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18 pages, 4308 KiB

Open AccessFeature PaperArticle

Raman Enhancement of Nanoparticle Dimers Self-Assembled Using DNA Origami Nanotriangles

by Sergio Kogikoski, Kosti Tapio, Robert Edler von Zander, Peter Saalfrank and Ilko Bald

Molecules 2021, 26(6), 1684; https://doi.org/10.3390/molecules26061684 - 17 Mar 2021

Cited by 9 | Viewed by 2561

Abstract

Surface-enhanced Raman scattering is a powerful approach to detect molecules at very low concentrations, even up to the single-molecule level. One important aspect of the materials used in such a technique is how much the signal is intensified, quantified by the enhancement factor [...] Read more.

Surface-enhanced Raman scattering is a powerful approach to detect molecules at very low concentrations, even up to the single-molecule level. One important aspect of the materials used in such a technique is how much the signal is intensified, quantified by the enhancement factor (EF). Herein we obtained the EFs for gold nanoparticle dimers of 60 and 80 nm diameter, respectively, self-assembled using DNA origami nanotriangles. Cy5 and TAMRA were used as surface-enhanced Raman scattering (SERS) probes, which enable the observation of individual nanoparticles and dimers. EF distributions are determined at four distinct wavelengths based on the measurements of around 1000 individual dimer structures. The obtained results show that the EFs for the dimeric assemblies follow a log-normal distribution and are in the range of 10⁶ at 633 nm and that the contribution of the molecular resonance effect to the EF is around 2, also showing that the plasmonic resonance is the main source of the observed signal. To support our studies, FDTD simulations of the nanoparticle’s electromagnetic field enhancement has been carried out, as well as calculations of the resonance Raman spectra of the dyes using DFT. We observe a very close agreement between the experimental EF distribution and the simulated values. Full article

(This article belongs to the Special Issue Biomolecular Materials: Self-Assembly, Structure, and Application)

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15 pages, 5632 KiB

Open AccessArticle

DNA-Mediated Stack Formation of Nanodiscs

by Madhumalar Subramanian, Charlotte Kielar, Satoru Tsushima, Karim Fahmy and Jana Oertel

Molecules 2021, 26(6), 1647; https://doi.org/10.3390/molecules26061647 - 16 Mar 2021

Cited by 2 | Viewed by 2979

Abstract

Membrane-scaffolding proteins (MSPs) derived from apolipoprotein A-1 have become a versatile tool in generating nano-sized discoidal membrane mimetics (nanodiscs) for membrane protein research. Recent efforts have aimed at exploiting their controlled lipid protein ratio and size distribution to arrange membrane proteins in regular [...] Read more.

Membrane-scaffolding proteins (MSPs) derived from apolipoprotein A-1 have become a versatile tool in generating nano-sized discoidal membrane mimetics (nanodiscs) for membrane protein research. Recent efforts have aimed at exploiting their controlled lipid protein ratio and size distribution to arrange membrane proteins in regular supramolecular structures for diffraction studies. Thereby, direct membrane protein crystallization, which has remained the limiting factor in structure determination of membrane proteins, would be circumvented. We describe here the formation of multimers of membrane-scaffolding protein MSP1D1-bounded nanodiscs using the thiol reactivity of engineered cysteines. The mutated positions N42 and K163 in MSP1D1 were chosen to support chemical modification as evidenced by fluorescent labeling with pyrene. Minimal interference with the nanodisc formation and structure was demonstrated by circular dichroism spectroscopy, differential light scattering and size exclusion chromatography. The direct disulphide bond formation of nanodiscs formed by the MSP1D1_N42C variant led to dimers and trimers with low yield. In contrast, transmission electron microscopy revealed that the attachment of oligonucleotides to the engineered cysteines of MSP1D1 allowed the growth of submicron-sized tracts of stacked nanodiscs through the hybridization of nanodisc populations carrying complementary strands and a flexible spacer. Full article

(This article belongs to the Special Issue Biomolecular Materials: Self-Assembly, Structure, and Application)

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14 pages, 1664 KiB

Open AccessArticle

Occurrence of Peptide-Peptide Interactions during the Purification of Self-Assembling Peptide f1-8 from a β-Lactoglobulin Tryptic Hydrolysate

by Mathilde Pimont-Farge, Amélie Bérubé, Véronique Perreault, Guillaume Brisson, Shyam Suwal, Yves Pouliot and Alain Doyen

Molecules 2021, 26(5), 1432; https://doi.org/10.3390/molecules26051432 - 06 Mar 2021

Cited by 3 | Viewed by 1584

Abstract

Self-assembling peptides have gained attention because of their nanotechnological applications. Previous work demonstrated that the self-assembling peptide f1-8 (Pf1-8) that is generated from the tryptic hydrolysis of β-lactoglobulin can form a hydrogel after several purification steps, including membrane filtration and consecutive washes. This [...] Read more.

Self-assembling peptides have gained attention because of their nanotechnological applications. Previous work demonstrated that the self-assembling peptide f1-8 (Pf1-8) that is generated from the tryptic hydrolysis of β-lactoglobulin can form a hydrogel after several purification steps, including membrane filtration and consecutive washes. This study evaluates the impact of each processing step on peptide profile, purity, and gelation capacity of each fraction to understand the purification process of Pf1-8 and the peptide-peptide interactions involved. We showed that peptide-peptide interactions mainly occurred through electrostatic and hydrophobic interactions, influencing the fraction compositions. Indeed, the purity of Pf1-8 did not correlate with the number of wash steps. In addition to Pf1-8, two other hydrophobic peptides were identified, peptide f15-20, and peptide f41-60. The gelation observed could be induced either through peptide-peptide interactions or through self-assembling, both being driven by non-covalent bond and more specifically hydrophobic interactions. Full article

(This article belongs to the Special Issue Biomolecular Materials: Self-Assembly, Structure, and Application)

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15 pages, 3831 KiB

Open AccessArticle

Protein-Assisted Room-Temperature Assembly of Rigid, Immobile Holliday Junctions and Hierarchical DNA Nanostructures

by Saminathan Ramakrishnan, Sivaraman Subramaniam, Charlotte Kielar, Guido Grundmeier, A. Francis Stewart and Adrian Keller

Molecules 2020, 25(21), 5099; https://doi.org/10.3390/molecules25215099 - 03 Nov 2020

Cited by 1 | Viewed by 2614

Abstract

Immobile Holliday junctions represent not only the most fundamental building block of structural DNA nanotechnology but are also of tremendous importance for the in vitro investigation of genetic recombination and epigenetics. Here, we present a detailed study on the room-temperature assembly of immobile [...] Read more.

Immobile Holliday junctions represent not only the most fundamental building block of structural DNA nanotechnology but are also of tremendous importance for the in vitro investigation of genetic recombination and epigenetics. Here, we present a detailed study on the room-temperature assembly of immobile Holliday junctions with the help of the single-strand annealing protein Redβ. Individual DNA single strands are initially coated with protein monomers and subsequently hybridized to form a rigid blunt-ended four-arm junction. We investigate the efficiency of this approach for different DNA/protein ratios, as well as for different DNA sequence lengths. Furthermore, we also evaluate the potential of Redβ to anneal sticky-end modified Holliday junctions into hierarchical assemblies. We demonstrate the Redβ-mediated annealing of Holliday junction dimers, multimers, and extended networks several microns in size. While these hybrid DNA–protein nanostructures may find applications in the crystallization of DNA–protein complexes, our work shows the great potential of Redβ to aid in the synthesis of functional DNA nanostructures under mild reaction conditions. Full article

(This article belongs to the Special Issue Biomolecular Materials: Self-Assembly, Structure, and Application)

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13 pages, 33329 KiB

Open AccessArticle

Seeding, Plating and Electrical Characterization of Gold Nanowires Formed on Self-Assembled DNA Nanotubes

by Dulashani R. Ranasinghe, Basu R. Aryal, Tyler R. Westover, Sisi Jia, Robert C. Davis, John N. Harb, Rebecca Schulman and Adam T. Woolley

Molecules 2020, 25(20), 4817; https://doi.org/10.3390/molecules25204817 - 20 Oct 2020

Cited by 6 | Viewed by 3281

Abstract

Self-assembly nanofabrication is increasingly appealing in complex nanostructures, as it requires fewer materials and has potential to reduce feature sizes. The use of DNA to control nanoscale and microscale features is promising but not fully developed. In this work, we study self-assembled DNA [...] Read more.

Self-assembly nanofabrication is increasingly appealing in complex nanostructures, as it requires fewer materials and has potential to reduce feature sizes. The use of DNA to control nanoscale and microscale features is promising but not fully developed. In this work, we study self-assembled DNA nanotubes to fabricate gold nanowires for use as interconnects in future nanoelectronic devices. We evaluate two approaches for seeding, gold and palladium, both using gold electroless plating to connect the seeds. These gold nanowires are characterized electrically utilizing electron beam induced deposition of tungsten and four-point probe techniques. Measured resistivity values for 15 successfully studied wires are between 9.3 × 10⁻⁶ and 1.2 × 10⁻³ Ωm. Our work yields new insights into reproducible formation and characterization of metal nanowires on DNA nanotubes, making them promising templates for future nanowires in complex electronic circuitry. Full article

(This article belongs to the Special Issue Biomolecular Materials: Self-Assembly, Structure, and Application)

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Review

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24 pages, 35222 KiB

Open AccessReview

The Art of Designing DNA Nanostructures with CAD Software

by Martin Glaser, Sourav Deb, Florian Seier, Amay Agrawal, Tim Liedl, Shawn Douglas, Manish K. Gupta and David M. Smith

Molecules 2021, 26(8), 2287; https://doi.org/10.3390/molecules26082287 - 15 Apr 2021

Cited by 16 | Viewed by 7197

Abstract

Since the arrival of DNA nanotechnology nearly 40 years ago, the field has progressed from its beginnings of envisioning rather simple DNA structures having a branched, multi-strand architecture into creating beautifully complex structures comprising hundreds or even thousands of unique strands, with the [...] Read more.

Since the arrival of DNA nanotechnology nearly 40 years ago, the field has progressed from its beginnings of envisioning rather simple DNA structures having a branched, multi-strand architecture into creating beautifully complex structures comprising hundreds or even thousands of unique strands, with the possibility to exactly control the positions down to the molecular level. While the earliest construction methodologies, such as simple Holliday junctions or tiles, could reasonably be designed on pen and paper in a short amount of time, the advent of complex techniques, such as DNA origami or DNA bricks, require software to reduce the time required and propensity for human error within the design process. Where available, readily accessible design software catalyzes our ability to bring techniques to researchers in diverse fields and it has helped to speed the penetration of methods, such as DNA origami, into a wide range of applications from biomedicine to photonics. Here, we review the historical and current state of CAD software to enable a variety of methods that are fundamental to using structural DNA technology. Beginning with the first tools for predicting sequence-based secondary structure of nucleotides, we trace the development and significance of different software packages to the current state-of-the-art, with a particular focus on programs that are open source. Full article

(This article belongs to the Special Issue Biomolecular Materials: Self-Assembly, Structure, and Application)

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28 pages, 6054 KiB

Open AccessReview

Constructing Large 2D Lattices Out of DNA-Tiles

by Johannes M. Parikka, Karolina Sokołowska, Nemanja Markešević and J. Jussi Toppari

Molecules 2021, 26(6), 1502; https://doi.org/10.3390/molecules26061502 - 10 Mar 2021

Cited by 14 | Viewed by 5334

Abstract

The predictable nature of deoxyribonucleic acid (DNA) interactions enables assembly of DNA into almost any arbitrary shape with programmable features of nanometer precision. The recent progress of DNA nanotechnology has allowed production of an even wider gamut of possible shapes with high-yield and [...] Read more.

The predictable nature of deoxyribonucleic acid (DNA) interactions enables assembly of DNA into almost any arbitrary shape with programmable features of nanometer precision. The recent progress of DNA nanotechnology has allowed production of an even wider gamut of possible shapes with high-yield and error-free assembly processes. Most of these structures are, however, limited in size to a nanometer scale. To overcome this limitation, a plethora of studies has been carried out to form larger structures using DNA assemblies as building blocks or tiles. Therefore, DNA tiles have become one of the most widely used building blocks for engineering large, intricate structures with nanometer precision. To create even larger assemblies with highly organized patterns, scientists have developed a variety of structural design principles and assembly methods. This review first summarizes currently available DNA tile toolboxes and the basic principles of lattice formation and hierarchical self-assembly using DNA tiles. Special emphasis is given to the forces involved in the assembly process in liquid-liquid and at solid-liquid interfaces, and how to master them to reach the optimum balance between the involved interactions for successful self-assembly. In addition, we focus on the recent approaches that have shown great potential for the controlled immobilization and positioning of DNA nanostructures on different surfaces. The ability to position DNA objects in a controllable manner on technologically relevant surfaces is one step forward towards the integration of DNA-based materials into nanoelectronic and sensor devices. Full article

(This article belongs to the Special Issue Biomolecular Materials: Self-Assembly, Structure, and Application)

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17 pages, 5295 KiB

Open AccessReview

Increasing Complexity in Wireframe DNA Nanostructures

by Petteri Piskunen, Sami Nummelin, Boxuan Shen, Mauri A. Kostiainen and Veikko Linko

Molecules 2020, 25(8), 1823; https://doi.org/10.3390/molecules25081823 - 16 Apr 2020

Cited by 21 | Viewed by 5598

Abstract

Structural DNA nanotechnology has recently gained significant momentum, as diverse design tools for producing custom DNA shapes have become more and more accessible to numerous laboratories worldwide. Most commonly, researchers are employing a scaffolded DNA origami technique by “sculpting” a desired shape from [...] Read more.

Structural DNA nanotechnology has recently gained significant momentum, as diverse design tools for producing custom DNA shapes have become more and more accessible to numerous laboratories worldwide. Most commonly, researchers are employing a scaffolded DNA origami technique by “sculpting” a desired shape from a given lattice composed of packed adjacent DNA helices. Albeit relatively straightforward to implement, this approach contains its own apparent restrictions. First, the designs are limited to certain lattice types. Second, the long scaffold strand that runs through the entire structure has to be manually routed. Third, the technique does not support trouble-free fabrication of hollow single-layer structures that may have more favorable features and properties compared to objects with closely packed helices, especially in biological research such as drug delivery. In this focused review, we discuss the recent development of wireframe DNA nanostructures—methods relying on meshing and rendering DNA—that may overcome these obstacles. In addition, we describe each available technique and the possible shapes that can be generated. Overall, the remarkable evolution in wireframe DNA structure design methods has not only induced an increase in their complexity and thus expanded the prevalent shape space, but also already reached a state at which the whole design process of a chosen shape can be carried out automatically. We believe that by combining cost-effective biotechnological mass production of DNA strands with top-down processes that decrease human input in the design procedure to minimum, this progress will lead us to a new era of DNA nanotechnology with potential applications coming increasingly into view. Full article

(This article belongs to the Special Issue Biomolecular Materials: Self-Assembly, Structure, and Application)

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