This paper discusses an approach developed for exploiting the local elementary movements of evolution to study complex networks in terms of shared common embedding and, consequently, shared fractal properties. This approach can be useful for the anal...
Monte Carlo simulations can quantify various types of DNA damage to evaluate the biological effects of ionizing radiation at the nanometer scale. This work presents a study simulating the DNA target response after proton irradiation. A chromatin fibe...
Regular device-scale DNA waves for high DNA concentrations and flow velocities have been shown to emerge in quadratic micropillar arrays with potentially strong relevance for a wide range of microfluidic applications. Hexagonal arrays constitute anot...
The regulation of superhelical stress, mediated by the combined action of topoisomerases and fork rotation, is crucial for DNA replication. The conformational changes during DNA replication are still experimentally challenging, mainly due to the rapi...
Patterning of surfaces with a simple strategy provides insights into the functional interfaces by suitable modification of the surface by novel techniques. Especially, highly ordered structural topographies and chemical features from the wide range o...
The proton transfer (PT) complexation reaction between 3,4-diaminopyridine (3,4-DAP), an important drug, and 2,6-dichloro-4-nitrphenole (DCNP) was investigated experimentally and theoretically. The experimental results indicated a chemical reaction o...
Muscle energetics reflects the ability of myosin motors to convert chemical energy into mechanical energy. How this process takes place remains one of the most elusive questions in the field. Here, we combined experimental measurements of in vitro sl...
The conformation and distribution of a flexible and semiflexible chain confined in an array of nanoposts arranged in parallel way in a square-lattice projection of their cross-section was investigated using coarse-grained molecular dynamics simulatio...
This paper presents and visualizes examples of large amounts of genetic information using a new class of cognitive computer graphics algorithms. These algorithms are related to the semiotics of perception and allow the interpretation of those propert...
Molecular dynamics simulations and geometry optimizations carried out at the quantum level as well as by quantum mechanical/molecular mechanics methods predict that short, single-stranded DNA oligonucleotides adopt conformations very similar to those...
This study delves into the intricate interaction between DNA and nanosystems, exploring its potential implications for biomedical applications. The focus lies in understanding the adsorption geometry of DNA when in proximity to plasmonic nanoparticle...
DNA nanotechnology offers a fine control over biochemistry by programming chemical reactions in DNA templates. Coupled to microfluidics, it has enabled DNA-based reaction-diffusion microsystems with advanced spatio-temporal dynamics such as traveling...
Radiopharmaceutical therapy (RPT) is evolving as a promising strategy for treating cancer. As interest grows in short-range particles, like Auger electrons, understanding the dose–response relationship at the deoxyribonucleic acid (DNA) level h...
Transient or long-term DNA self-assembly participates in essential genetic functions. The present review focuses on tight DNA-DNA interactions that have recently been found to play important roles in both controlling DNA higher-order structures and t...
Vanadium compounds have been set in various fields as anticancer, anti-diabetic, anti-parasitic, anti-viral, and anti-bacterial agents. This study reports the synthesis and structural characterization of oxidovanadium(IV)-based imidazole drug complex...
Thiosemicarbazones and their transition metal complexes are biologically active compounds and anticancer agents with versatile structural properties. In this contribution, the structural features and stability of four pyridoxal-thiosemicarbazone (PLT...
In this study we investigated the contact characteristics of human prostate cancer cells (PC3) on silicon micropillar arrays with complex shapes by using high-resolution confocal fluorescence microscopy techniques. These arrays consist of micropillar...
In the present work, the procedures for the creation of self-assembled DNA nanostructures in aqueous and non-aqueous media are described. DNA-Surfactant complex formation renders the DNA soluble in organic solvents offering an exciting way to bridge...
The (4′→6′)-linked DNA homolog 2′,3′-dideoxy-β-D-glucopyranosyl nucleic acid (dideoxy-glucose nucleic acid or homo-DNA) exhibits stable self-pairing of the Watson–Crick and reverse-Hoogsteen types, but does not...
The development of new convenient tools for the design of multicomponent nucleic acid (NA) complexes is one of the challenges in biomedicine and NA nanotechnology. In this paper, we analyzed the formation of hybrid RNA/DNA concatemers and self-limite...
Double-strand breaks (DSBs) in nuclear DNA represents radiation-induced damage that has been identified as particularly deleterious. Calculating this damage using Monte Carlo track structure modeling could be a suitable indicator to better assess and...
Biosensors are favored devices for the fast and cost-effective detection of biological species without the need for laboratories. Microfluidic integration with biosensors has advanced their capabilities in selectivity, sensitivity, controllability, a...
Six new organotin(IV) compounds of Schiff bases derived from S-R-dithiocarbazate [R = benzyl (B), 2- or 4-methylbenzyl (2M and 4M, respectively)] condensed with 2-hydroxy-3-methoxybenzaldehyde (oVa) were synthesised and characterised by elemental ana...
Genome compaction is one of the important subject areas for understanding the mechanisms regulating genes’ expression and DNA replication and repair. The basic unit of DNA compaction in the eukaryotic cell is the nucleosome. The main chromatin...
The rapid development of multidrug co-delivery and nano-medicines has made spontaneous progress in tumor treatment and diagnosis. DNA is a unique biological molecule that can be tailored and molded into various nanostructures. The addition of ligands...
While undergoing structural deformation, DNA experiences changes in the interactions between its internal base pairs, presenting challenges to conventional elastic methods. To address this, we propose the Discrete Critical State (DCS) model in this p...
The coordination chemistry, structural characterization, and biomolecular interactions of europium(III) and iron(III) complexes with the pyridoxal-semicarbazone (PLSC) ligand were thoroughly examined using experimental and computational approaches. S...
Ribonucleotides misincorporated in the human genome are the most abundant DNA lesions. The 2′-hydroxyl group makes them prone to spontaneous hydrolysis, potentially resulting in strand breaks. Moreover, their presence may decrease the rate of DNA rep...
DNA has shown great promise as a building material for self-assembling nanoscale structures. To further develop the potential of this technology, more methods are needed for functionalizing DNA-based nanostructures to increase their chemical diversit...
We report an efficient, high-yield method for synthesizing dumbbell-shaped conjugates composed of gold nanoparticles (AuNPs) connected by double-stranded (ds) DNA. The dsDNA, bearing terminal thiol groups, was covalently attached to two AuNPs to form...
Radiation therapy (RT) is a vital component of multimodal cancer treatment, and its immunomodulatory effects are a major focus of current therapeutic strategies. Macrophages are some of the first cells recruited to sites of radiation-induced injury w...
DNA nanostructures are well-established vectors for packaging diversified payloads for targeted cellular delivery. Here, DNA origami rectangular sheets were combined with Herpes Simplex Virus 1 (HSV1) capsids to demonstrate surface coverage of the pa...
Surface modification of nucleic acid-based electrochemical biosensors has been at the forefront of research since their inception. Effective modification ensures the optimization of the sensitivity, specificity, and stability of modern biosensors. Re...
By imposing finite order constraints on Fibonacci anyon braid relations, we construct the finite quotient
Biological processes often involve the attachment and detachment of extended molecules to substrates. Here, the classical dimer model is used to investigate these geometric effects on the free energy, which governs both the equilibrium state and the...
We performed molecular dynamics simulations of DNA polymer chains confined in helical nano-channels under compression in order to explore the potential of knot-factories with helical geometry to produce knots with a preferred handedness. In our simul...
In this study, we attempted to examine the biological activity of the copper(II)–based small molecule aquabis (1-formyl-2-naphtholato-k2O,O′)copper(II) (1) against colon cancer. The characterization of complex 1 was established by analyti...
We present a parallel DNA molecular analysis platform based on an array of plano-concave Fabry–Pérot (PC-FP) microcavity lasers that enables the simultaneous, sequence-specific detection of multiple DNA targets. Each PC-FP cavity is func...
In the search for novel anticancer complex, transition metal complexes of Schiff base derived from 2-aminopyrazine and salicylaldehyde were successfully synthesized and characterized based on elemental analyses, spectroscopic and thermal analysis. Th...
We propose a DNA nucleobase sequencing device composed of zigzag graphene nanoribbon electrodes connected with a porphyrin molecule via carbon chains (GEPM). The connecting geometry between the nanoribbons with an even width number and the carbon cha...
Zinc ions are the second most abundant ions found in humans. Their role in proteins can be merely structural but also catalytic, owing to their transition metal character. Modelling their geometric–coordination versatility by empirical force fi...
DNA is an exceptional building block for the fabrication of dynamic supramolecular systems with switchable geometries. Here, a self-assembled, tunable plasmonic–fluorescent nanostructure was developed. A precise sliding motion mechanism was ope...
DNA nanostructures enable the attachment of functional molecules to nearly any unique location on their underlying structure. Due to their single-base-pair structural resolution, several ligands can be spatially arranged and closely controlled accord...
DNA nanotechnology offers the possibility to rationally design structures with emergent properties by precisely controlling their geometry and functionality. Here, we demonstrate a DNA-based plasmonic metamolecule that is capable of sensing human thr...
A wide range of endogenous and exogenous alkylating agents attack DNA to generate various alkylation adducts. N7-methyl-2-deoxyguanosine (Fm7dG) is the most abundant alkylative DNA lesion. If not repaired, Fm7dG can undergo spontaneous depurination,...
Several classes of copper complexes are known to induce oxidative DNA damage that mediates cell death. These compounds are potentially useful anticancer agents and detailed investigation can reveal the mode of DNA interaction, binding strength, and t...
Evolution and geometry generate complexity in similar ways. Evolution drives natural selection while geometry may capture the logic of this selection and express it visually, in terms of specific generic properties representing some kind of advantage...
The compounds 7-ethyl-9-(N-methylamino)methyl-10-hydroxycamptothecin (2) and 7-ethyl-9-(N-morpholino)methyl-10-hydroxycamptothecin (3) are potential topoisomerase I poisons. Moreover, they were shown to have favorable anti-neoplastic effects on sever...
Several novel copper (II) complexes of reduced Schiff bases containing fluoride substituents were prepared and structurally characterized by single-crystal X-ray diffraction. The complexes exhibited diverse structures, with the central atom in distor...
Structure-related biological activities of flavanones are still considered largely unexplored. Since they exhibit various medicinal activities, it is intriguing to enter deeper into their chemical structures, electronic transitions or interactions wi...
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