## 1 Introduction  
The binding of proteins to nucleic acids (DNA and RNA) is central to all aspects of gene expression regulation. DNA-binding proteins include the transcription factor to bind to specific DNA sequences and control the transcription rate of genetic information from the DNA to RNA [1; 2]. Many DNA modifying enzymes are also included in the DNA binding protein, for example, repair enzymes [3; 4] and epigenetic modification enzymes. DNA methyl transferase is one of the epigenetic modification enzymes and catalyses the transfer of the methyl group to DNA modifying the function of genes and affecting gene expression [5; 6]. RNA-binding proteins have important functions in the post-transcriptional process, such as splicing regulation [7] and modulation of the mRNA translation. Recent studies have revealed that post-transcriptional gene regulation by non-coding RNAs is involved in most biological activities. The association of the RNA binding protein with ncRNA plays a crucial role in these biological functions [8; 9; 10]. The chemical tools for the control of the interaction between the nucleic acids-binding protein and nucleic acids have the potential for the development as the new strategy for artificial control of the gene expression. Crosslinking reactions between nucleic acids and binding proteins are powerful tools for analyzing these interactions. Photoreactive functional groups, such as diazirines and benzophenones,were utilized for DNA or RNA-protein crosslinking [11; 12; 13; 14], but lack selectivity for the target amino acid. Furthermore, due to their intrinsic reactivity, these groups react with water and other reactive chemical species resulting in low yields. Oligodeoxynucleotides (ODN) with reactive groups are exploited for their effective DNA-protein crosslinking reactions by the proximity effect of the specific DNA recognition with the binding protein. The reactive groups activated by oxidation, such as a diol [15] and furan [16], react with a proximal lysine or arginine in the protein or peptides. [PERSON] et al. reported that the ODN bearing a vinylsulfone amide [17] or chloroacetamide group [18] efficiently cross-linked with the p53 protein through alkylation of the cysteine in the proximal position with the reactive groups. Recently, they demonstrated that ODN with 2-vinylhypoxantine reacted with a thiol-containing minor groove binding peptide by proximity effect [19]. In our previous study, we reported the synthesis of the ODN bearing 4-amino-6-oxo-2-vinyltriazine with an ethyl linker (Et-AOVT: (**1**)) as a cross linkable derivative and an evaluation of its properties [20]. ODN showed a relatively high reactivity with the pyrimidine nucleobases of the complementary DNAs and the lowest reactivity to guanine. We hypothesized that the AOVT base would form a stable base pair with guanine (G) by three hydrogen bonds to be positioned at the vinyl group in the DNA major groove. In this study, we have designed an AOVT derivative with an acyclic linker (_acy_AOVT: (**2**)) as a cross-linkable probe of the nucleic acids-binding protein. The distance between the reactive base and sugar moiety of **2** is shorter than that of **1**, and consequently, the _acy_AOVT (**2**) should form a base pair with guanine (G) similar to the natural cytosine (C)-G pair. This assumption is supported by the molecular modeling shown in Figure 1. The molecular modeling revealed that the structure of the base pair of _acy_AOVT (**2**)-G and the natural C-G significantly overlap each other (Figure 1C). On the other hand, the structure of Et-AOVT (**1**)-G is subtly shifted from the natural base pair one (Figure 1B). The duplex DNA containing the _acy_AOVT (**2**)-G is expected to bind to the nucleic acid binding proteins similar to the natural duplex and form covalent linkages with the nucleophilic residues of the protein in the proximal position of the vinyl group (Figure 2).