No abstract

DNA molecular glue is a small synthetic ligand that can adhere two single-stranded DNAs that do not spontaneously hybridize with each other. For reversible control of DNA hybridization by an external light stimulus, we have developed a photoswitchable molecular glue for DNA. The photoswitchable molecular glue, NCDA, consists of two guanine-recognizing naphthyridine moieties connected with a photochromic azobenzene unit. Azobenzene undergoes a reversible cis/trans isomerization by photoirradiation, which changes the relative orientations and positions of the naphthyridine moieties, resulting into photoswitching of NCDA binding to the DNA containing GG-mismatch. NCDA in the cis configuration binds to a GG-mismatch sequence and induces the formation of the DNA duplex. Using the photoswitchable binding property of NCDA, the hybridization event of two natural unmodified DNAs can be reversibly controlled by an external light stimulus.

mM NaCl, and 25 µM Co(NH 3 ) 5 Cl 2+ was irradiated for ten minutes at 436 nm followed by enzymatic digestion. (C) The CP G/Rh assembly (5 µM) in 20 mM Tris-Cl (pH 8.1), 10 mM NaCl was irradiated at 365 nm for ten minutes followed by enzymatic digestion.

Supporting Information

The phenothiazinium dye thionine has a high excited state reduction potential and is quenched by guanine on the femtosecond time scale. Here, we show by gel electrophoresis that irradiation of thionine with 599 nm light in the presence of an oligonucleotide duplex does not produce permanent DNA damage. Upon photoexcitation of thionine weakly associated with guanosine-5'-monophosphate, the reduced protonated thionine radical and neutral guanine radical are detected by transient absorption spectroscopy, indicating that the quenching of thionine by guanine occurs via an electron-transfer mechanism. The observation of radical formation without permanent guanine damage indicates that fast back electron transfer plays a critical role in governing the yield of damage by DNA-binding molecules.