OligoCalc Chemical Modifications

When available, mousing over the modification name will give the chemical name

When available, clicking on the modification name will display the structure

Absorptivity is given at 260nm in Moles-1 cm-1

Chemical `Modification	MW	5'	3'	Absorption max (nm)	Emission max (nm)	Absorptivity
Amino dT (C2)	402	X				8700
Amino dT (C6)	458.41	X				8700
5'-BHQ-1 (Black Hole Quencher)	538.49	X		534		8000
3'-BHQ-1 (Black Hole Quencher)	554.49		X	534		8000
BHQ-2 (Black Hole Quencher)	540.47		X	579		8000
5'-Biotin	405.45	X				no absorbance
3'-Biotin	435.48		X			no absorbance
Biotin TEG (Triethyleneglycol)	570		X			no absorbance
Bromo-dC	368	X
Bromo-dU	369	X
C12-Aminolink	263.32	X
C6-Aminolink	179.16	X
C7-Aminolink	209.18		X
Carboxy-dT	360.22		X	297		14700
Cholesterol-TEG	755.97	X
Cholesterol-TEG-Link	855		X
Cyanine (CY) 3.5	607.7	X		591	604	24000
Cyanine (CY) 5.5	633.74	X		688	707	21500
Cyanine (CY) 3	507.59	X		547	563	4930
Cyanine (CY) 3	587		X	546	563	5000
Cyanine (CY) 3 NHS Ester	766	X
Cyanine (CY) 5	533.63	X		646	662	10000
Cyanine (CY) 5	613		X	646	662	10000
Cyanine (CY) 5 Ester	820	X
Dabsyl	498.49		X	453	none	32000 (Lamda max)
2',3'-ddA	297.21		X
2',3'-ddC	273.18		X
2',3'-ddT	288.19		X
Digoxigenin	724	X
Dig with C7 Spacer	754		X
dSpacer	180.1	X
dUridine	290.17	X
3'-Fluorescein (6-FAM)	569.46		X	495	521	20960
5'-Fluorescein (6-FAM)	537.46	X		495	521	20960
5'-Fluorescein	598.56	X		495	520	13700
3'-Fluorescein	598.56		X	494	522	13700
3'-(6-Fluorescein)	566.48		X	494	522	13700
5'-Hexachloro-Fluorescein (HEX)	744.13	X		537	556	31580
3'-Hexachloro-Fluorescein (HEX)	1216		X
Inosine	314.19		X			7200
5-iodo-2'-dCytidine	415.08	X				3300
5-iodo-2'-dUridine	416.07	X
IRDye 700 chromophore	753	X
IRDye 800 chromophore	861	X
JOE chromophore	667	X		520	548	75000 (L. max)
JOE chromophore	697		X
LightCycler Red 610	825	X
LightCycler Red 640	904	X
LightCycler Red 640	934		X
LightCycler Red 670	534	X
LightCycler Red 705	634	X
MethylCytosine	303.21	X
Oregon Green 488	574	X		496	524	76000 (L. max)
32-P labeled	80.0	X
33-P labeled	81.0-	X
Phosphorylated	79.0	X
Psoralen C6-Linker	420.4	X
Psoralen TEG-Linker	453	X
Rhodamine Fluorophore	727	X		572	596	92500 (L. max)
Rhodamine Fluorophore	757		X
Rhodamine-Green	536	X		505	527	68000 (L. max)
6-Carboxy-X-rhodamine (ROX)	698	X		575	602	82000 (L. max)
6-Carboxy-X-rhodamine (ROX)	1104		X
ROX Ester	715		X
Spacer-18	344.3	X
Spacer-C12	264.3	X
Spacer-C3	138.06	X
Spacer-C6	180	X
Tetramethyl-rhodamine (TAMRA)	576	X		560	583	31980
Tetramethyl-rhodamine (TAMRA)	623.6		X	556	580	32300
5'-Tetrachloro-Fluorescein (TET)	675.24	X		519	539	16255
3'-Tetrachloro-Fluorescein (TET)	1147		X
Texas Red Fluorophore	882	X		595	615	80000 (L. max)
Thiol-Modifier C6 S-S	196.2	X
Thiol-Modifier C3 S-S	154.12		X

Please note that many of the chemical structures are for the phosphoramidite form of the compound before it is incorporated into the oligonucleotide, not the modification alone or after incorporation.

Most of the structures were courtesy of Glen Research at http://www.glenres.com/.