	backbone	N/A	Latham and Cech, 1989; Wang and Padgett, 1989
	Nicotinoyl Azide (Naz)	l	G C8, A C8	N/A	Feng et al., 2018