Table 1.

Spectral and biophysical characteristics of commonly used fluorogenic RNA aptamers

RNA aptamer	Fluorophore	KD (nM)	Ex/Em (nm)	ɛ (M−1 cm−1)	ɸ	Length (nt)	Ref.
Spinach	DFHBI	540	469/501	24,300	0.72	98	102
Spinach2	DFHBI-1T	560	482/505	31000	0.94	95	174
Spinach2	DFHBI	530	447/501	22000	0.72	95	174
Spinach2	DFHBI-2T	1300	500/523	29000	0.12	95	174
Spinach2	DFHBI-CM	N/A	447/502	N/A	N/A	95	175
Broccoli	DFHBI-1T	360	472/507	29600	0.94	49	103
Broccoli	BI	51	470/505	33600	0.67	49	113
Red Broccoli	DFHO	206	518/582	35000	0.34	49	105
Orange Broccoli	DFHO	230	513/562	34000	0.28	49	105
Red Broccoli	OBI	23	541/590	47300	0.67	54	126
Corn	DFHO	70	505/545	29000	0.25	36	105
Mango	TO1-Biotin	3.6	510/535	77500	0.16	29	104
Mango II	TO1-Biotin	0.7	510/535	77000	0.2	29	176
Mango III	TO1-Biotin	5.6	510/535	77000	0.56	29	176
Mango IV	TO1-Biotin	11.1	510/535	77000	0.42	29	176
DIR2s-Apt	DIR-pro	252	600/658	164000	0.33	57	177
DIR2s-Apt	OTB-SO3	662	380/421	73000	0.51	57	177
Chili	DMHBI+	63	413/542	21000	0.4	52	178
Chili	DMHBO+	12	456/592	22000	0.1	52	178
SiRA	SiR	430	649/662	86000	0.98	46	179
Pepper485	HBC485	8	443/485	49100	0.42	43	106
Pepper497	HBC497	6.7	435/497	54700	0.57	43	106
Pepper508	HBC508	27	458/508	42500	0.3	43	106
Pepper514	HBC514	12	458/514	44100	0.45	43	106
Pepper525	HBC525	3.8	491/525	74100	0.7	43	106
Pepper530	HBC530	3.5	485/530	65300	0.66	43	106
Pepper599	HBC599	18	515/599	54400	0.43	43	106
Pepper620	HBC620	6.1	577/620	100000	0.58	43	106
SRB-2	SR-DN	1400	579/596	N/A	0.65	54	108
o-Coral	Gemini-561	73	580/596	141000	0.58	150	180
RhoBAST	TMR-DN	15	564/590	96000	0.57	55	181
DNB	TMR-DN	350	555/582	47150	0.9	75	107
DNB	SR-DN	800	572/591	50250	0.98	75	107
BHQ apt (A1)	Cy3-BHQ1	4700	520/565	N/A	N/A	60	182

N/A, not available; ɛ, absorption coefficient; ɸ, quantum yield;

E_x/E_m, excitation/emission wavelength peak value.