Alexandru Rotaru

Single molecule atomic force microscopy studies of photosensitized singlet oxygen behavior on a DNA origami template.

DNA origami, the folding of a long single-stranded DNA sequence (scaffold strand) by hundreds of short synthetic oligonucleotides (staple strands) into parallel aligned helices, is a highly efficient method to form advanced self-assembled DNA-architectures. Since molecules and various materials can be conjugated to each of the short staple strands, the origami method offers a unique possibility of arranging molecules and materials in well-defined positions on a structured surface. Here we combine the action of light with AFM and DNA nanostructures to study the production of singlet oxygen from a single photosensitizer molecule conjugated to a selected DNA origami staple strand on an origami structure. We demonstrate a distance-dependent oxidation of organic moieties incorporated in specific positions on DNA origami by singlet oxygen produced from a single photosensitizer located at the center of each origami.

Sequence dependence of electron-induced DNA strand breakage revealed by DNA nanoarrays

The electronic structure of DNA is determined by its nucleotide sequence, which is for instance exploited in molecular electronics. Here we demonstrate that also the DNA strand breakage induced by low-energy electrons (18 eV) depends on the nucleotide sequence. To determine the absolute cross sections for electron induced single strand breaks in specific 13 mer oligonucleotides we used atomic force microscopy analysis of DNA origami based DNA nanoarrays. We investigated the DNA sequences 5′-TT(XYX)3TT with X = A, G, C and Y = T, BrU 5-bromouracil and found absolute strand break cross sections between 2.66 · 10−14 cm2 and 7.06 · 10−14 cm2. The highest cross section was found for 5′-TT(ATA)3TT and 5′-TT(ABrUA)3TT, respectively. BrU is a radiosensitizer, which was discussed to be used in cancer radiation therapy. The replacement of T by BrU into the investigated DNA sequences leads to a slight increase of the absolute strand break cross sections resulting in sequence-dependent enhancement factors between 1.14 and 1.66. Nevertheless, the variation of strand break cross sections due to the specific nucleotide sequence is considerably higher. Thus, the present results suggest the development of targeted radiosensitizers for cancer radiation therapy.

DNA-assisted decoration of single-walled carbon nanotubes with gold nanoparticles for applications in surface-enhanced Raman scattering imaging of cells

AbstractSingle-walled carbon nanotubes (SWNTs) are 1D nanostructures with distinct physical and chemical properties that have shown great promise for applications in many fields, including biomedicine. Since for biomedical application the water solubility is crucial and SWNTs have low solubility, various methods (including polymer and biopolymer wrapping, chemical modifications) have been developed to solubilize and disperse them in water. Due to their unique optical properties such as photoluminescence in the NIR and strong resonant Raman signatures, they can be used as nanoprobes in biomedical imaging and phototherapies. Furthermore, decoration of SWNTs with noble metal nanoparticles will induce an excellent surface-enhanced Raman scattering (SERS) effect of the nanoparticles-SWNTs composites, with applications in cell imaging. Herein, we present a new and facile strategy for the DNA-assisted decoration of SWNTs with gold nanoparticles (AuNPs) and their application in SERS imaging. By ultrasonication at room temperature of SWNTs with AuNPs functionalized with synthetic DNA, SWNT-AuNPs nanocomposites with enhanced Raman signal were obtained. Among the important advantages of the proposed method are the presence of the free DNA overhangs around the SWNT-AuNPs suitable for post-synthetic modification of nanocomposite through hybridization of complementary DNA strands containing molecules of interest attached by well-developed bio-conjugation chemistry. Graphical abstractᅟ

New conjugates of calix[4]arenes bearing dipyridine and indolizine heterocycles

A simple route to introduce various heterocycles, derivatives of dipyridyls and indolizines on the lower rim of the para-tert-butylcalix[4]arene via ester bond formation to afford 1,3-disubstituted conjugates is described. The conformation of the new compounds and some intermolecular interactions are discussed on the basis of X-ray and NMR analyses. Preliminary complexation properties of some of the new tert-butylcalix[4]arene heterocyclic conjugates with Cu (II), Co (II) and Ni (II) were studied by means of UV–Vis titration.

Synthesis, structure, computational modeling, and biological activity of two novel bimesitylene derivatives

Tetrazole- and nitrile-containing bimesitylene derivatives with potential use in coordination chemistry were synthesized and characterized, and their structural particularities are discussed. For the bimesitylene bistetrazole derivative, geometry optimization was carried out by quantum-chemical calculations using density functional theory together with vibrational frequencies, natural bond orbitals, and highest occupied molecular orbital (HOMO)–lowest unoccupied molecular orbital (LUMO) calculations. The newly synthesized bimesitylene derivatives were also evaluated for their antimicrobial activity against three different reference strains, namely Escherichia coli, Staphylococcus aureus, and Candida albicans.

Optimization of Polyplex Formation between DNA Oligonucleotide and Poly(ʟ-Lysine): Experimental Study and Modeling Approach

The polyplexes formed by nucleic acids and polycations have received a great attention owing to their potential application in gene therapy. In our study, we report experimental results and modeling outcomes regarding the optimization of polyplex formation between the double-stranded DNA (dsDNA) and poly(l-Lysine) (PLL). The quantification of the binding efficiency during polyplex formation was performed by processing of the images captured from the gel electrophoresis assays. The design of experiments (DoE) and response surface methodology (RSM) were employed to investigate the coupling effect of key factors (pH and N/P ratio) affecting the binding efficiency. According to the experimental observations and response surface analysis, the N/P ratio showed a major influence on binding efficiency compared to pH. Model-based optimization calculations along with the experimental confirmation runs unveiled the maximal binding efficiency (99.4%) achieved at pH 5.4 and N/P ratio 125. To support the experimental data and reveal insights of molecular mechanism responsible for the polyplex formation between dsDNA and PLL, molecular dynamics simulations were performed at pH 5.4 and 7.4.