Excess Electron Transfer through DNA Duplexes Comprising a Metal-Mediated Base Pair.

Excess electron transfer through one set of DNA duplexes comprising either one or two metal-mediated thymine-HgII -thymine base pairs was studied. Towards this end, the metal-mediated base pair(s) were introduced between an artificial nucleoside bearing a N,N,N',N'-tetramethyl-1,5-diaminonaphthalene derivative (dN, acting as a photoinducible electron donor) and 5-bromo-2'-deoxyuridine (dB, acting as an electron acceptor). Upon one-electron reduction, dB loses a bromide ion. The amount of unreacted dB remaining after irradiation-determined by LC/ICP-MS-was used to evaluate the charge-transfer efficiency across the metal-mediated base pair(s). Reference measurements with canonical adenine:thymine base pairs prove the applicability of this approach for the detection of charge transfer in DNA. The data indicate that, for the set of DNA duplexes under investigation, excess electron transfer across a thymine-HgII -thymine base pair proceeds with low efficiency, comparable to the transfer across a thymine:thymine mispair. Two contiguous thymine-HgII -thymine base pairs effectively shut down excess electron transfer.

Sequence-Dependent Duplex Stabilization upon Formation of a Metal-Mediated Base Pair.

An artificial nucleoside surrogate with 1H-imidazo[4,5-f][1,10]phenanthroline (P) acting as an aglycone has been introduced into DNA oligonucleotide duplexes. This nucleoside surrogate can act as a bidentate ligand, and so is useful in the context of metal-mediated base pairs. Several duplexes involving a hetero base pair with an imidazole nucleoside have been investigated. The stability of DNA duplexes incorporating the respective Ag(I) -mediated base pairs strongly depends on the sequence context. Quantum mechanical/molecular mechanical (QM/MM) calculations have been performed in order to gain insight into the factors determining this sequence dependence. The results indicated that, in addition to the stabilizing effect that results from the formation of coordinative bonds, destabilizing effects may occur when the artificial base pair does not fit optimally into the surrounding B-DNA duplex.

A metal-mediated base pair that discriminates between the canonical pyrimidine nucleobases.

A nucleoside analogue comprising the ligand 1H-imidazo[4,5-f][1,10]phenanthroline (P) was applied to develop a molecular beacon capable of discriminating the canonical nucleobases cytosine and thymine. The beacon is based on the formation of a stable Ag+-mediated base pair between P and cytosine, whereas the presence of Ag+ strongly destabilizes nucleic acids comprising an artificial base pair between P and thymine. Metal-mediated base pair formation was investigated by temperature-dependent UV spectroscopy and CD spectroscopy and complemented by extensive DFT calculations. The molecular beacon significantly extends the application spectrum of nucleic acids with metal-mediated base pairs. It is of potential use in the detection of single-nucleotide polymorphisms.