Diarylethene-modified nucleotides for switching optical properties in DNA

Abstract

Diarylethenes were attached to the 5-position of 2'-deoxyuridine in order to yield three different photochromic nucleosides. All nucleosides were characterized with respect to their absorption and photochromic properties. Based on these results, the most promising photochromic DNA base modification was incorporated into representative oligonucleotides by using automated phosphoramidite chemistry. The switching of optical properties in DNA can be achieved selectively at 310 nm (forward) and 450 nm (backward); both wavelengths are outside the normal nucleic acid absorption range. Moreover, this nucleoside was proven to be photochemically stable and allows switching back and forth several times. These results open the way for the use of diarylethenes as photochromic compounds in DNA-based architectures.

Keywords: absorption; cross coupling; molecular switches; oligonucleotide; palladium; photochromism.

Scheme 1

Spiropyran as DNA base surrogate 1, DNA base modifications 2 and 3, and diarylethene-modified nucleosides 4–6. Photoswitching is representatively shown for nucleoside 4.

Scheme 2

Synthesis of diarylethene-modified 2’-deoxyuridines 4 [30], 5 and 6.

Figure 1

Photoswitching properties of nucleosides 4–6 (each 20 mM in MeCN, rt). Top: Irradiation of 4 at 242 nm (A, left) and irradiation of 4 alternating at 242 nm and 450 nm (B, right). Middle: Irradiation of 5 at 250 nm (C, left) and irradiation of 5 alternating at 250 nm and 450 nm (D, right). Bottom: Irradiation of 6 at 254 nm (E, left) and plots of kinetic traces of absorption changes at 450 nm of all nucleosides 4–6 irradiated at the corresponding wavelength until 30 min, then at 450 nm (F, right).

Scheme 3

Synthesis of DNA building block 17 [30] and sequences of diarylethene-modified DNA1–DNA4.

Figure 2

Irradiation of dsDNA2 at 310 nm (A, left) and plot of kinetic trace of absorption changes at 450 nm of dsDNA2 irradiated at 310 nm until 30 min, then 450 nm (B, right).

Figure 3

UV–vis absorption spectra of ssDNA1–ssDNA4 (2.5 μM in 50 mM Na–Pi buffer, pH 7, 250 mM NaCl, rt).