Reasons and remedies for the agglomeration of multilayered graphene and carbon nanotubes in polymers

• Rasheed Atif and
• Fawad Inam

Beilstein J. Nanotechnol. 2016, 7, 1174–1196, doi:10.3762/bjnano.7.109

• osteoblasts (bone-forming cells) and neurons, and found to be effective nano-carriers for several biomolecules such as proteins, DNA and carbohydrates [4]. Recently, MLG/CNT–polymer nanocomposites have been explored as scaffolds for cell growth and load-bearing implant materials for replacing defective human

High antiviral effect of TiO₂·PL–DNA nanocomposites targeted to conservative regions of (−)RNA and (+)RNA of influenza A virus in cell culture

• Asya S. Levina,
• Marina N. Repkova,
• Elena V. Bessudnova,
• Ekaterina I. Filippova,
• Natalia A. Mazurkova and
• Valentina F. Zarytova

Beilstein J. Nanotechnol. 2016, 7, 1166–1173, doi:10.3762/bjnano.7.108

• TiO2·PL–DNA nanocomposite consisting of titanium dioxide nanoparticles and polylysine (PL)-containing oligonucleotides. Results: The TiO2·PL–DNA nanocomposites bearing the DNA fragments targeted to different conservative regions of (−)RNA and (+)RNA of segment 5 of influenza A virus (IAV) were studied

• for their antiviral activity in MDCK cells infected with the H1N1, H5N1, and H3N2 virus subtypes. Within the negative strand of each of the studied strains, the efficiency of DNA fragments increased in the direction of its 3’-end. Thus, the DNA fragment aimed at the 3’-noncoding region of (−)RNA was

• the most efficient and inhibited the reproduction of different IAV subtypes by 3–4 orders of magnitude. Although to a lesser extent, the DNA fragments targeted at the AUG region of (+)RNA and the corresponding region of (−)RNA were also active. For all studied viral subtypes, the nanocomposites

Multiwalled carbon nanotube hybrids as MRI contrast agents

• Nikodem Kuźnik and
• Mateusz M. Tomczyk

Beilstein J. Nanotechnol. 2016, 7, 1086–1103, doi:10.3762/bjnano.7.102

• been applied in MWCNT CA candidates, an example of SWCNT separation in the magnetic field was described by Choi [6]. Nanotubes with SPIO anchored at one of the ends were combined with DNA chains. Then the dispersion of hybrids was placed over a 0.5 T magnetic array for two days. The hybrids arranged

Dielectrophoresis of gold nanoparticles conjugated to DNA origami structures

• Anja Henning-Knechtel,
• Matthew Wiens,
• Mathias Lakatos,
• Andreas Heerwig,
• Frieder Ostermaier,
• Nora Haufe and
• Michael Mertig

Beilstein J. Nanotechnol. 2016, 7, 948–956, doi:10.3762/bjnano.7.87

• Chemistry, University of Alberta, Edmonton, T6G2G2, Canada Kurt-Schwabe-Institut für Mess- und Sensortechnik Meinsberg e.V., 04736 Waldheim, Germany 10.3762/bjnano.7.87 Abstract DNA nanostructures are promising construction materials to bridge the gap between self-assembly of functional molecules and

• conventional top-down fabrication methods in nanotechnology. Their positioning onto specific locations of a microstructured substrate is an important task towards this aim. Here we study manipulation and positioning of pristine and of gold nanoparticle-conjugated tubular DNA origami structures using ac

• dielectrophoresis. The dielectrophoretic behavior was investigated employing fluorescence microscopy. For the pristine origami, a significant dielectrophoretic response was found to take place in the megahertz range, whereas, due to the higher polarizability of the metallic nanoparticles, the nanoparticle/DNA

Improved biocompatibility and efficient labeling of neural stem cells with poly(L-lysine)-coated maghemite nanoparticles

• Igor M. Pongrac,
• Marina Dobrivojević,
• Lada Brkić Ahmed,
• Michal Babič,
• Miroslav Šlouf,
• Daniel Horák and
• Srećko Gajović

Beilstein J. Nanotechnol. 2016, 7, 926–936, doi:10.3762/bjnano.7.84

• electrostatic interaction between negatively charged ions of the cell membrane and the surface of the culture plate. Due to the presence of NH2 groups, which promote cell adhesion, PLL is as well used as a non-viral transfection agent for gene delivery and DNA complexation [20]. Our previous studies showed that

Reconstitution of the membrane protein OmpF into biomimetic block copolymer–phospholipid hybrid membranes

• Matthias Bieligmeyer,
• Franjo Artukovic,
• Stephan Nussberger,
• Thomas Hirth,
• Thomas Schiestel and
• Michaela Müller

Beilstein J. Nanotechnol. 2016, 7, 881–892, doi:10.3762/bjnano.7.80

• lipid membranes with high fidelity and selectivity. In the field of biotechnology, they are particularly attractive for single-molecule DNA sequencing [1][2][3][4][5] and stochastic sensing of ions and macromolecules [6][7][8][9][10]. The well-defined dimensions of the protein pores furthermore offer a

Hierarchical coassembly of DNA–triptycene hybrid molecular building blocks and zinc protoporphyrin IX

• Rina Kumari,
• Sumit Singh,
• Mohan Monisha,
• Sourav Bhowmick,
• Anindya Roy,
• Neeladri Das and
• Prolay Das

Beilstein J. Nanotechnol. 2016, 7, 697–707, doi:10.3762/bjnano.7.62

• composite DNA nanostructures by the self-assembly of complementary symmetrical 2,6,14-triptycenetripropiolic acid (TPA)–DNA building blocks and zinc protoporphyrin IX (Zn PpIX). DNA–organic molecule scaffolds for the composite DNA nanostructure were constructed through covalent conjugation of TPA with 5

• ′-C12-amine-terminated modified single strand DNA (ssDNA) and its complementary strand. The repeated covalent conjugation of TPA with DNA was confirmed by using denaturing polyacrylamide gel electrophoresis (PAGE), reverse-phase high-performance liquid chromatography (RP-HPLC) and matrix-assisted laser

• desorption/ionization time-of-flight (MALDI-TOF). The biologically relevant photosensitizer Zn PpIX was used to direct the hybridization-mediated self-assembly of DNA–TPA molecular building blocks as well as a model guest molecule within the DNA–TPA supramolecular self-assembly. The formation of fiber-like

Unraveling the neurotoxicity of titanium dioxide nanoparticles: focusing on molecular mechanisms

• Bin Song,
• Yanli Zhang,
• Jia Liu,
• Xiaoli Feng,
• Ting Zhou and
• Longquan Shao

Beilstein J. Nanotechnol. 2016, 7, 645–654, doi:10.3762/bjnano.7.57

• signaling pathways, dysregulated neurotransmitters and synaptic plasticity have also been shown to contribute to neurotoxicity of TiO2 NPs. Recently, studies on autophagy and DNA methylation have shed some light on possible mechanisms of nanotoxicity. Therefore, we offer a new perspective that autophagy and

• DNA methylation could contribute to neurotoxicity of TiO2 NPs. Undoubtedly, more studies are needed to test this idea in the future. In short, to fully understand the health threats posed by TiO2 NPs and to improve the bio-safety of TiO2 NPs-based products, the neurotoxicity of TiO2 NPs must be

• investigated comprehensively through studying every possible molecular mechanism. Keywords: autophagy; brain; DNA methylation; neurotoxicity; titanium dioxide nanoparticles; Introduction Titanium dioxide nanoparticles, smaller than 1 μm in at least one dimension, possess specific physico-chemical

Novel roles for well-known players: from tobacco mosaic virus pests to enzymatically active assemblies

• Claudia Koch,
• Fabian J. Eber,
• Carlos Azucena,
• Alexander Förste,
• Stefan Walheim,
• Thomas Schimmel,
• Alexander M. Bittner,
• Holger Jeske,
• Hartmut Gliemann,
• Sabine Eiben,
• Fania C. Geiger and
• Christina Wege

Beilstein J. Nanotechnol. 2016, 7, 613–629, doi:10.3762/bjnano.7.54

• viruses consist of genetic DNA or RNA material surrounded by a protein coat (capsid), and optionally a lipid envelope. Since virus genomes do not encode all biochemical mechanisms necessary for their own replication and spread, they exploit the genetic repertoire of the infected host cells, which are re

• the fabrication of microfluidic devices by master-replication techniques, was already shown to allow a site-specific bottom-up integration of TMV carrier sticks [60]. This was achieved via isothiocyanate- (ITC-) based coupling of single-stranded (ss) DNA anchors, subsequent trapping of the 3'-ends of

• might enable a fine-tuned adjustment of rod orientations in the desired dimensions (Figure 8B): Substrates coated with DNA anchors were equipped with a nano-perforated metal-organic layer via metal polymer blend lithography [178][179], and its topographical contrast amplified by a metal-organic build-up

Investigating organic multilayers by spectroscopic ellipsometry: specific and non-specific interactions of polyhistidine with NTA self-assembled monolayers

• Ilaria Solano,
• Pietro Parisse,
• Ornella Cavalleri,
• Federico Gramazio,
• Loredana Casalis and
• Maurizio Canepa

Beilstein J. Nanotechnol. 2016, 7, 544–553, doi:10.3762/bjnano.7.48

• form a solid analytical background towards the study of layered systems of greater complexity such as the interaction of NTA with His6-tag proteins, or the DNA/DNA hybridization, which is ongoing in our laboratories. Further, this paper describes a quite general method, which can be applied to other

Comparison of the interactions of daunorubicin in a free form and attached to single-walled carbon nanotubes with model lipid membranes

• Dorota Matyszewska

Beilstein J. Nanotechnol. 2016, 7, 524–532, doi:10.3762/bjnano.7.46

• in the treatment of various types of cancer including leukemia, breast cancer, ovarian cancer, lung carcinoma and several sarcomas (Figure 1). Its mode of action consists in the intercalation into DNA double strand, which leads to the inhibition of the process of duplication and transcription of mRNA

• as well as DNA damage by the inhibition of topoisomerase II [1][2]. However, the second mechanism involving the increased production of ceramides inside cells has been recently postulated [3]. Application of this drug in the cancer treatment is limited because of serious side effects including drug

• -stranded DNA or RNA sequences showing high specificity and affinity to their targets, which were employed as molecular targeting agents for targeted drug transport. Carbon nanotubes (CNTs) are among the promising drug delivery systems. They attract scientists’ attention due to their properties such as

Antibacterial activity of silver nanoparticles obtained by pulsed laser ablation in pure water and in chloride solution

• Brunella Perito,
• Emilia Giorgetti,
• Paolo Marsili and
• Maurizio Muniz-Miranda

Beilstein J. Nanotechnol. 2016, 7, 465–473, doi:10.3762/bjnano.7.40

• the microbial cell, which disturbs the power functions of the cell membrane and causes structural damage; (b) the generation of reactive oxygen species (ROS), which damage the cell membrane; and (c) the interference with DNA replication and inhibition of enzymes and other proteins [13][17][18][19][20

Length-extension resonator as a force sensor for high-resolution frequency-modulation atomic force microscopy in air

• Hannes Beyer,
• Tino Wagner and
• Andreas Stemmer

Beilstein J. Nanotechnol. 2016, 7, 432–438, doi:10.3762/bjnano.7.38

• in air or liquid have been reported so far, for example on mica [13][15], Si(111) [16], on a grating [17], HOPG, and DNA origami [18]. Froning et al. [18] also discussed the influence of the environmental conditions on the sensor properties. Temperature and humidity changes lead to variations in

Invariance of molecular charge transport upon changes of extended molecule size and several related issues

• Ioan Bâldea

Beilstein J. Nanotechnol. 2016, 7, 418–431, doi:10.3762/bjnano.7.37

• dimensional, is described by a Hermitean Hamiltonian matrix, H≡ = H†, whose elements (possibly complex numbers) are arbitrary. Real systems described within the framework provided by Equation 9 and Equation 10 include atomic chains, quantum wires, carbon nanotubes, and (possibly DNA-based) bio- and larger

• within this framework include, e.g., atomic chains, quantum wires, carbon nanotubes, and (possibly DNA-based) bio and large organic molecules. To determine the model parameter values, density functional based tight binding (DFTB) frameworks [18][19][20] represent the state-of-the-art. It is worth

Rigid multipodal platforms for metal surfaces

• Michal Valášek,
• Marcin Lindner and
• Marcel Mayor

Beilstein J. Nanotechnol. 2016, 7, 374–405, doi:10.3762/bjnano.7.34

Hemolysin coregulated protein 1 as a molecular gluing unit for the assembly of nanoparticle hybrid structures

• Tuan Anh Pham,
• Andreas Schreiber,
• Elena V. Sturm (née Rosseeva),
• Stefan Schiller and
• Helmut Cölfen

Beilstein J. Nanotechnol. 2016, 7, 351–363, doi:10.3762/bjnano.7.32

• , Habsburgerstrasse 49, D-79104 Freiburg, Germany 10.3762/bjnano.7.32 Abstract Hybrid nanoparticle (NP) structures containing organic building units such as polymers, peptides, DNA and proteins have great potential in biosensor and electronic applications. The nearly free modification of the polymer chain, the

• variation of the protein and DNA sequence and the implementation of functional moieties provide a great platform to create inorganic structures of different morphology, resulting in different optical and magnetic properties. Nevertheless, the design and modification of a protein structure with functional

• particular, a template-free approach is more difficult to achieve since specific interactions in terms of chemical and spatial interplay have to be ensured. The controlled assembly of NPs using organic compounds such as polymers [3][4][5][6][7], peptides [8][9] and DNA [10][11][12][13][14] demonstrate great

Mismatch detection in DNA monolayers by atomic force microscopy and electrochemical impedance spectroscopy

• Maryse D. Nkoua Ngavouka,
• Pietro Capaldo,
• Elena Ambrosetti,
• Giacinto Scoles,
• Loredana Casalis and
• Pietro Parisse

Beilstein J. Nanotechnol. 2016, 7, 220–227, doi:10.3762/bjnano.7.20

• University of Trieste, Via Valerio 9, Trieste, Italy Department of Medical and Biological Sciences, University of Udine, Udine, Italy 10.3762/bjnano.7.20 Abstract Background: DNA hybridization is at the basis of most current technologies for genotyping and sequencing, due to the unique properties of DNA

• differentiate devices read-out of fully and partially matching sequences. Results: We present here two platforms based on different sensing strategies, to detect mismatched and/or perfectly matched complementary DNA strands hybridization into ssDNA oligonucleotide monolayers. The first platform exploits atomic

• microRNAs or in genomic DNA. Keywords: atomic force microscopy; DNA monolayers; electrochemical impedance spectroscopy; hybridization; mismatches; Introduction Most current technologies for genotyping and sequencing are based on DNA hybridization, exploiting the high grade of selectivity due to the unique

Characterisation of thin films of graphene–surfactant composites produced through a novel semi-automated method

• Nik J. Walch,
• Alexei Nabok,
• Frank Davis and
• Séamus P. J. Higson

Beilstein J. Nanotechnol. 2016, 7, 209–219, doi:10.3762/bjnano.7.19

• coverage) were obtained by using a simple technique of electrostatic layer-by-layer (LbL) deposition, a well-established technique developed first for polyelectrolytes [10] and later adapted for deposition of other objects, such as nanoparticles and biomolecules (proteins, antibodies, enzymes, DNA) [9][11

Single-molecule mechanics of protein-labelled DNA handles

• Vivek S. Jadhav,
• Dorothea Brüggemann,
• Florian Wruck and
• Martin Hegner

Beilstein J. Nanotechnol. 2016, 7, 138–148, doi:10.3762/bjnano.7.16

• .7.16 Abstract DNA handles are often used as spacers and linkers in single-molecule experiments to isolate and tether RNAs, proteins, enzymes and ribozymes, amongst other biomolecules, between surface-modified beads for nanomechanical investigations. Custom DNA handles with varying lengths and chemical

• end-modifications are readily and reliably synthesized en masse, enabling force spectroscopic measurements with well-defined and long-lasting mechanical characteristics under physiological conditions over a large range of applied forces. Although these chemically tagged DNA handles are widely used

• , their further individual modification with protein receptors is less common and would allow for additional flexibility in grabbing biomolecules for mechanical measurements. In-depth information on reliable protocols for the synthesis of these DNA–protein hybrids and on their mechanical characteristics

Linear and nonlinear optical properties of hybrid metallic–dielectric plasmonic nanoantennas

• Mario Hentschel,
• Bernd Metzger,
• Bastian Knabe,
• Karsten Buse and
• Harald Giessen

Beilstein J. Nanotechnol. 2016, 7, 111–120, doi:10.3762/bjnano.7.13

• achieve this goal. In all these cases, these techniques such as high-resolution electron beam lithography [78][79], self-assembled molecular monolayers [77], spacer layer engineering via atomic layer deposition [45], self-assembly of metallic nanoparticles with DNA and other molecular binding units [46

Single pyrimidine discrimination during voltage-driven translocation of osmylated oligodeoxynucleotides via the α-hemolysin nanopore

• Yun Ding and
• Anastassia Kanavarioti

Beilstein J. Nanotechnol. 2016, 7, 91–101, doi:10.3762/bjnano.7.11

• the pore. With the assistance of a processing enzyme to slow down translocation, nanopore-based DNA sequencing is now a commercially available platform. However, accurate base calling is challenging because α-HL senses a sequence, and not a single nucleotide. Osmylated DNA was recently proposed as a

• above detection limits, may be further optimized, and clear the way for nanopore-based sequencing using osmylated DNA. Keywords: DNA sequencing; α-hemolysin; ion-channel measurements; nanopore; osmium tetroxide bipyridine; osmylated oligos; osmylation; single-stranded DNA (ssDNA); Introduction

• thin layers of inorganic materials [6][7][8][9] has led to exploration of both natural and synthetic pores for a number of applications [10][11]. The concept, reintroduced independently by David Deamer and George Church in the context of DNA sequencing, is based on applying a potential across an open

Counterion effects on nano-confined metal–drug–DNA complexes

• Nupur Biswas,
• Sreeja Chakraborty,
• Alokmay Datta,
• Munna Sarkar,
• Mrinmay K. Mukhopadhyay,
• Mrinal K. Bera and
• Hideki Seto

Beilstein J. Nanotechnol. 2016, 7, 62–67, doi:10.3762/bjnano.7.7

• Accelerator Research Organization, Tsukuba 305-0801, Japan 10.3762/bjnano.7.7 Abstract We have explored morphology of DNA molecules bound with Cu complexes of piroxicam (a non-steroidal anti-inflammatory drug) molecules under one-dimensional confinement of thin films and have studied the effect of

• counterions present in a buffer. X-ray reflectivity at and away from the Cu K absorption edge and atomic force microscopy studies reveal that confinement segregates the drug molecules preferentially in a top layer of the DNA film, and counterions enhance this segregation. Keywords: confinement; metal–drug

• –DNA composites; polyelectrolyte; X-ray scattering; Introduction Condensed state behaviour of DNA, the best-known biopolymer, in a confined space is a matter of interest due to its relevance in living systems. Within cells DNA molecules remain in a confined space crowded by other molecules and ions

Application of biclustering of gene expression data and gene set enrichment analysis methods to identify potentially disease causing nanomaterials

• Andrew Williams and
• Sabina Halappanavar

Beilstein J. Nanotechnol. 2015, 6, 2438–2448, doi:10.3762/bjnano.6.252

• black (CB) or carbon nanotubes (CNTs) to determine the disease significance of these data-driven gene sets. Results: Biclusters representing inflammation (chemokine activity), DNA binding, cell cycle, apoptosis, reactive oxygen species (ROS) and fibrosis processes were identified. All of the NM studies

• fibrosis. The pro-fibrogenic potential of CNTs is well established. Although CB has not been shown to induce fibrosis, it induces stronger inflammatory, oxidative stress and DNA damage responses than nano-TiO2 particles. Conclusion: The results of the analysis correctly identified all NMs to be

• (NAAC; which resulted in no observed tumors). DNA replication for the GO term (FDR p-value = 4.1 × 10−3) and KEGG pathway (FDR p-value = 4.1 × 10−3) were significant. The only other significant GO term was DNA replication initiation (FDR p-value = 0.028). A few genes showed association with matrix

Ultrastructural changes in methicillin-resistant Staphylococcus aureus induced by positively charged silver nanoparticles

• Dulce G. Romero-Urbina,
• Humberto H. Lara,
• J. Jesús Velázquez-Salazar,
• M. Josefina Arellano-Jiménez,
• Eduardo Larios,
• Anand Srinivasan,
• Jose L. Lopez-Ribot and
• Miguel José Yacamán

Beilstein J. Nanotechnol. 2015, 6, 2396–2405, doi:10.3762/bjnano.6.246

• permeability [38]. After penetrating the cell membrane, AgNPs can also alter sulfur-containing amino acids and phosphorus (a main constituent of DNA), inhibiting replication via attaching to the bacterial ribosome [39][40]. The proteomic signatures of AgNP-treated E. coli demonstrated an accumulation of

• interacting with their cell walls, resulting in imbalances and increased porosity of their cell membranes and a resultant loss of cytoplasmic content. EDS analyses showed the presence of smaller AgNPs in the cytoplasms of cells that possibly interacted with DNA material (Figure 10). Furthermore, the MIC

Green and energy-efficient methods for the production of metallic nanoparticles

• Mitra Naghdi,
• Mehrdad Taheran,
• Satinder K. Brar,
• M. Verma,
• R. Y. Surampalli and
• J. R. Valero

Beilstein J. Nanotechnol. 2015, 6, 2354–2376, doi:10.3762/bjnano.6.243

• preventive or protective properties with regard to human health. They are not essential for the human body to survive but they can act as antioxidant, enzyme stimulator, or antibacterial agent, and they can interfere with DNA to prevent the multiplication of cancer cells. Researchers found that several