A General Design for Caging Groups

To improve caging groups for the use of different applications such as photolithography or DNA arrays several types of caging groups have been designed. Figure 1 illustrated a general chemical structure for a variety of approaches used for the design of caged molecules.

Figure 1: Chemical structure for the general design of caging groups.

Y = amino acids, XNH-, or C5¹ oxygen on DNA or RNA,

R₁ and R₂ = Hydrogen, alkyl, aryl, benzyl, halogen, hydroxyl, alkoxyl, thiol, thioether, amino, nitro, carboxyl, formate, formido, sulfide, phosphidogroup,

R₃ = alkoxy, aryl, alkenyl, hydrogen group.

{Source: Patent WO 1992010092 A1; 1992}.

The perturbation effect for each caging group can vary based on oligonucleotide function, the number of caged nucleobases used per oligonucleotide, as well as the position of the caging group within the oligonucleotide probe. However, often a single caging group placed at a crucial site is sufficient for blocking activities, for example, to interfere with or study protein interactions or catalytic DNAzyme activities. Multiple caging groups are often required for the regulation of base-pairing interactions between oligonucleotides. Studies have shown that in general one caging group placed every 5 to 6 bases and evenly spaced throughout an oligonucleotide can fully abrogate or block hybridization to the complement. Removing the caging groups through irradiation will allow restoring hybridization.

To conclude, well designed photo-caged oligonucleotides or probes can be used for the study of biological processes via light- or optochemical-regulation. However, recent scientific reports indicate that the scope of application for this technology is much wider. Caged oligonucleotides may enable new types of applications in DNA based computation, DNA/RNA sensing, as well as DNA nanotechnologies. The future may see their use for the study of gene functions, effects of non-coding RNA, in embryo development, cell motility, and other research areas. Also, caging groups can be combined with other modified nucleobases such as bridged nucleic acids (BNAs) to design new types of oligonucleotide based probes and tools.

Reference

Adrian Dussy, Christoph Meyer, Edith Quennet, Thomas A. Bickle, Bernd Giese and Andreas Marx; New Light-Sensitive Nucleosides for Caged DNA Strand Breaks. Volume 3, Issue 1, pages 54–60, January 4, 2002.

G C Ellis-Davies, J H Kaplan; Nitrophenyl-EGTA, a photolabile chelator that selectively binds Ca2+ with high affinity and releases it rapidly upon photolysis. Proc Natl Acad Sci U S A. 1994 January 4; 91(1): 187–191. PMCID: PMC42911.

Ting R, Lermer L, Perrin DM. Triggering DNAzymes with light: A photoactive C8 thioetherlinked adenosine. J Am Chem Soc. 2004; 126:12720–12721. [PubMed: 15469235].