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

Electrochemical coating of dental implants with anodic porous titania for enhanced osteointegration

• Amirreza Shayganpour,
• Alberto Rebaudi,
• Pierpaolo Cortella,
• Alberto Diaspro and
• Marco Salerno

Beilstein J. Nanotechnol. 2015, 6, 2183–2192, doi:10.3762/bjnano.6.224

• is essential to all living cells for its interaction with polyphosphate compounds such as ATP, DNA and RNA, required by many enzymes for their functioning, and present in many pharmaceutical products. In the research literature, Mg has also been added to hydroxylapatite to support to bone formation

Electrochemical behavior of polypyrrol/AuNP composites deposited by different electrochemical methods: sensing properties towards catechol

• Celia García-Hernández,
• Cristina García-Cabezón,
• Cristina Medina-Plaza,
• Fernando Martín-Pedrosa,
• Yolanda Blanco,
• José Antonio de Saja and
• María Luz Rodríguez-Méndez

Beilstein J. Nanotechnol. 2015, 6, 2052–2061, doi:10.3762/bjnano.6.209

• been reported that the insertion of NPs into the sensing layer provides remarkable properties compared to conventional polymeric matrices. Several examples have been reported in the literature. For instance, electrochemically deposited Ppy/AuNP films have demonstrated a great potential to detect DNA

Nanocuration workflows: Establishing best practices for identifying, inputting, and sharing data to inform decisions on nanomaterials

• Christina M. Powers,
• Karmann A. Mills,
• Stephanie A. Morris,
• Fred Klaessig,
• Sharon Gaheen,
• Nastassja Lewinski and
• Christine Ogilvie Hendren

Beilstein J. Nanotechnol. 2015, 6, 1860–1871, doi:10.3762/bjnano.6.189

• developed a curation workflow that uses standardized file formats for both metadata and raw DNA sequence data for submissions into standard repositories [9]. A validation tool (Picard, http://broadinstitute.github.io/picard/) is then used to verify that the data fits the standard. An example of the second

NanoE-Tox: New and in-depth database concerning ecotoxicity of nanomaterials

• Katre Juganson,
• Angela Ivask,
• Irina Blinova,
• Monika Mortimer and
• Anne Kahru

Beilstein J. Nanotechnol. 2015, 6, 1788–1804, doi:10.3762/bjnano.6.183

• ][183], oxidative stress [71][73][89][175][176][184][185], DNA damage/genotoxicity [102][186][187], and binding to sulfhydryl groups [100]. Similar effects were also demonstrated in case of ZnO NPs [84][85][86][188][189][190]. The mechanism of toxic action of insoluble ENMs like CeO2 [109][110], CNTs

Analysis of soil bacteria susceptibility to manufactured nanoparticles via data visualization

• Rong Liu,
• Yuan Ge,
• Patricia A. Holden and
• Yoram Cohen

Beilstein J. Nanotechnol. 2015, 6, 1635–1651, doi:10.3762/bjnano.6.166

• communities [18][19]; quantum dots (QDs) were linked to DNA damage of both freshwater mussels and gills [24]; and carbon nanotubes have been found to induce harmful effects to various organs (such as aquatic animals, bacteria, and plants) [25]. MNPs in soil can cause compositional changes to soil bacterial

• datasets of high dimensionality (e.g., over 105 soil DNA sequences extracted for a treatment) [18][19]. Therefore, advanced data exploration/visualization approaches are required to allow researchers to design subsequent confirmatory experiments and/or perform detailed statistical analyses. Graphical

• day controls (without MNPs) [18]. Soil DNA sequences were recovered for the above 15 treatments (in quadruplicate). The recovered DNA sequences were clustered into 31,621 bacterial operational taxonomic units (OTUs) [18], with the number of DNA sequences clustered into the same OTU counted to quantify

Influence of surface chemical properties on the toxicity of engineered zinc oxide nanoparticles to embryonic zebrafish

• Zitao Zhou,
• Jino Son,
• Bryan Harper,
• Zheng Zhou and
• Stacey Harper

Beilstein J. Nanotechnol. 2015, 6, 1568–1579, doi:10.3762/bjnano.6.160

• (lacking surface ligands) are known to cause delayed embryo hatching, developmental abnormalities [12] through dissolution and release of ionic zinc [13][14] as well as induction of DNA damage through generation of reactive oxidative species (ROS) [12][15]. ZnO NPs are often coated with a variety of

DNA–melamine hybrid molecules: from self-assembly to nanostructures

• Rina Kumari,
• Shib Shankar Banerjee,
• Anil K. Bhowmick and
• Prolay Das

Beilstein J. Nanotechnol. 2015, 6, 1432–1438, doi:10.3762/bjnano.6.148

• Technology Kharagpur, Kharagpur 721302, India 10.3762/bjnano.6.148 Abstract Single-stranded DNA–melamine hybrid molecular building blocks were synthesized using a phosphoramidation cross-coupling reaction with a zero linker approach. The self-assembly of the DNA–organic hybrid molecules was achieved by DNA

• hybridization. Following self-assembly, two distinct types of nanostructures in the form of linear chains and network arrays were observed. The morphology of the self-assembled nanostructures was found to depend on the number of DNA strands that were attached to a single melamine molecule. Keywords: DNA

• –organic hybrid; melamine; nanostructures; phosphoramidation; self-assembly; Findings The importance of DNA in the field of nanotechnology stems from the fact that DNA is a macromolecule on the nanoscale with self-assembling properties [1][2]. The molecular recognition through base pairing in DNA makes it

Natural and artificial binders of polyriboadenylic acid and their effect on RNA structure

• Giovanni N. Roviello,
• Domenica Musumeci,
• Valentina Roviello,
• Marina Pirtskhalava,
• Alexander Egoyan and
• Merab Mirtskhulava

Beilstein J. Nanotechnol. 2015, 6, 1338–1347, doi:10.3762/bjnano.6.138

• molecules but also by interaction with nucleopeptides, metal–amino acid complexes, nanotubes, etc. Indeed, from a structural point of view, numerous studies were conducted in the last forty years describing in detail the properties of poly(rA) and its complexes with various molecules, such as DNA

• isoquinoline compound with poly(rA) concerned berberine [24]. In particular, this alkaloid was found to bind poly(rA) with greater affinity than double-stranded B-DNA or tRNA [24]. Recently, the ability of berberine to interact with single-stranded poly(rA) was the object of another investigation presented by

• study the same authors also studied the interaction of this alkaloid, already known for its binding to DNA, with double-stranded poly(rA) [34]. From fluorescence and UV studies a strong interaction of this alkaloid with poly(rA) double helix clearly emerged, and this binding was characterized by (a) an

PLGA nanoparticles as a platform for vitamin D-based cancer therapy

• Maria J. Ramalho,
• Joana A. Loureiro,
• Bárbara Gomes,
• Manuela F. Frasco,
• Manuel A. N. Coelho and
• M. Carmo Pereira

Beilstein J. Nanotechnol. 2015, 6, 1306–1318, doi:10.3762/bjnano.6.135

• performed in propidium iodide (PI)-stained S2-013, hTERT-HPNE and A549 cells after treatment with free calcitriol and calcitriol-loaded PLGA NPs at 1.2 µM for 72 h. PI counterstaining was used for DNA quantification. The differences in the DNA content between the cell population allowed the cell cycle

• calcitirol. The sub-G1 group represents the apoptotic cells with fractional DNA, which appear as cells with hypodiploid DNA content [27]. These data suggest that calcitriol antiproliferative effects, observed in cytotoxicity assays, could occur in consequence of cell cycle arrest. Discussion The

• harvested and fixed with 70% v/v ethanol. The cells were then stained with a DNA staining solution (0.1% v/v TritonX-100, 20 µg/mL PI and 35 µg/mL of RNase A in PBS) at a cell density of 106 cells/mL. FCM (FACSCalibur, BD Biosciences, CA, USA) was performed by plotting 12,000 gated events per sample. The