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Synthesis of light-activated antisense oligodeoxynucleotide

Nature Protocols volume 1, pages 3041–3048 (2006)Cite this article

Abstract

The activity of a 20-mer antisense oligodeoxynucleotide (asODN) is transiently blocked by attaching a partially complementary sense strand (sODN) via a heterobifunctional photocleavable linker (PL). The asODN-PL-sODN conjugate forms a DNA hairpin-like structure that is considerably more stable than the corresponding asODN/sODN duplex. In conjugate form, the asODN is prevented from hybridizing to exogenous RNA or DNA molecules. Activity is restored after modest exposure to UV light (λ ≈ 365 nm). Here, we provide a detailed procedure for synthesizing photoactive asODNs in good yields. Synthesis, purification and analysis of the light-activated asODN can be completed within 1–2 weeks.

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Figure 1
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Figure 5: HPLC traces (Step 34) observed under different reaction conditions to generate PL-oligonucleotide in Step 30: (a) 1 h at room temperature; (b) 2 h at 35 °C or 40 min at over 50 °C; (c) 40 min at 35 °C.
Figure 6

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Acknowledgements

Support for this work came from grants from the Penn Genomics Institute (PGI) and Penn Institute for Medicine and Engineering (IME), and startup funds provided to I.J.D. by the Department of Chemistry at the University of Pennsylvania.

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  1. Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, 19104-6323, Pennsylvania, USA

    XinJing Tang & Ivan J Dmochowski

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Correspondence to Ivan J Dmochowski.

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Tang, X., Dmochowski, I. Synthesis of light-activated antisense oligodeoxynucleotide. Nat Protoc 1, 3041–3048 (2006). https://doi.org/10.1038/nprot.2006.462

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