Interstrand cross-link of DNA by covalently linking a pair of abasic sites.

A pair of apurinic/apyrimidinic sites formed in DNA has been covalently connected with bis(aminooxy) derivatives. The efficacy of the interstrand cross-link is associated with the structural tethering of two aminooxy groups. The interstrand cross-link constructed stable DNA scaffolds for enzyme alignment.

Construction of highly reactive probes for abasic site detection by introduction of an aromatic and a guanidine residue into an aminooxy group.

Abasic sites (AP sites) arise from hydrolysis of glycosidic bonds of DNA that is damaged by various external and internal processes; unrepaired AP sites give rise to genetic mutations. We have constructed highly reactive AP-site-detecting probes by introducing a hydrophobic and a hydrophilic residue in an aminooxy group. Synthesized probes containing either a naphthalene or a guanidine residue conjugate effectively with AP sites.

Development of novel chemical probes to detect abasic sites in DNA.

We chemically synthesized a series of aminooxy derivatives to develop novel probes for sensitive detection of abasic (AP) sites in DNA. The results of the conjugation reactions showed that the probes could efficiently react to AP sites by introducing an aromatic or a guanidino group in their structures. In particular, the probe having both functional groups showed the most effective reactivity, indicating that hydrophobic and electrostatic interactions cooperatively acted in the reaction of the probe to AP sites.

Efficient synthesis of oligonucleotide conjugates on solid-support using an (aminoethoxycarbonyl)aminohexyl group for 5'-terminal modification.

Solid-support conjugation at the 5'-terminal primary amine of oligonucleotides is a convenient and powerful method for introducing various functional groups. However, conventional aliphatic amines do not necessarily provide conjugates with sufficient yields. To improve the modification efficacy, we used the amino-linker (aminoethoxycarbonyl)aminohexyl group (ssH-linker), for solid-support conjugation.

Comparison of the chemical properties of a novel amino-linker with various amino modifications.

We previously reported a series of new amino-linkers, consisting of an aminoethyl carbamate structure (Komatsu, 2008). We have now examined the chemical properties of oligonucleotides modified with an ssH-linker, which is the simplest and most cost-effective derivative of the series. Although it was previously shown that monomethoxytrityl protection on a primary amine of the ssH-linker was cleaved under weakly acidic conditions (1% acetic acid), we found that the deprotection also proceeded in aqueous buffer solutions (pH 6.

Construction of an aminooxy derivative for RNA and DNA labeling.

We previously reported that the reactivity of a primary amine is increased by connecting the amine to an aromatic residue with an alkyl linker. This strategy was applied to the construction of a reagent that could form a covalent bond with an aldehyde group. We synthesized a new reagent that consisted of aminooxy and aromatic groups and biotin.