Photochemical modifications for DNA/RNA oligonucleotides^e.

#	Photoreaction type	Photoreactive group	Structure	Reaction wavelength (nm)	Reversible?b	T m effect	Photoreaction time scale	Nucleic acid position	Biological application
1	(I) Photocleavage – irreversible	o-Nitrobenzyla (& NPE, NPM, NPOM, PNVOM, NDBF, etc)		345–420	No	↓	sec–min	Bases, backbone, ribose	Variety of biological systems (see text)
2	(I) Photocleavage – irreversible	p-Hydroxyphenacyl (& HBT)		295–405	No	↓	msec–sec	G, T bases	Control of antisense RNA annealing
3	(I) Photocleavage – irreversible	TEEP-OH		300–365	No	ND	min	Phosphate backbone on DNA	Regulation of DNAzyme activity
4	(I) Photocleavage – irreversible	Aryl sulfide		350	No	↓	μsec–min	U, T bases	Control of RNA riboswitch folding
5	(I) Photocleavage – irreversible	Nitroindole		350	No	↓	min	Deoxyribose as a purine analogue	Catch and Release DNA Decoys
6	(I) Photocleavage – irreversible	Benzophenone, acetophenone		365	No	ND	min	G, C bases	Regulation of mRNA translation; photocrosslink with bound proteins
7	(I) Photocleavage – irreversible, (II) Intermolecular photocrosslinking via [2 + 2] cycloaddition – reversible	Coumarin (& DEACM, Bhc; quinoline. Cf. psoralen)		350–470	No for cleavage; Yes for crosslinking (254)	↓	sec–min	G, T bases, phosphate, backbone linker	Catch-and-release DNA decoy, regulation of mRNA caging, transient DNA polymerization, aptamer
8	(II) Intermolecular photocrosslinking via [2 + 2] cycloaddition – reversible	Carbazolea (&CNVK, CNVD, PCX, and PCXD)		365–450	Yes (312)	↓↑	sec–min	Nucleoside	RNA FISH, plasmid labeling, antisense DNA, regulation of DNAzyme activity
9	(II) Intermolecular photocrosslinking via [2 + 2] cycloaddition – reversible, (III). Cis–trans photoisomerization – reversible	Vinyl-derivative (& stilbazole, cyanostilbene, styrylpyrene; 8ST, 8NV and 8FV)		340–465c, 370–420d	Yes (≤300–340c) (254–310d)	↓↑	min–hour	Nucleoside, G base	DNA hybridization, regulation of gene expression
10	(III) Cis–trans photoisomerization – reversible	Azobenzenea		365	Yes (400–420)	↓↑	sec–min	Nucleoside backbone linker, G, A bases	Variety of biological systems (see text)
11	(IV) Intramolecular photocyclization – reversible	Spiropyrans		365	Yes (400–520)	ND	min–hour	Backbone	ND
12	(IV) Intramolecular photocyclization – reversible	Diarylethene		250–370	Yes (>400)	↓	sec–min	U, C bases, A analogue (deazapurine)	ND

^aSome derivatives (e.g., d-tAzo) are commercially available.

^bWavelengths in parentheses indicate those for the reverse, uncrosslinking reactions.

^cWavelengths for (un)crosslinking reaction.

^dWavelengths for cis–trans/trans–cis isomerization.

^eN.B. All modifications can be incorporated in solid-phase oligonucleotide syntheses (e.g. via phosphoramidite chemistry) unless otherwise noted (e.g., DMNEC as a part of oNB, TEEP-OH, and DPMTC as a part of coumarin).