Abstract
Selective photocrosslinking reaction between 3-cyanovinylcarbazole nucleoside (CNVK) and 5-methylcytosine (mC), which is known as epigenetic modification in genomic DNA, was developed. The reaction was completely finished within 5 s of 366 nm irradiation, and the rate of this photocrosslinking reaction was ca. 30-fold higher than that in the case of unmodified normal cytosine. There were no significant differences in the thermodynamic parameters and the kinetics of hybrid formation of oligonucleotide (ODN) containing CNVK and its complementary ODN containing C or mC at the photocrosslinking site, and suggesting that the quick and selective photoreaction has potential for the selective detection of mC in the DNA strand via the photocrosslinking reaction.
Highlights
Selective photocrosslinking reaction between 3-cyanovinylcarbazole nucleoside (CNVK) and 5-methylcytosine, which is known as epigenetic modification in genomic
(Figure 1, left), the photocrosslinking reaction between CNVK-ODN and ODN(C) occurred, the reaction rate was low compared with the case of ODN(mC)
We found that ODN having CNVK can rapidly photocrosslink to mC in a complementary DNA strand and that the photocrosslinking reaction has a C5 methylation selective manner
Summary
5-Methylcytosine (mC) is the most abundant epigenetic modification in genomic DNA and plays a role in the epigenetic regulation of gene expression, genomic imprinting, cell differentiation, and tumorigenesis [1,2]. If the rapid photocrosslinking reaction of CNVK had the selectivity for mC like VU derivatives having hydrophobic group, rapid and selective detection of mC in the target DNA sequence will be possible. Such a quick and selective photocrosslinking reaction might be a basic reaction for in situ mC mapping and imaging in genomic DNA. In this manuscript, we describe the mC selective photocrosslinking reaction of ODNs containing. K and describe what causes the selective photocrosslinking reaction from the viewpoint of the difference of thermodynamic, kinetic and electronic properties of the ODN duplex containing CNVK and mC or C
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