Oligoamine-acridine conjugates for promotion of gap-selective DNA hydrolysis by Ce(IV)/EDTA complex

Synthesis of [12]aneN3-dipeptide conjugates as metal-free DNA nucleases

In this Letter, a series of macrocyclic polyamine [12]aneN(3)-dipeptide conjugates as a new type of metal-free nucleases were synthesized and fully characterized with (1)H NMR, (13)C NMR, IR, and HR-MS. Results indicate that these conjugates can bind to calf thymus DNA mainly through electrostatic interaction and can cleave the plasmid DNA at 200 μM (pH 7.2, 37°C), with an acceleration of 10(6)-fold via hydrolytic pathway.

Site-selective DNA hydrolysis by Ce(IV)-EDTA with the use of one oligonucleotide additive bearing two monophosphates

Two deoxyuridine derivatives each bearing a monophosphate group at the 5-position with a C3 linker, were incorporated into an oligonucleotide. By using this modified oligonucleotide, a bulge was formed at a predetermined position in a DNA substrate, and two monophosphate groups were placed at both junctions of the bulge. Upon treatment of the mixture with Ce(IV)-EDTA at pH 7.0, the phosphodiester linkages at the bulge site were selectively and efficiently hydrolyzed. The monophosphate groups introduced into the bulge site greatly accelerated site-selective DNA scission. Compared with the previously reported two-additive system, which combines two oligonucleotide additives each with a monophosphate at their termini, the present one-additive system is simpler and more convenient. Furthermore, site-selective DNA hydrolysis by using this one-additive system is successful even at high reaction temperatures (e.g., 55 degrees C). This reflects the thermodynamic stability of the duplexes formed between the substrate and the additive DNA.

Oligonucleotide bearing ethylenediamine-N,N,N'-Triacetates for gap-selective DNA hydrolysis by Ce4+/EDTA

With the use of two oligonucleotides bearing ethylenediamine-N,N,N'-triacetate groups as additives, gap sites were formed at predetermined sites in substrate DNA. Upon treating these systems with a Ce(4+)/EDTA complex at pH 7.0 and 37 degrees C, the phosphodiester linkages at the gap site were selectively hydrolyzed. The DNA scission was greatly promoted by the introduction of ethylenediaminetriacetate groups, and the scission efficiency increased as the number of these groups increased. Even a one-base gap was successfully hydrolyzed when three ethylenediaminetriacetate groups were placed consecutively at both edges of the gap, although the scission was minimal in the absence of these groups. The site-selective scission could be also achieved at higher temperatures without any significant loss of site-selectivity.