Application Description
Psoralen Labelling:
Psoralen is the parent compound in a family of natural products known as furocoumarins and have been used for centuries to treat skin and tumor diseases. In addition, Psoralen is capable of intercalating between nucleobases of a duplex, and cross-link with bases in both double-stranded and triple-stranded oligonucleotides. Psoralen modified DNA is used in the elucidation of nucleic acid structure and nucleic acid/protein interactions.1
Psoralen reacts with DNA and RNA by a two-step mechanism. First, the planar Psoralen molecule intercalates within a double helical region of nucleic acid. Second, when exposed to long-wavelength UV (350 nm) intercalated Psoralen becomes covalently attached to DNA via a [2 + 2] cycloaddition reaction with pyrimidine bases, predominantly with thymine. Initially it forms mono-adduct, in which the psoralen moiety binds to one adjacent thymidine on the same or complimentary strand. Since Psoralen is bi-functional, the photoreaction can lead to di-adducts, in which Psoralen binds to two thymidines adjacent to it, either on the same or complimentary strand.1,2 Di-adducts formed between adjacent thymidines are photo-reversible with short wavelength UV light (254 nm).3 When attached to the terminal of triplex forming oligonucleotide (TFO), Psoralens intercalate into the neighboring duplex and stabilize the triple-stranded complex.4 By forming covalent cross-links with base-paired structures, psoralens can probe both static and dynamic structural features. This allows both the occurrence of the interaction to be established and its position within the structure to be mapped. This advanced state of chemical control makes the Psoralens extremely versatile reagents.
We offer Psoralen phosphoramidites with various linker lengths (C2, C4, C6 and C18 spacer arm) in order to facilitate a Psoralen-modified oligonucleotide’s ability to intercalate and cross-link with double and triple-stranded RNA.
Our Psoralen CPG support (N-9375-05) allows attachment of Psoralen at the 3’-end oligo chain.
Psoralen phosphoramidites with shorter linker (CLP-6647 with C2 spacer arm and CLP-6647 with C4 spacer arm) are capable of forming adducts between double-stranded DNA.
Psoralen amidite with longer linker arm (CLP-6641 with C6 spacer arm and CLP-6642 with 18 atom spacer) arm have the ability to form adducts between triple-stranded DNA.
References
1. Cimino, G. D. et. al. Annu. Rev. Biochem. 1985 54, 1151.
2. a) Turner, S. et. al. Biochem. 1983 22, 4159; b) Garrett-Wheeler E. et. al. Nucl. Acids Res. 1984, 12, 3405.
3. Shi, Y. et. al. Biochem. 1987, 26, 3786.
4. Helene, C. et. al. Proc. Natl. Acad. Sci. U.S.A. 1991 88, 5602-5606Li, H. et. al. Bioconj. Chem. 2006, 17, 1561-1567.
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