. Author manuscript; available in PMC: 2011 May 5.

Published in final edited form as: J Am Chem Soc. 2010 May 5;132(17):6183–6193. doi: 10.1021/ja100710j

Table 1.

Synthesized caged and non-caged deoxyoligonucleotide sequences.

DNA	Sequence 5’ → 3’
D1	CGCACCCAGGCTAGCTACAACGACTCTCTCCG
D2	CGCACCCAGGCT₁₂AGCTACAACGACTCTCTCCG
D3	CGCACCCAGGCTAGCT₁₆ACAACGACTCTCTCCG
D4	CGCACCCAGGCTAGCTACAACGACT₂₅CTCTCCG
D5	CGCACCCAGGCTAGCTACAACGACTCT₂₇CTCCG
D6	CGCACCCAGGCTAGCTACAACGACTCTCT₂₉CCG
D7	CGCACCCAGGCTAGCTACAACGACT₂₅CT₂₇CT₂₉CCG
DD1	GGAGAGAGATGGGTGCG
DD2	GGAGAGAGAT₁₀GGGT₁₄GCG
DD3	TCGTTGTAGCTAGCC
DD4	T₁CGT₄TGTAGCT₁₁AGCC
HP1	CTAGCCTGGTGCGTTTTCGCACCCAGGCTAGCTACAACGACTCTCTCCG
HP2	CCTGGTGCGTTTTCGCACCCAGGCTAGCTACAACGACTCTCTCCG
HP3	CT₂AGCCT₇GGT₁₀GCGTTTTCGCACCCAGGCTAGCTACAACGACTCTCTCCG
R1	GCGCGCGAAACGCGCGCTACAACTCGGTGATGAGGCTAGCTACAACGAGTTCTCGGAGGAGCGGCGCGCGCAAAGCGCGCG
R2	GCGCGCGAAACGCGCGCTACAACTCGGTGATGAGGCT₃₇AGCTACAACGAGTTCTCGGAGGAGCGGCGCGCGCAAAGCGCGCG
R3	GCGCGCGAAACGCGCGCTACAACTCGGTGATGAGGCA₃₇AGCTACAACGAGTTCTCGGAGGAGCGGCGCGCGCAAAGCGCGCG
R4	GCGCGCGAAACGCGCGCTACAACTCGGTGATGAGTTCTCGGAGGAGCGGCGCGCGCAAAGCGCGCG
R5	GCGCGCGAAACGCGCGCTACAACT₂₄CGGTGAT₃₁GAGGCTAGCTACAACGAGTTCTCGGAGGAGCGGCGCGCGCAAAGCGCGCG
R6	AT₂CACCGAGT₁₀TGT₁₃AGCGCGCGAAACGCGCGCTACAACTCGGTGATGAGTTCTCGGAGGAGCGGCGCGCGCAAAGCGCGCG
R7	GCGCGCGAAACGCGCGCCGCACCCAGGCTAGCTACAACGACTCTCTCCCGCGCGCGCAAAGCGCGCG

T_nn = caged thymidine; underline = self-complementary region for hairpin formation; italics = protective hairpin formation for intracellular stabilization; A₃₇ = mutation from thymidine to adenosine.