Effect of substitution of photo-cross-linker in photochemical cytosine to uracil transition in DNA

Abstract

Genome editing is an important technique for protein engineering, treatment of genetic disorders, and production of non-native proteins. A shortcoming of current enzymatic and chemical methods for genome editing is their limited applicability for in vivo studies. In addition, non-enzymatic methods, such as photochemical DNA editing using 3-cyanovinylcarbazole (^CNVK), require high temperatures to affect cytosine to uracil transformations. To overcome this limitation, we developed new photo-cross-linkers based on ^CNVK, 3-methoxycarbonlycarbazole, 3-carboxyvinylcarbazole, and 3-carbonylamidevinylcarbazole. The use of 3-carboxyvinylcarbazole resulted in greater acceleration of the deamination reaction than that achieved with ^CNVK. The most likely factors affecting the ability of ultrafast photo-responsive nucleosides to accelerate the deamination reaction are polarity and hydrophilicity of the oligodeoxyribonucleotides that contain photo-cross-linker.

Keywords: C to U transition; DNA photo-cross-linking; Vinyl-carbazole derivatives.