A Photo‐responsive Small‐Molecule Approach for the Opto‐epigenetic Modulation of DNA Methylation

Abstract

Controlling the functional dynamics of DNAwithin living cells is essential in biomedical research. Epigenetic modifications such as DNAmethylation play akey role in this endeavour.D NA methylation can be controlled by genetic means.Y et there are few chemical tools available for the spatial and temporal modulation of this modification. Herein, we present as mall-molecule approach to modulate DNAm ethylation with light. The strategy uses aphoto-tuneable version of ac linically used drug (5-aza-2'-deoxycytidine) to alter the catalytic activity of DNAmethyltransferases,the enzymes that methylate DNA. After uptake by cells,t he photo-regulated molecule can be light-controlled to reduce genome-wide DNA methylation levels in proliferating cells.T he chemical tool complements genetic,b iochemical, and pharmacological approaches to study the role of DNAm ethylation in biology and medicine.The methylation of DNAatposition 5ofcytosine residues is chemically av ery simple but biologically one of the most important modifications of DNA. It influences many biological processes in humans such as the regulation of cell function, cellular reprogramming,a nd organismal development. [1][2][3][4][5][6][7] Biological effects of higher methylation levels at promoters are mediated by lowering the transcription of genes either by blocking the binding of transcription factors or by recruiting unique methyl-recognizing proteins that lower gene expression. Altered levels of methylation are also associated with several diseases [8][9][10][11] including cancer. [8,[12][13][14][15][16] Driven by the growing importance of DNAmethylation in biomedical research, there is as trong interest to experimentally lower or increase methylation levels [17][18][19][20][21][22][23] to study,f or example,t he role of epigenetic reprogramming in tissue development or regenerative medicine. [24,25] Optical control is of particular relevance given the high spatial and temporal resolution of light. Often, the approach is implemented with photosensitive small molecules of tuneable bioactivity. [26][27][28][29][30][31] These can be used without the need for genetic engineering of cells leading to powerful applications within cell biology. [32] Yet, despite the importance of DNAm ethylation in biology, no light-tuneable small-molecule tool has been developed to manipulate methylation levels in cells.Herein, we present ap hoto-mediated small-molecule strategy that modulates methylation in light-exposed cells. At the approachsc entre is an inhibitor that interferes with DNAmethyltransferases (DNMTs), the enzymes responsible for DNAm ethylation [33] including the maintenance DNA methyltransferase 1( DNMT1). [34] Thei nhibitorsb ioactivity becomes tuneable with light by the chemical derivatization with ap hotocage.A ss chematically illustrated in Figure 1a, the attached photocage renders the inhibitor biologically inactive.However, light exposure cleaves off the photocage to restore the original inhibitory effect (Figure 1a). Thep hotocaged molecule is hence expected...

Exploring the Relationship between BODIPY Structure and Spectroscopic Properties to Design Fluorophores for Bioimaging

“…When compared to their reference compounds 5 and 8,t he solvatochromic shift between the two solvents is also almostt wice as large with the mono-substituted compound 16 than with the double- substituted compound 15.T his is due to the introductiono f the diethylamino group only present in compound 16. [28,29] Finally,b and gaps for all compoundsw ere computationally calculated by using time-dependant density functional theory (TD-DFT) calculations. For the calculations of compounds 11 and 12,i odine was substituted by bromine as iodine is not compatible with this calculation base.…”

“…[5] Furthermore, to induce strong solvatochromism,w hichi se ssential for environmental sensing,t wo diethyl-amino groups were installed ( Figure 3). [28,29] Amino groupsc an render fluorophores highly sensitivet os olventp olarity [30] and also contribute to longer absorption wavelengths. [29] Thec ompact amphiphilic design of HiBO is aimed to counter commoni ssues of other long wavelength,y et lipophilic non-BODIPY probes, such as poor biological compatibility,c ompromised fluorescencee missiona nd limited retention within membranes.…”

Solvent-dependent photophysics of a red-shifted, biocompatible coumarin photocage

“…The extinction coefficient ε of (1a) in water is 1.04 × 10 4 M −1 cm −1 (Table 1) which is in the range observed for coumarins. 20 Furthermore, the absorption characteristics of (1a) are strongly dependent on the solvent (ESI Fig. S1, † Table 1).…”

“…Longer wavelengths are less mutagenic to biological cells, 5 reach deeper into biological tissues, 11 and help create scope for using a second orthologous photocage. 11 Synthetic strategies to increase the absorption wavelength are to add auxochromes, 12,20 extend the conjugated system, 13 substitute oxygen in carbonyls or lactones, 14 and combinations thereof. 13 Yet, achieving long wavelength absorption and a high photolysis quantum yield within one photocage is usually difficult.…”

“…Organic solvents are often used in photophysical studies 18,19 but biological use requires understanding from water-based data. A final question relates to the photolysis product as the expected release of both uncaged molecule and reformed photocage can be experimentally confirmed, 20 while sometimes only the uncaged molecule is traced. 13 Here we pioneer a new coumarin photocage with long maximum wavelength of absorption and high photolysis quantum yield.…”