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

• , 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

• implemented (not shown) and test configurations in which a prospective biomolecular construct was directly grafted to the sphere surfaces. To simulate in situ tethering to complex biomolecules, we used PDHs to grasp single DNA molecules in situ (Figure 1d,e). For experimental configurations illustrated in

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

• place for 2 h and the C=O and C–O groups in the extract stabilized NPs. They also concluded that the water-soluble polyhydroxy biomolecules, such as flavonoids and sugars, are accountable for the reduction of metallic ions [106]. Swamy et al. reduced AgNO3 to Ag NPs using methanolic leaf extract of

Silica-coated upconversion lanthanide nanoparticles: The effect of crystal design on morphology, structure and optical properties

• Uliana Kostiv,
• Miroslav Šlouf,
• Hana Macková,
• Alexander Zhigunov,
• Hana Engstová,
• Katarína Smolková,
• Petr Ježek and
• Daniel Horák

Beilstein J. Nanotechnol. 2015, 6, 2290–2299, doi:10.3762/bjnano.6.235

• specific application. Thus, various ligands and functionalities have to be attached to the particle surface to provide efficient drug delivery, to ensure engulfment by the cells, or to control the release of biomolecules and their specific target. Finally, the surface modification must ensure that the

• particles to be considered as probes of target proteins, oligonucleotides and other biomolecules in cells and tissues. DLS experiments showed that the average hydrodynamic particle size in water was large (Dh = 163–265 nm), suggesting the formation of particle aggregates. DLS provides the z-average of the

Orthogonal chemical functionalization of patterned gold on silica surfaces

• Francisco Palazon,
• Didier Léonard,
• Thierry Le Mogne,
• Francesca Zuttion,
• Céline Chevalier,
• Magali Phaner-Goutorbe,
• Éliane Souteyrand,
• Yann Chevolot and
• Jean-Pierre Cloarec

Beilstein J. Nanotechnol. 2015, 6, 2272–2277, doi:10.3762/bjnano.6.233

• hot spot areas. Orthogonal surface chemical functionalization appears to enable such directed anchoring of target biomolecules (Figure 1) [6][8][9]. Despite the aforementioned publications, there is still much to be investigated regarding the orthogonal functionalization of patterned metal on

• . Second, while biotinylated poly(ethylene glycol) [5][6][7][8] may be well suited to immobilize some biomolecules (avidin derivatives), it is worth considering other surface chemistries. For instance, carboxylic acid-based [10][11][12][13][14][15][16][17][18][19][20][21], amine-based [22][23][24][25][26

• ] or other [27][28] self-assembled monolayers may provide a higher diversity of potential biomolecules to immobilize. Shorter spacer chains (e.g., short alkyl chains) may also be useful to immobilize the target as close to the metal surface (i.e., the maximum intensity of the evanescent field) as

A simple and efficient quasi 3-dimensional viscoelastic model and software for simulation of tapping-mode atomic force microscopy

• Santiago D. Solares

Beilstein J. Nanotechnol. 2015, 6, 2233–2241, doi:10.3762/bjnano.6.229

• interactions. A few examples of these processes include viscoelastic deformation, irreversible molecular structure changes (e.g., in biomolecules) and plastic deformation in crystals. These phenomena bring challenges into AFM characterization primarily in two ways. First, in delicate samples, such as

• biomolecules, it becomes necessary to control the maximum tip–sample interaction forces and stresses, such that undesirable irreversible changes do not occur in the sample. Second, the interpretation of the experiment requires the user to make assumptions and/or develop models that properly account for the

Au nanoparticle-based sensor for apomorphine detection in plasma

• Chiara Zanchi,
• Andrea Lucotti,
• Matteo Tommasini,
• Sebastiano Trusso,
• Ugo de Grazia,
• Emilio Ciusani and
• Paolo M. Ossi

Beilstein J. Nanotechnol. 2015, 6, 2224–2232, doi:10.3762/bjnano.6.228

• colloids synthesized by laser ablation in liquids, suitably functionalized and tagged with Raman reporters, have effectively revealed specific biomolecules, even in chemically complex environments such as cells [9][10][11][12]. On the other hand, silver and gold colloids produced by chemical routes can be

Selective porous gates made from colloidal silica nanoparticles

• Roberto Nisticò,
• Paola Avetta,
• Paola Calza,
• Debora Fabbri,
• Giuliana Magnacca and
• Dominique Scalarone

Beilstein J. Nanotechnol. 2015, 6, 2105–2112, doi:10.3762/bjnano.6.215

• the separation of chemical species, ions and biomolecules in solution is a field of increasing interest for researchers involved in microfiltration and separation science [1][2][3][4][5][6][7]. In this topic, it is important to remind that microfiltration is one of the oldest processes optimized since

Light-powered, artificial molecular pumps: a minimalistic approach

• Giulio Ragazzon,
• Massimo Baroncini,
• Serena Silvi,
• Margherita Venturi and
• Alberto Credi

Beilstein J. Nanotechnol. 2015, 6, 2096–2104, doi:10.3762/bjnano.6.214

• ]. Indeed, owing to the progress in molecular biology, we know that living beings are endowed with biomolecules that can replicate genetic material, transport substances inside cells or across membranes, and can be switched on and off in response to external stimuli [3]. Other classes of proteins

Optimized design of a nanostructured SPCE-based multipurpose biosensing platform formed by ferrocene-tethered electrochemically-deposited cauliflower-shaped gold nanoparticles

• Wicem Argoubi,
• Maroua Saadaoui,
• Sami Ben Aoun and
• Noureddine Raouafi

Beilstein J. Nanotechnol. 2015, 6, 1840–1852, doi:10.3762/bjnano.6.187

• recent works support the fact the electron-transfer rates can be enhanced by the conformational changes especially of long alkyl chains and biomolecules used to tether ferrocene to a gold surface [31][32][33][34]. The current variation stopped at high concentration because of the saturation of all the

Towards multifunctional inorganic materials: biopolymeric templates

• Claudia Steinem and
• Joachim Bill

Beilstein J. Nanotechnol. 2015, 6, 1698–1699, doi:10.3762/bjnano.6.172

• Forschungsgemeinschaft in Germany. Correspondingly, this Thematic Series addresses multifunctional, inorganic materials generated by templating with biomolecules. The reader of this series will gain a comprehensive overview about the general ideas and principles of biopolymeric templating by means of selected examples

Synthesis, characterization and in vitro biocompatibility study of Au/TMC/Fe₃O₄ nanocomposites as a promising, nontoxic system for biomedical applications

• Hanieh Shirazi,
• Maryam Daneshpour,
• Soheila Kashanian and
• Kobra Omidfar

Beilstein J. Nanotechnol. 2015, 6, 1677–1689, doi:10.3762/bjnano.6.170

• biocompatibility), they can be utilized as catalysts, labels, and as a protective substrate, especially for immobilization of biomolecules in various fields of modern science [29][30]. Au nanoparticles are extensively used in the design and construction of fuel cells and many types of sensors (e.g

Fulleropeptide esters as potential self-assembled antioxidants

• Mira S. Bjelaković,
• Tatjana J. Kop,
• Jelena Đorđević and
• Dragana R. Milić

Beilstein J. Nanotechnol. 2015, 6, 1065–1071, doi:10.3762/bjnano.6.107

• contribution to the development of carriers for biomolecules [21]. Higashi and co-workers have reported the aggregation properties and a high superoxide scavenging activity of fullerene–poly(Glu)peptide nanoparticles as self-assembled structures [22]. Fullerene C60 and fulleropyrrolidine derivatives showed

A simple approach to the synthesis of Cu_1.8S dendrites with thiamine hydrochloride as a sulfur source and structure-directing agent

• Xiaoliang Yan,
• Sha Li,
• Yun-xiang Pan,
• Zhi Yang and
• Xuguang Liu

Beilstein J. Nanotechnol. 2015, 6, 881–885, doi:10.3762/bjnano.6.90

• -friendly preparation of metal sulfide nano/micro-materials is sought for. Biomolecules have been widely used as a sulfur sources and structure-directing agents in the synthesis of metal sulfides [11][12]. Kim et al. used 2-mercaptoethanol to synthesize high-aspect ratio and single-crystalline nanowires of

• investigated the morphology evolution of Cu1.8S as a function of the hydrothermal process time. Burford et al. reported that the functional groups in biomolecules, e.g., –NH2, –COOH, and –S–, are strongly inclined to interact with inorganic cations based on a mass spectrometry study [13]. This indicates that

• metal ions could interact with biomolecules to form stable complexes. In this experiment, copper nitrate and thiamine hydrochloride is dissolved in water to form a mixture in which Cu2+ ions coordinate with thiamine hydrochloride to form a complex. When the mixture was sealed and kept at 180 °C under

Protein corona – from molecular adsorption to physiological complexity

• Lennart Treuel,
• Dominic Docter,
• Michael Maskos and
• Roland H. Stauber

Beilstein J. Nanotechnol. 2015, 6, 857–873, doi:10.3762/bjnano.6.88

• Hospital of Mainz, Langenbeckstrasse 1, 55101 Mainz, Germany 10.3762/bjnano.6.88 Abstract In biological environments, nanoparticles are enshrouded by a layer of biomolecules, predominantly proteins, mediating its subsequent interactions with cells. Detecting this protein corona, understanding its

• to high electrolyte concentrations and sometimes even due to interaction with biomolecules. Not only do the subsequent agglomeration processes lead to a loss of accessible surface area, they also lead to changes in diffusion properties and, in case of larger agglomerates, give rise to sedimentation

Influence of gold, silver and gold–silver alloy nanoparticles on germ cell function and embryo development

• Ulrike Taylor,
• Daniela Tiedemann,
• Christoph Rehbock,
• Wilfried A. Kues,
• Stephan Barcikowski and
• Detlef Rath

Beilstein J. Nanotechnol. 2015, 6, 651–664, doi:10.3762/bjnano.6.66

• medical and consumer products. Gold and silver nanoparticles play an important role in the current increase of nanoparticle usage. However, our understanding concerning possible side effects of this increased exposure to particles, which are frequently in the same size regime as medium sized biomolecules

• ) and oligonucleotide conjugated AuNP (diameter 7.3 nm, 94 biomolecules per particle, Zeta potential −32 mV) which were tested by using bovine sperm, as well as bovine serum albumin (BSA) coated gold (diameter 6–20 nm), silver (diameter 11 nm; AgNP) and various gold silver alloy nanoparticles (silver

• ]. The ex situ method is an alternative approach where the ablation site is physically separated from bioconjugation [80]. To this end laser ablation is carried out in a flow through reactor, while biomolecules are added at specified time delays. Innate to the in situ bioconjugation method is a distinct

Silica micro/nanospheres for theranostics: from bimodal MRI and fluorescent imaging probes to cancer therapy

• Shanka Walia and
• Amitabha Acharya

Beilstein J. Nanotechnol. 2015, 6, 546–558, doi:10.3762/bjnano.6.57

• materials [8], for controlled delivery [9], and in biotechnology for the controlled release of biomolecules such as small drugs [10], therapeutic proteins [11], antibiotics [12], and antibodies [13]. In MRI, the relative difference of the signal intensity between two adjoining tissues can be improved by

Hollow plasmonic antennas for broadband SERS spectroscopy

• Gabriele C. Messina,
• Mario Malerba,
• Pierfrancesco Zilio,
• Ermanno Miele,
• Michele Dipalo,
• Lorenzo Ferrara and
• Francesco De Angelis

Beilstein J. Nanotechnol. 2015, 6, 492–498, doi:10.3762/bjnano.6.50

• be considered that some of the biomolecules of interest are present in very low concentrations. Therefore, monitoring such an environment requires techniques that can offer both flexibility and high sensitivity for all cases. In other words, the investigation of the biological functions of living

• ][18] and magnetic field enhancement [19]. In these various disciplines, the rise of a trend targeting high performance spectroscopy techniques for biomolecules and cells can be recognized. Raman spectroscopy has already been implemented for whole live cell imaging [20] as well as its biological

Biological responses to nanoscale particles

• Reinhard Zellner

Beilstein J. Nanotechnol. 2015, 6, 380–382, doi:10.3762/bjnano.6.37

• . The key differences are (i) an increased relative surface area and (ii) quantum size effects. Since the growth, catalytic activity and the various interactions with molecules (including biomolecules) occur at the surface of nanoparticles, a given mass of material in nanoparticle form will be much more

• potential biomolecules and cells, thus creating a large parameter space to be examined. With these shortcomings in mind, we initiated a national Priority Program (Schwerpunktprogramm SPP1313) in Germany in 2007 at the Deutsche Forschungsgemeinschaft (DFG) entitled, “Biological Responses to Nanoscale

• conjugates of biomolecules, magnetism, radioactivity, Janus particles and core–shell particles were combined. In particular, the use of fluorescently labeled particles has become one of the preferred tools to track nanoparticles inside cells and tissue. When nanoparticles are exposed to biological fluids

Overview about the localization of nanoparticles in tissue and cellular context by different imaging techniques

• Anja Ostrowski,
• Daniel Nordmeyer,
• Alexander Boreham,
• Cornelia Holzhausen,
• Lars Mundhenk,
• Christina Graf,
• Martina C. Meinke,
• Annika Vogt,
• Sabrina Hadam,
• Jürgen Lademann,
• Eckart Rühl,
• Ulrike Alexiev and
• Achim D. Gruber

Beilstein J. Nanotechnol. 2015, 6, 263–280, doi:10.3762/bjnano.6.25

• bioapplications are typically composed of a semiconductor core (e.g., cadmium sulfide), an outer shell of a higher band semiconducting material (e.g., zinc sulfide) and a surface functionalization which may consist of various hydrophilic organic molecules including biomolecules or polymers [86]. QD with their

• [126]. However, one disadvantage is that only low signal intensities are emitted by biomolecules themselves [132]. Advanced Raman techniques, such as surface-enhanced Raman spectroscopy (SERS), coherent anti-Stokes Raman spectroscopy (CARS), and stimulated Raman spectroscopy (SRS) have been used in the

Tailoring the ligand shell for the control of cellular uptake and optical properties of nanocrystals

• Johannes Ostermann,
• Christian Schmidtke,
• Christopher Wolter,
• Jan-Philip Merkl,
• Hauke Kloust and
• Horst Weller

Beilstein J. Nanotechnol. 2015, 6, 232–242, doi:10.3762/bjnano.6.22

• based on specific chemical groups like amines, carboxyl and hydroxyl functions [31]. Functional groups are not only useful for typical coupling strategies of biomolecules, but also for the determination of the surface properties of the final nanocontainers. Differently charged particles show different

Functionalization of α-synuclein fibrils

• Simona Povilonienė,
• Vida Časaitė,
• Virginijus Bukauskas,
• Arūnas Šetkus,
• Juozas Staniulis and
• Rolandas Meškys

Beilstein J. Nanotechnol. 2015, 6, 124–133, doi:10.3762/bjnano.6.12

• factors including temperature, pH, and ionic strength. An incubation temperature of 4 °C was chosen to preserve the neutravidin-conjugated nanoparticles. Discussion Self-assembling biomolecules such as DNA, peptides or proteins are of special interest in the design and construction of nanoscale materials

Proinflammatory and cytotoxic response to nanoparticles in precision-cut lung slices

• Stephanie Hirn,
• Nadine Haberl,
• Kateryna Loza,
• Matthias Epple,
• Wolfgang G. Kreyling,
• Barbara Rothen-Rutishauser,
• Markus Rehberg and
• Fritz Krombach

Beilstein J. Nanotechnol. 2014, 5, 2440–2449, doi:10.3762/bjnano.5.253

• -NPs were shown to dissolve after immersion in water in the presence of oxygen under the release of Ag+ ions [30][41]. However, their dissolution in biological environments is still poorly understood and will be influenced by the presence of biomolecules such as proteins [42][43]. Taken together, the

Functionalized polystyrene nanoparticles as a platform for studying bio–nano interactions

• Cornelia Loos,
• Tatiana Syrovets,
• Anna Musyanovych,
• Volker Mailänder,
• Katharina Landfester,
• G. Ulrich Nienhaus and
• Thomas Simmet

Beilstein J. Nanotechnol. 2014, 5, 2403–2412, doi:10.3762/bjnano.5.250

• effects on cell growth [4]. Nanoparticles Nanoparticles, limited in size to 100 nm in either two or three dimensions [18], fill the gap between molecules and bulk material and between biomolecules and cells. The atoms located at the surface of a nanoparticle have less neighbors than atoms of a bulk

Nanoparticle interactions with live cells: Quantitative fluorescence microscopy of nanoparticle size effects

• Li Shang,
• Karin Nienhaus,
• Xiue Jiang,
• Linxiao Yang,
• Katharina Landfester,
• Volker Mailänder,
• Thomas Simmet and
• G. Ulrich Nienhaus

Beilstein J. Nanotechnol. 2014, 5, 2388–2397, doi:10.3762/bjnano.5.248

• machinery. An interesting aspect in this process is that, in the biological milieu, the NPs typically adsorb dissolved biomolecules, so that they are enshrouded by a so-called ‘protein corona’ [6][7][8]. NPs interact with cells via this layer of biomolecules, at least during the initial encounter, so that

• vesicle contains receptor proteins that recognize specific chemical groups on the biomolecules to be internalized. It is finally pinched off so as to generate a vesicle in the cytoplasm that contains the internalized material (Figure 1). Different pinocytosis mechanisms are being distinguished, depending

Inorganic Janus particles for biomedical applications

• Isabel Schick,
• Steffen Lorenz,
• Dominik Gehrig,
• Stefan Tenzer,
• Wiebke Storck,
• Karl Fischer,
• Dennis Strand,
• Frédéric Laquai and
• Wolfgang Tremel

Beilstein J. Nanotechnol. 2014, 5, 2346–2362, doi:10.3762/bjnano.5.244

• solvents [2], specificity towards small molecules or larger biomolecules [3], suppression of nonspecific adsorption [4], adjustment of net electric charge [5], to electrochemical activity [6]. Although it has been shown that synthetic and natural systems share a number of similarities, the degree of

• based on the little two photon-cross-section of most biomolecules leading to less auto-fluorescence, enhanced penetration depth within biological samples by tuning the excitation light to the biological window, near IR range 700–1000 nm. Furthermore, the effect of photobleaching can be reduced by

• an aqueous environment. This is a key point regarding the use of nanoparticles for biomedical applications for sensing biomolecules, cells, and diagnosis of diseases, and intracellular delivery [99][100][101]. There are different surface modification strategies, such as ligand exchange to bind