Excited States in Single-Stranded and i-Motif DNA with Silver Ions.

We have studied the excited states and structural properties for the complexes of cytosine (dC)10 chains with silver ions (Ag+) in a wide range of the Ag+ to DNA ratio (r) and pH conditions using circular dichroism, steady-state absorption, and fluorescence spectroscopy along with the ultrafast fluorescence upconversion technique. We also calculated vertical electronic transition energies and determined the nature of the corresponding excited states in some models of the cytosine-Ag+ complexes. We show that (dC)10 chains in the presence of silver ions form a duplex stabilized by C-Ag+-C bonds. It is also shown that the i-motif structure formed by (dC)10 chains is destabilized in the presence of Ag+ ions. The excited-state properties in the studied complexes depend on the amount of binding ions and the binding sites, which is supported by the calculations. In particular, new low-lying excited states appear when the second Ag+ ion interacts with the O atom of cytosine in the C-Ag+-C pairs. A similar picture is observed in the case when one Ag+ ion interacts with one cytosine via the N7 atom.

Rapid and selective colorimetric determination of L-DOPA in human serum with silver nanoparticles.

L-DOPA, or l-3,4-dihydroxyphenylalanine is an aromatic amino acid, which plays a significant role in human metabolism as a precursor of important neurotransmitters. We develop a fast and simple colorimetric method for the detection of L-DOPA in biological fluids. The method is based on the reduction of silver ions with L-DOPA and the subsequent formation of L-DOPA stabilized silver nanoparticles (Ag NPs). In this novel approach, L-DOPA works as both reducing and stabilizing agent, which provides selectivity and simplifies the procedure. HR-TEM images show very narrow Ag NPs distribution with an average size of 24 nm. Such sensor design is suggested for the first time. We also calculate vertical ionization potential, vertical electron affinity, and Gibbs free energy change of different ionic forms of L-DOPA and amino acids at the M06-2X/def2-TZVP level for the gas phase in comparison with that of silver. A model of silver ions reduction by aromatic amino acids is proposed: the ionic forms with charge -1 are suggested to reduce silver ions. High selectivity against aromatic amino acids, dopamine and serotonin is achieved by tuning pH and involving two L-DOPA forms with charged both hydroxyphenolate and carboxylate groups in the stabilization of uniform-sized Ag NPs. The method is applicable for the determination of L-DOPA in human serum with the 50 nM limit of detection and the linear range up to 5 µM. Ag NPs formation and coloring the solution proceeds in a few minutes. The suggested colorimetric method has potential application in clinical trials.

Exciton Absorption and Luminescence in i-Motif DNA.

We have studied the excited-state dynamics for the i-motif form of cytosine chains (dC)10, using the ultrafast fluorescence up-conversion technique. We have also calculated vertical electronic transition energies and determined the nature of the corresponding excited states in a model tetramer i-motif structure. Quantum chemical calculations of the excitation spectrum of a tetramer i-motif structure predict a significant (0.3 eV) red shift of the lowest-energy transition in the i-motif form relative to its absorption maximum, which agrees with the experimental absorption spectrum. The lowest excitonic state in i-(dC)10 is responsible for a 2 ps red-shifted emission at 370 nm observed in the decay-associated spectra obtained on the femtosecond time-scale. This delocalized (excitonic) excited state is likely a precursor to a long-lived excimer state observed in previous studies. Another fast 310 fs component at 330 nm is assigned to a monomer-like locally excited state. Both emissive states form within less than the available time resolution of the instrument (100 fs). This work contributes to the understanding of excited-state dynamics of DNA within the first few picoseconds, which is the most interesting time range with respect to unraveling the photodamage mechanism, including the formation of the most dangerous DNA lesions such as cyclobutane pyrimidine dimers.

Structure of DNA obtained during the ab initio synthesis by Bst DNA polymerase in the presence of the nicking endonuclease from Bacillus stearothermophilus (Nt.BstNBI).

Communicated by Ramaswamy H. Sarma.

DNA as UV light-harvesting antenna.

The ordered structure of UV chromophores in DNA resembles photosynthetic light-harvesting complexes in which quantum coherence effects play a major role in highly efficient directional energy transfer. The possible role of coherent excitons in energy transport in DNA remains debated. Meanwhile, energy transport properties are greatly important for understanding the mechanisms of photochemical reactions in cellular DNA and for DNA-based artificial nanostructures. Here, we studied energy transfer in DNA complexes formed with silver nanoclusters and with intercalating dye (acridine orange). Steady-state fluorescence measurements with two DNA templates (15-mer DNA duplex and calf thymus DNA) showed that excitation energy can be transferred to the clusters from 21 and 28 nucleobases, respectively. This differed from the DNA-acridine orange complex for which energy transfer took place from four neighboring bases only. Fluorescence up-conversion measurements showed that the energy transfer took place within 100 fs. The efficient energy transport in the Ag-DNA complexes suggests an excitonic mechanism for the transfer, such that the excitation is delocalized over at least four and seven stacked bases, respectively, in one strand of the duplexes stabilizing the clusters. This result demonstrates that the exciton delocalization length in some DNA structures may not be limited to just two bases.

DNA with Ionic, Atomic, and Clustered Silver: An XPS Study.

The rapidly developing field of bionanotechnology requires detailed knowledge of the mechanisms of interaction between inorganic matter and biomolecules. Under conditions different from those in an aqueous solution, however, the chemistry of these systems is elusive and may differ dramatically from their interactions in vitro and in vivo. Here, we report for the first time a photoemission study of a metal silver-DNA interface, formed in vacuo, in comparison with DNA-Ag+ and fluorescent DNA-Ag complexes formed in solution. The high-resolution photoelectron spectra reveal that in vacuo silver atoms interact mainly with oxygen atoms of the phosphodiester bond and deoxyribose in DNA, in contrast to the behavior of silver ions, which interact preferentially with the nitrogen atoms of the bases. This offers new insight into the mechanism of DNA metallization, which is of importance in creating metal-bio interfaces for nanotechnology applications.

Ag-DNA Emitter: Metal Nanorod or Supramolecular Complex?

Ligand-stabilized luminescent metal clusters, in particular, DNA-based Ag clusters, are now employed in a host of applications such as sensing and bioimaging. Despite their utility, the nature of their excited states as well as detailed structures of the luminescent metal-ligand complexes remain poorly understood. We apply a new joint experimental and theoretical approach based on QM/MM-MD simulations of the fluorescence excitation spectra for three Ag clusters synthesized on a 12-mer DNA. Contrary to a previously proposed "rod-like" model, our results show that (1) three to four Ag atoms suffice to form a partially oxidized nanocluster emitting in visible range; (2) charge transfer from Ag cluster to DNA contributes to the excited states of the complexes; and (3) excitation spectra of the clusters are strongly affected by the bonding of Ag atoms to DNA bases. The presented approach can also provide a practical way to determine the structure and properties of other luminescent metal clusters.