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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biophysics".

Deadline for manuscript submissions: closed (30 April 2023) | Viewed by 15352

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Dr. Massimiliano Magro

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Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell’Università 16, 35020 Legnaro, Italy
Interests: protein corona; theranostic nanodevices; endogenous protein recognition; smart nanomaterial surfaces; iron oxide nanoparticles; selective protein binding; biosensing; drug delivery; stealth nanomaterials; biochemistry and biophysics
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Special Issue Information

Dear Colleagues,

I would like to invite you to submit a high-quality research paper for the Special Issue titled “Bio-Nano Interactions 2.0” of the International Journal of Molecular Sciences. The story of materials from living (biotic) organisms is intensely intertwined with the one of inanimate (abiotic) materials, which might have played a crucial role in the chemical evolution in the prebiotic era and, therefore, in the origin of life. Nanoparticles and proteins are entities of the same size range and the understanding and the prediction of the interactions between proteins and nanoparticles represents the Holy Grail in nanoscience. Indeed, the crucial challenge is to endow nanoparticles of protein-like specificity with the ability to enable the abiotic material to specifically interact with all components of biological systems such as peptides, proteins, lipids, DNA, receptors, cells and whole organisms, including humans or animals.

The Special Issue “Bio-Nano Interactions 2.0” encourages the publication of papers which expand the existing perspectives on smart synthetic nanomaterials and on their interplay with biological interfaces.

Dr. Massimiliano Magro
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

nanoparticles
proteins
smart nanomaterial surfaces
selective protein binding
nanomaterials
abiotic material
biological systems

Published Papers (7 papers)

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Editorial

Jump to: Research, Review

3 pages, 503 KiB

Open AccessEditorial

Special Issue “Bio-Nano Interactions 2.0”

by Aura Cencini and Massimiliano Magro

Int. J. Mol. Sci. 2024, 25(3), 1667; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms25031667 - 30 Jan 2024

Viewed by 518

Abstract

In 1961, USA’s blues legend Howlin’ Wolf released the single entitled “Down in the Bottom” (Figure 1) [...] Full article

(This article belongs to the Special Issue Bio-Nano Interactions 2.0)

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Research

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14 pages, 2581 KiB

Open AccessCommunication

Template-Assisted Assembly of Hybrid DNA/RNA Nanostructures Using Branched Oligodeoxy- and Oligoribonucleotides

by Alesya Fokina, Yulia Poletaeva, Svetlana Dukova, Kristina Klabenkova, Zinaida Rad’kova, Anastasia Bakulina, Timofei Zatsepin, Elena Ryabchikova and Dmitry Stetsenko

Int. J. Mol. Sci. 2023, 24(21), 15978; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms242115978 - 5 Nov 2023

Viewed by 1114

Abstract

A template-assisted assembly approach to a C₂₄ fullerene-like double-stranded DNA polyhedral shell is proposed. The assembly employed a supramolecular oligonucleotide dendrimer as a 3D template that was obtained via the hybridization of siRNA strands and a single-stranded DNA oligonucleotide joined to three- or four-way branched junctions. A four-way branched oligonucleotide building block (a starlet) was designed for the assembly of the shell composed of three identical self-complementary DNA single strands and a single RNA strand for hybridization to the DNA oligonucleotides of the template. To prevent premature auto-hybridization of the self-complementary oligonucleotides in the starlet, a photolabile protecting group was introduced via the N³-substituted thymidine phosphoramidite. Cleavable linkers such as a disulfide linkage, RNase A sensitive triribonucleotides, and di- and trideoxynucleotides were incorporated into the starlet and template at specific points to guide the post-assembly disconnection of the shell from the template, and enzymatic disassembly of the template and the shell in biological media. At the same time, siRNA strands were modified with 2′-OMe ribonucleotides and phosphorothioate groups in certain positions to stabilize toward enzymatic digestion. We report herein a solid-phase synthesis of branched oligodeoxy and oligoribonucleotide building blocks for the DNA/RNA dendritic template and the branched DNA starlet for a template-assisted construction of a C₂₄ fullerene-like DNA shell after initial molecular modeling, followed by the assembly of the shell around the DNA-coated RNA dendritic template, and visualization of the resulting nanostructure by transmission electron microscopy. Full article

(This article belongs to the Special Issue Bio-Nano Interactions 2.0)

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14 pages, 3226 KiB

Open AccessArticle

Adsorption of Ferritin at Nanofaceted Al₂O₃ Surfaces

by Bhanu K. Pothineni, Sabrina Kollmann, Xinyang Li, Guido Grundmeier, Denise J. Erb and Adrian Keller

Int. J. Mol. Sci. 2023, 24(16), 12808; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms241612808 - 15 Aug 2023

Viewed by 982

Abstract

The influence of nanoscale surface topography on protein adsorption is highly important for numerous applications in medicine and technology. Herein, ferritin adsorption at flat and nanofaceted, single-crystalline Al₂O₃ surfaces is investigated using atomic force microscopy and X-ray photoelectron spectroscopy. The nanofaceted surfaces are generated by the thermal annealing of Al₂O₃ wafers at temperatures above 1000 °C, which leads to the formation of faceted saw-tooth-like surface topographies with periodicities of about 160 nm and amplitudes of about 15 nm. Ferritin adsorption at these nanofaceted surfaces is notably suppressed compared to the flat surface at a concentration of 10 mg/mL, which is attributed to lower adsorption affinities of the newly formed facets. Consequently, adsorption is restricted mostly to the pattern grooves, where the proteins can maximize their contact area with the surface. However, this effect depends on the protein concentration, with an inverse trend being observed at 30 mg/mL. Furthermore, different ferritin adsorption behavior is observed at topographically similar nanofacet patterns fabricated at different annealing temperatures and attributed to different step and kink densities. These results demonstrate that while protein adsorption at solid surfaces can be notably affected by nanofacet patterns, fine-tuning protein adsorption in this way requires the precise control of facet properties. Full article

(This article belongs to the Special Issue Bio-Nano Interactions 2.0)

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24 pages, 13751 KiB

Open AccessArticle

Red Blood Cell Substitutes: Liposome Encapsulated Hemoglobin and Magnetite Nanoparticle Conjugates as Oxygen Carriers

by Saleha Hafeez and Najam Us Sahar Sadaf Zaidi

Int. J. Mol. Sci. 2023, 24(2), 1618; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms24021618 - 13 Jan 2023

Cited by 1 | Viewed by 2155

Abstract

The established blood donation and transfusion system has contributed a lot to human health and welfare, but for this system to function properly, it requires a sufficient number of healthy donors, which is not always possible. Pakistan was a country hit hardest by COVID-19 which additionally reduced the blood donation rates. In order to address such challenges, the present study focused on the development of RBC substitutes that can be transfused to all blood types. This paper reports the development and characterization of RBC substitutes by combining the strategies of conjugated and encapsulated hemoglobin where magnetite nanoparticles would act as the carrier of hemoglobin, and liposomes would separate internal and external environments. The interactions of hemoglobin variants with bare magnetite nanoparticles were studied through molecular docking studies. Moreover, nanoparticles were synthesized, and hemoglobin was purified from blood. These components were then used to make conjugates, and it was observed that only the hemoglobin HbA1 variant was making protein corona. These conjugates were then encapsulated in liposomes to make negatively charged RBC substitutes with a size range of 1–2 μm. Results suggest that these RBC substitutes work potentially in a similar way as natural RBCs work and can be used in the time of emergency. Full article

(This article belongs to the Special Issue Bio-Nano Interactions 2.0)

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16 pages, 13323 KiB

Open AccessArticle

Upconverting Nanoparticles as a New Bio-Imaging Strategy—Investigating Intracellular Trafficking of Endogenous Processes in Neural Tissue

by Karolina Zajdel, Justyna Janowska, Małgorzata Frontczak-Baniewicz, Joanna Sypecka and Bożena Sikora

Int. J. Mol. Sci. 2023, 24(2), 1122; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms24021122 - 6 Jan 2023

Cited by 3 | Viewed by 2228

Abstract

In recent years, rare-earth-doped upconverting nanoparticles (UCNPs) have been widely used in different life sciences due to their unique properties. Nanoparticles have become a multifunctional and promising new approach to neurobiological disorders and have shown extraordinary application potential to overcome the problems related to conventional treatment strategies. This study evaluated the internalization mechanisms, bio-distribution, and neurotoxicity of NaYF₄:20%Yb³⁺,2%Er³⁺ UCNPs in rat organotypic hippocampal slices. TEM results showed that UCNPs were easily internalized by hippocampal cells and co-localized with selected organelles inside neurons and astrocytes. Moreover, the UCNPs were taken into the neurons via clathrin- and caveolae-mediated endocytosis. Propidium iodide staining and TEM analysis did not confirm the adverse effects of UCNPs on hippocampal slice viability and morphology. Therefore, UCNPs may be a potent tool for bio-imaging and testing new therapeutic strategies for brain diseases in the future. Full article

(This article belongs to the Special Issue Bio-Nano Interactions 2.0)

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18 pages, 2930 KiB

Open AccessArticle

Acidic Shift of Optimum pH of Bovine Serum Amine Oxidase upon Immobilization onto Nanostructured Ferric Tannates

by Graziano Rilievo, Alessandro Cecconello, Simone Molinari, Andrea Venerando, Lavinia Rutigliano, Gayathri T. Govardhan, Dinusha H. Kariyawasam, Ruth J. Arusei, Lucio Zennaro, Maria L. Di Paolo, Enzo Agostinelli, Fabio Vianello and Massimiliano Magro

Int. J. Mol. Sci. 2022, 23(20), 12172; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms232012172 - 12 Oct 2022

Cited by 2 | Viewed by 1487

Abstract

Protein–nanoparticle hybrids represent entities characterized by emerging biological properties that can significantly differ from those of the parent components. Herein, bovine serum amine oxidase (i.e., BSAO) was immobilized onto a magnetic nanomaterial constituted of surface active maghemite nanoparticles (i.e., SAMNs, the core), surface-modified with tannic acid (i.e., TA, the shell), to produce a biologically active ternary hybrid (i.e., SAMN@TA@BSAO). In comparison with the native enzyme, the secondary structure of the immobilized BSAO responded to pH variations sensitively, resulting in a shift of its optimum activity from pH 7.2 to 5.0. Conversely, the native enzyme structure was not influenced by pH and its activity was affected at pH 5.0, i.e., in correspondence with the best performances of SAMN@TA@BSAO. Thus, an extensive NMR study was dedicated to the structure–function relationship of native BSAO, confirming that its low activity below pH 6.0 was ascribable to minimal structural modifications not detected by circular dichroism. The generation of cytotoxic products, such as aldehydes and H₂O₂, by the catalytic activity of SAMN@TA@BSAO on polyamine oxidation is envisaged as smart nanotherapy for tumor cells. The present study supports protein–nanoparticle conjugation as a key for the modulation of biological functions. Full article

(This article belongs to the Special Issue Bio-Nano Interactions 2.0)

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Review

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28 pages, 2492 KiB

Open AccessReview

Significance of Capping Agents of Colloidal Nanoparticles from the Perspective of Drug and Gene Delivery, Bioimaging, and Biosensing: An Insight

by Rabia Javed, Anila Sajjad, Sania Naz, Humna Sajjad and Qiang Ao

Int. J. Mol. Sci. 2022, 23(18), 10521; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms231810521 - 10 Sep 2022

Cited by 25 | Viewed by 5839

Abstract

The over-growth and coagulation of nanoparticles is prevented using capping agents by the production of stearic effect that plays a pivotal role in stabilizing the interface. This strategy of coating the nanoparticles’ surface with capping agents is an emerging trend in assembling multipurpose nanoparticles that is beneficial for improving their physicochemical and biological behavior. The enhancement of reactivity and negligible toxicity is the outcome. In this review article, an attempt has been made to introduce the significance of different capping agents in the preparation of nanoparticles. Most importantly, we have highlighted the recent progress, existing roadblocks, and upcoming opportunities of using surface modified nanoparticles in nanomedicine from the drug and gene delivery, bioimaging, and biosensing perspectives. Full article

(This article belongs to the Special Issue Bio-Nano Interactions 2.0)

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