Alexei I. Kononov

Fluorescent Silver Nanoclusters in Condensed DNA

We study the formation and fluorescent properties of silver nanoclusters encapsulated in condensed DNA nanoparticles. Fluorescent globular DNA nanoparticles are formed using a dsDNA-cluster complex and polyallylamine as condensing agents. The fluorescence emission spectrum of single DNA nanoparticles is obtained using tip-enhanced fluorescence microscopy. Fluorescent clusters in condensed DNA nanoparticles appear to be more protected against destructive damage in solution compared to clusters synthesized on a linear polymer chain. The fluorescent clusters on both dsDNA and ssDNA exhibit the same emission bands (at 590 and 680 nm) and the same formation efficiency, which suggests the same binding sites. By using density functional theory, we show that the clusters may bind to the Watson-Crick guanine-cytosine base pairs and to single DNA bases with about the same affinity.

Noncanonical Stacking Geometries of Nucleobases as a Preferred Target for Solar Radiation

Direct DNA absorption of UVB photons in a spectral range of 290-320 nm of terrestrial solar radiation is responsible for formation of cyclobutane pyrimidine dimers causing skin cancer. Formation of UVB-induced lesions is not random, and conformational features of their hot spots remain poorly understood. We calculated the electronic excitation spectra of thymine, cytosine, and adenine stacked dimers with ab initio methods in a wide range of conformations derived from PDB database and molecular dynamics trajectory of thymine-containing oligomer. The stacked dimers with reduced interbase distances in curved, hairpin-like, and highly distorted DNA and RNA structures exhibit excitonic transitions red-shifted up to 0.6 eV compared to the B-form of stacked bases, which makes them the preferred target for terrestrial solar radiation. These results might have important implications for predicting the hot spots of UVB-induced lesions in nucleic acids.

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.

DNA as UV light–harvesting antenna

Abstract 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.

Triplet state generation by furocoumarins revisited: a combined QSPR/DFT approach

Furocoumarins (psoralens and angelicins) are often used for the photo-treatment of psoriasis, vitiligo, atopic dermatitis and other dermatological pathologies. The mechanism of furocoumarin action in vivo is as follows: furocoumarin enters the cells and intercalates between DNA base pairs. Upon exposure to UVA, furocoumarin absorbs photons, becomes chemically activated, and covalently binds to DNA base pairs, forming cross-links and cyclobutane type adducts with DNA. The triplet state formation by furocoumarins is a key process, which leads not only to covalent binding to DNA, but also to the generation of reactive oxygen species and photooxidation reactions. Our goal was to develop a quantitative structure–property relationship (QSPR) model for the fast virtual screening and prediction of the efficiency of triplet state generation by furocoumarins. We performed QSPR analysis of 26 furocoumarin compounds (including widely known 8-methoxypsoralen and 5-methoxypsoralen) for their ability to form triplet excited states. Quantum-chemical descriptors were calculated using the HF, B3LYP and PBE0 methods. The ability of furocoumarins to generate triplet states was found to be significantly correlated with the T1 triplet state energy (R2 = 0.627) and the Jhetv descriptor. The best QSPR model “structure–triplet state generation” possesses high internal stability (q2 = 0.865) and a high predicting ability for the test set (pred_R2 = 0.897). The evaluation of reactive oxygen species generation feasibility using Density Functional Theory (DFT) was also performed. We hope that the QSPR model developed in this study will be useful in the development of new synthetic psoralens and angelicins for medicinal purposes.

Electronic excitation energy transport in a DNA-Ag cluster complex

We study electronic excitation transfer in the complexes of Ag clusters with oligonucleotides. Steady-state fluorescence excitation spectra show that the excitation energy is transferred to Ag cluster from all the 30 nucleobases of a 15-mer DNA duplex. This is in contrast to DNA-dyes complexes, where the energy transfer to the dye occurs from neighboring DNA bases only. Fluorescence decay curve for the DNA duplex shows that the process of energy transfer occurs within <100 fs. The obtained results suggest coherent excitonic type of the transfer rather than trivial Forster mechanism.

Structure of fluorescent metal clusters on a DNA template.

Luminescent metal clusters are a subject of growing interest in recent years due to their bright emission from visible to near infrared range. Detailed structure of the fluorescent complexes of Ag and other metal clusters with ligands still remains a challenging task. In this joint experimental and theoretical study we synthesized Ag-DNA complexes on a DNA oligonucleotide emitting in violet- green spectral range. The structure of DNA template was determined by means of various spectral measurements (CD, MS, XPS). Comparison of the experimental fluorescent excitation spectra and calculated absorption spectra for different QM/MM optimized structures allowed us to determine the detailed structure of the green cluster containing three silver atoms in the stem of the DNA hairpin structure stabilized by cytosine-Ag+-cytosine bonds.