Instance maps as an organising concept for complex experimental workflows as demonstrated for (nano)material safety research

• Benjamin Punz,
• Maja Brajnik,
• Joh Dokler,
• Jaleesia D. Amos,
• Litty Johnson,
• Katie Reilly,
• Anastasios G. Papadiamantis,
• Amaia Green Etxabe,
• Lee Walker,
• Diego S. T. Martinez,
• Steffi Friedrichs,
• Klaus M. Weltring,
• Nazende Günday-Türeli,
• Claus Svendsen,
• Christine Ogilvie Hendren,
• Mark R. Wiesner,
• Martin Himly,
• Iseult Lynch and
• Thomas E. Exner

Beilstein J. Nanotechnol. 2025, 16, 57–77, doi:10.3762/bjnano.16.7

• investigate the influence of nanotopography on the protein binding capacity and its impact on epitope integrity. Johnson et al. [53] reported that structural alterations of proteins bound to nanomaterials impact the antigen-processing machinery in APCs and could, thus, impact the outcome in terms of

Interaction of graphene oxide with tannic acid: computational modeling and toxicity mitigation in C. elegans

• Romana Petry,
• James M. de Almeida,
• Francine Côa,
• Felipe Crasto de Lima,
• Diego Stéfani T. Martinez and
• Adalberto Fazzio

Beilstein J. Nanotechnol. 2024, 15, 1297–1311, doi:10.3762/bjnano.15.105

• biosynthesis protein COQ7 [51][53][54][55]. The co-exposure of GO with antioxidant molecules, such as ʟ-cysteine and ascorbate, can mitigate the oxidative effects of the material and minimize GO’s toxicity [35][53]. Moreover, GO also shows important neuronal effects; for example, it influences protein–protein

• binding in the organism, activating or suppressing neuronal receptors and influencing the neurotransmission process in C. elegans [34][35][56]. GO’s toxicity is highly related to its surface chemistry; changes of the functional groups of the surface impact its biological effects. Yang et al. [57] showed

Entry of nanoparticles into cells and tissues: status and challenges

• Kirsten Sandvig,
• Tore Geir Iversen and
• Tore Skotland

Beilstein J. Nanotechnol. 2024, 15, 1017–1029, doi:10.3762/bjnano.15.83

• ]. Thus, more studies are required to investigate if and how in vitro protein binding studies can help us to explain the in vivo behavior of NPs. Following i.v. injection of NPs with a diameter of 5 nm, approximately half of the injected dose can be expected to be rapidly excreted in urine, whereas there

Multiscale modelling of biomolecular corona formation on metallic surfaces

• Parinaz Mosaddeghi Amini,
• Ian Rouse,
• Julia Subbotina and
• Vladimir Lobaskin

Beilstein J. Nanotechnol. 2024, 15, 215–229, doi:10.3762/bjnano.15.21

• predictions of the binding strength, preferred orientations, and relative abundance of the specified molecules on the specified material surfaces or NPs and, thus, gives an insight into the mechanisms of bionano interaction. We can compare different materials in terms of the protein binding affinity and

Study of the reusability and stability of nylon nanofibres as an antibody immobilisation surface

• Inés Peraile,
• Matilde Gil-García,
• Laura González-López,
• Nushin A. Dabbagh-Escalante,
• Juan C. Cabria-Ramos and
• Paloma Lorenzo-Lozano

Beilstein J. Nanotechnol. 2024, 15, 83–94, doi:10.3762/bjnano.15.8

• stability of the nylon nanofibres. To achieve this, we analysed any loss of immunocapture ability of well-oriented antibodies anchored both to the nylon nanofibres and to a specialised surface with high protein binding capacity. The nanofibre immunocapture system maintained an unchanged immunocapture

Recognition mechanisms of hemoglobin particles by monocytes – CD163 may just be one

• Jonathan-Gabriel Nimz,
• Pichayut Rerkshanandana,
• Chiraphat Kloypan,
• Ulrich Kalus,
• Saranya Chaiwaree,
• Axel Pruß,
• Radostina Georgieva,
• Yu Xiong and
• Hans Bäumler

Beilstein J. Nanotechnol. 2023, 14, 1028–1040, doi:10.3762/bjnano.14.85

• site within the Hb α chain is freely accessible (exclusively β-crosslinked Hb vs α-crosslinked Hb) [27]. Intermolecular modifications changing the molecular or polymer size of HBOCs [16][19][30] are relevant for protein binding as well. Hemoglobin sub-micron particles (HbMPs) obtained via

Polymer nanoparticles from low-energy nanoemulsions for biomedical applications

• Santiago Grijalvo and
• Carlos Rodriguez-Abreu

Beilstein J. Nanotechnol. 2023, 14, 339–350, doi:10.3762/bjnano.14.29

•  5) with viabilities higher than 70% for HeLa cells are promising candidates for gene therapy (e.g., gene vaccines). Protein binding on PLGA nanoparticles prepared from nanoemulsions has also been studied [62]. After incubation with human serum, afamin was one of the specific proteins bound to PLGA

Microneedle-based ocular drug delivery systems – recent advances and challenges

• Piotr Gadziński,
• Anna Froelich,
• Monika Wojtyłko,
• Antoni Białek,
• Julia Krysztofiak and
• Tomasz Osmałek

Beilstein J. Nanotechnol. 2022, 13, 1167–1184, doi:10.3762/bjnano.13.98

• . For comparison, the cornea permeates substances with a mass not greater than 1 kDa [28]. Unfortunately, transscleral absorption is often reduced by elimination via nasolacrimal drainage pathways, tear protein binding, or drug metabolism [44]. The treatment efficiency is also decreased by constant

DNA aptamer selection and construction of an aptasensor based on graphene FETs for Zika virus NS1 protein detection

• Nathalie B. F. Almeida,
• Thiago A. S. L. Sousa,
• Viviane C. F. Santos,
• Camila M. S. Lacerda,
• Thais G. Silva,
• Rafaella F. Q. Grenfell,
• Flavio Plentz and
• Antero S. R. Andrade

Beilstein J. Nanotechnol. 2022, 13, 873–881, doi:10.3762/bjnano.13.78

• average behavior of this group of sensing devices with respect to protein addition. We evaluated the sensor responses as percentage changes in graphene resistance (ΔRSD) at VG = 0.2 V caused by aptamer–protein binding. For more details on how the variations in graphene resistances were measured, see Table

Design and selection of peptides to block the SARS-CoV-2 receptor binding domain by molecular docking

• Kendra Ramirez-Acosta,
• Ivan A. Rosales-Fuerte,
• J. Eduardo Perez-Sanchez,
• Alfredo Nuñez-Rivera,
• Josue Juarez and
• Ruben D. Cadena-Nava

Beilstein J. Nanotechnol. 2022, 13, 699–711, doi:10.3762/bjnano.13.62

• of RBD–ligand by PRODIGY The protein binding energy prediction (PRODIGY) web server is an effective predictive model based on intermolecular contacts in protein–protein complexes based on their 3D structure [39]. This tool predicts the binding free energy between protein complexes with great accuracy

• the entry of viruses to the cell host through the ACE2 cellular receptor. Binding energy by protein binding energy prediction ADV has been widely used to predict the alignment of small ligands within the binding cavity of a given protein and to evaluate the pose quality of the docked ligand in terms

Identification of physicochemical properties that modulate nanoparticle aggregation in blood

• Ludovica Soddu,
• Duong N. Trinh,
• Eimear Dunne,
• Dermot Kenny,
• Giorgia Bernardini,
• Ida Kokalari,
• Arianna Marucco,
• Marco P. Monopoli and
• Ivana Fenoglio

Beilstein J. Nanotechnol. 2020, 11, 550–567, doi:10.3762/bjnano.11.44

• protein binding to these surfaces [26]. Both SNPs and CNPs interact with plasma proteins forming a protein corona. The presence of the protein corona clearly induced platelet-independent agglomeration of carbon nanoparticles but not for silica (Figure 8). Notably, aggregation was observed for medium size

Multilayer capsules made of weak polyelectrolytes: a review on the preparation, functionalization and applications in drug delivery

• Varsha Sharma and
• Anandhakumar Sundaramurthy

Beilstein J. Nanotechnol. 2020, 11, 508–532, doi:10.3762/bjnano.11.41

• , the poly(ethylene glycol) (PEG)-based post-functionalization of pH-responsive click capsules of biodegradable PLL and poly(ʟ-glutamic acid) (PGA) rendered their low fouling capability against specific protein binding [94]. Hydrogen bonded films and hollow capsules of alkyne-modified PVP and PMA were

Rational design of block copolymer self-assemblies in photodynamic therapy

• Maxime Demazeau,
• Laure Gibot,
• Anne-Françoise Mingotaud,
• Patricia Vicendo,
• Clément Roux and
• Barbara Lonetti

Beilstein J. Nanotechnol. 2020, 11, 180–212, doi:10.3762/bjnano.11.15

Wafer-scale bioactive substrate patterning by chemical lift-off lithography

• Chong-You Chen,
• Chang-Ming Wang,
• Hsiang-Hua Li,
• Hong-Hseng Chan and
• Wei-Ssu Liao

Beilstein J. Nanotechnol. 2018, 9, 311–320, doi:10.3762/bjnano.9.31

• material, which can also be lifted off by activated PDMS stamps in the CLL operation [21]. After the ligand–protein binding process, a sandwich-like assay is employed via the sequential attachment of primary and reporter-labelled secondary antibodies. This bulky assay design requires the spatial

Phospholipid arrays on porous polymer coatings generated by micro-contact spotting

• Sylwia Sekula-Neuner,
• Monica de Freitas,
• Lea-Marie Tröster,
• Tobias Jochum,
• Pavel A. Levkin,
• Michael Hirtz and
• Harald Fuchs

Beilstein J. Nanotechnol. 2017, 8, 715–722, doi:10.3762/bjnano.8.75

• . Biotin lipid arrays were prepared by admixing 4 mol % biotin lipid (1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine-N-(cap biotinyl)) into the DOPC carrier. It was shown previously [24], that this percentage admixture of biotin saturates the number of available biotin headgroups for protein binding [24

• for spot size versus dwell time analysis, a dwell time of 2 s was used for target patterns and 1 s for optical reference patterns. Protein binding Streptavidin-FITC (Streptavidin, Fluorescein Conjugate) was purchased from Calbiochem and Streptavidin-Cy3 (recombinant from Streptomyces avidinii, Cy3

• labelled) was purchased from Sigma. Prior to protein binding on biotin lipid arrays, samples were blocked in 10% BSA (Sigma-Aldrich) solution in PBS (Gibco) for 20 min at room temperature. After washing with PBS, 0.5 µg solution of STV-Cy3 in PBS was incubated for 30 min on the substrate. Samples were

Dispersion of single-wall carbon nanotubes with supramolecular Congo red – properties of the complexes and mechanism of the interaction

• Anna Jagusiak,
• Barbara Piekarska,
• Tomasz Pańczyk,
• Małgorzata Jemioła-Rzemińska,
• Elżbieta Bielańska,
• Barbara Stopa,
• Grzegorz Zemanek,
• Janina Rybarska,
• Irena Roterman and
• Leszek Konieczny

Beilstein J. Nanotechnol. 2017, 8, 636–648, doi:10.3762/bjnano.8.68

• red shows unusual protein-binding properties – it preferentially interacts with partly unfolded beta-sheets and thus stabilizes unstable structural states that may emerge as a result of conformational changes linked with the biologic activity of some proteins (e.g., the alpha-1-proteinase inhibitor

• binding to carbon nanotubes but also for interaction with proteins (as it can adapt to the protein binding site) [31][34]. At solutions of low ionic strength, when CR supramolecular properties are much weaker, its interaction with SWNTs is greatly decreased. At higher ionic strength of the solution, which

Impact of surface wettability on S-layer recrystallization: a real-time characterization by QCM-D

• Jagoba Iturri,
• Ana C. Vianna,
• Alberto Moreno-Cencerrado,
• Dietmar Pum,
• Uwe B. Sleytr and
• José Luis Toca-Herrera

Beilstein J. Nanotechnol. 2017, 8, 91–98, doi:10.3762/bjnano.8.10

• recrystallization processes on both the nature-mimicking SCWP and the hydrophobic SiO2. This is a remarkable outcome: The natural case is featured by, among others, specific protein–carbohydrate interactions involved in the S-layer formation [25], while on fluorinated-SiO2 the protein binding and crystal formation

Tight junction between endothelial cells: the interaction between nanoparticles and blood vessels

• Yue Zhang and
• Wan-Xi Yang

Beilstein J. Nanotechnol. 2016, 7, 675–684, doi:10.3762/bjnano.7.60

• . Research using endothelial cell cultures in order to quantify the uptake of PLGA NPs showed a concentration-dependent uptake of PLGA [47]. Several NPs (COOH100, PEG100, Methyl100, Lysine100) associate with cells through the ability of protein binding on their surfaces [48]. SiO2 causes inflammation and

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

• the adsorption of His6 on the Ni-free NTA layer, due to non specific interactions, from the formation of a neatly thicker His6 film induced by the Ni(II)-loading of the NTA SAM. Keywords: His-tag; nitrilotriacetic acid (NTA); protein binding; self-assembled monolayers (SAMs); spectroscopic

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

• peak of Au NP at 520 nm shifts very slightly to 522 nm (Figure 2A,B), which indicates the protein binding to Au NP [23]. This observation is consistent with previously published results [22] which report on M2F03-antibody-functionalized Au NPs. In solution, these exhibit an increasing antigen

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

• , Ireland) or neutravidin (Pierce, Fisher Scientific, Dublin, Ireland) (both with approx. 60 kDa = 9.96 × 10−20 g each) at different ratios ranging from 100 to 500 proteins per DNA molecule. During incubation (30 min up to 48 h) the reactions were gently shaken to ensure efficient protein binding at the

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

• was attributed to an exacerbated macrophage response as a consequence of reduced protein binding onto the PEG-coated surfaces [142]. Interestingly, the systemic behavior of PEG-coated NPs was also reported to be changed, demonstrated by a decreased renal clearance of PEG coated NPs [143], especially

• from [8]. Copyright 2014 American Chemical Society. Tenzer et al. [10] revealed in a correlation analysis distinct kinetic protein-binding modalities during the temporal evolution of the serum protein corona. (a–c): Protein abundance profiles of AmSil30 (SiNP), time smoothes and normalized signals. (a

The fate of a designed protein corona on nanoparticles in vitro and in vivo

• Denise Bargheer,
• Julius Nielsen,
• Gabriella Gébel,
• Markus Heine,
• Sunhild C. Salmen,
• Roland Stauber,
• Horst Weller,
• Joerg Heeren and
• Peter Nielsen

Beilstein J. Nanotechnol. 2015, 6, 36–46, doi:10.3762/bjnano.6.5

• directly with the nanomaterial surface and is therefore tightly bound (hard corona), and a secondary layer (soft corona) that interacts with a weak protein–protein binding and exhibits dynamic exchange, if competing protein is added [8][9][10][11]. It is also reported that in the presence of plasma

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

• the protein corona of silica nanoparticles. Moreover, no size-dependent particle-protein binding effect was observed while studying nanoparticles with a diameter of 125 nm, 20 nm, and 8 nm [114]. Introducing the anisotropy of Janus particles as another variable to the formation/analysis of the protein

Coating with luminal gut-constituents alters adherence of nanoparticles to intestinal epithelial cells

• Heike Sinnecker,
• Katrin Ramaker and
• Andreas Frey

Beilstein J. Nanotechnol. 2014, 5, 2308–2315, doi:10.3762/bjnano.5.239

• lectin Ricinus communis agglutinin I (RCA I, Vector Laboratories, Burlingame, USA) to visualize the cell surface. Therefore the fixed cells were incubated with 50 mM NH4Cl in PBS (15 min at rt), washed again, and incubated with 0.2% gelatin in PBS (60 min at rt) to block nonspecific protein binding sites