Browsing by Author "Julin, Sofia"
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- Assembly and optically triggered disassembly of lipid-DNA origami fibers
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä(2023-12-25) Julin, Sofia; Best, Nadine; Anaya-Plaza, Eduardo; Enlund, Eeva; Linko, Veikko; Kostiainen, Mauri A.The co-assembly of lipids and other compounds has recently gained increasing interest. Here, we report the formation of stimuli-responsive lipid-DNA origami fibers through the electrostatic co-assembly of cationic lipids and 6-helix bundle (6HB) DNA origami. The photosensitive lipid degrades when exposed to UV-A light, which allows a photoinduced, controlled release of the 6HBs from the fibers. The presented complexation strategy may find uses in developing responsive nanomaterials e.g. for therapeutics. - DNA nanostructure-directed assembly of metal nanoparticle superlattices
A2 Katsausartikkeli tieteellisessä aikakauslehdessä(2018-05-01) Julin, Sofia; Nummelin, Sami; Kostiainen, Mauri A.; Linko, VeikkoStructural DNA nanotechnology provides unique, well-controlled, versatile, and highly addressable motifs and templates for assembling materials at the nanoscale. These methods to build from the bottom-up using DNA as a construction material are based on programmable and fully predictable Watson-Crick base pairing. Researchers have adopted these techniques to an increasing extent for creating numerous DNA nanostructures for a variety of uses ranging from nanoelectronics to drug-delivery applications. Recently, an increasing effort has been put into attaching nanoparticles (the size range of 1–20 nm) to the accurate DNA motifs and into creating metallic nanostructures (typically 20–100 nm) using designer DNA nanoshapes as molds or stencils. By combining nanoparticles with the superior addressability of DNA-based scaffolds, it is possible to form well-ordered materials with intriguing and completely new optical, plasmonic, electronic, and magnetic properties. This focused review discusses the DNA structure-directed nanoparticle assemblies covering the wide range of different one-, two-, and three-dimensional systems. - DNA Origami as a Tool for Assembling Functional Biohybrid Nanomaterials
School of Chemical Technology | Doctoral dissertation (article-based)(2023) Julin, SofiaRecent advances in nanotechnology have given us a versatile toolbox of nanoscale objects with different functionalities. However, approaches for constructing stimuli-responsive and highly ordered macroscopic materials from these nanometer-sized components are still needed. The DNA origami technique enables the fabrication of custom-designed, well-defined, and highly addressable DNA-based structures and could therefore aid in the development of more advanced nanomaterials. In this doctoral thesis, the use of DNA origami in bottom-up nanofabrication was explored with the aim to construct functional biohybrid nanomaterials with high structural order. In publications I and II, the co-assembly of (negatively charged) DNA origami and cationic lipids was studied. The results demonstrated that DNA origami may serve as templates and nucleation sites for the formation of ordered lipid assemblies. The formed lipid matrix encapsulated the DNA origami, which also enhanced the DNA origami stability against endonuclease digestion. Moreover, the encapsulated DNA origami could be released from the lipid assemblies on demand by addition of competitive polyanions (publication I) or by illumination with long-wavelength UV light (publication II). In publication III, for one, highly ordered gold nanoparticle (AuNP) superlattices were assembled by employing electrostatic interactions between the cationic AuNPs and DNA origami. The ionic strength of the solution was used to control the assembly, and well-defined three-dimensional tetragonal superlattices were formed by gradually decreasing the salt concentration. Finally, in publication IV, pH-responsive and dynamically reconfigurable DNA-origami based lattices were constructed. Two pH-sensitive latches relying on Hoogsteen-type triplex formation were incorporated into the arms of the lattice-forming DNA origami unit, and thus the unit and the whole lattice could switch between an open and a closed state depending on the pH of the surrounding solution. The work shows that the library of stimuli-responsive elements initially developed for small DNA-based devices could be used to induce dynamicity also in considerably larger, hierarchical DNA origami lattices. In conclusion, the results demonstrate that DNA origami could function as a versatile self-assembling building block for advanced nanomaterials. The thesis highlights the potential of using DNA origami to fabricate highly ordered nanomaterials by electrostatic self-assembly and contributes to a broader understanding of such assemblies in bottom-up nanofabrication. In addition, the developed methods could aid in the engineering of more sophisticated stimuli-responsive hierarchical nanomaterials. - DNA origami directed 3D nanoparticle superlattice via electrostatic assembly
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä(2019-03-14) Julin, Sofia; Korpi, Antti; Nonappa; Shen, Boxuan; Liljeström, Ville; Ikkala, Olli; Keller, Adrian; Linko, Veikko; Kostiainen, Mauri A.The arrangements of metal nanoparticles into spatially ordered structures is still challenging, but DNA-based nanostructures have proven to be feasible building blocks in directing the higher-ordered arrangements of nanoparticles. However, an additional DNA functionalization of the particles is often required to link them to the DNA frames. Herein, we show that ordered 3D metal nanoparticle superlattices could be formed also by plainly employing electrostatic interactions between particles and DNA nanostructures. By utilizing the negatively charged DNA origami surface, we were able to assemble 6-helix bundle DNA origami and cationic gold nanoparticles (AuNPs) into well-ordered 3D tetragonal superlattices. Further, the results reveal that shape and charge complementarity between the building blocks are crucial parameters for lattice formation. Our method is not limited to only AuNPs and the origami shapes presented here, and could therefore be used in construction of a variety of functional materials. - DNA Origami-Mediated Substrate Nanopatterning of Inorganic Structures for Sensing Applications
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä(2019-09-27) Piskunen, Petteri; Shen, Boxuan; Julin, Sofia; Ijäs, Heini; Toppari, J. Jussi; Kostiainen, Mauri A.; Linko, VeikkoStructural DNA nanotechnology provides a viable route for building from the bottom-up using DNA as construction material. The most common DNA nanofabrication technique is called DNA origami, and it allows high-throughput synthesis of accurate and highly versatile structures with nanometer-level precision. Here, it is shown how the spatial information of DNA origami can be transferred to metallic nanostructures by combining the bottom-up DNA origami with the conventionally used top-down lithography approaches. This allows fabrication of billions of tiny nanostructures in one step onto selected substrates. The method is demonstrated using bowtie DNA origami to create metallic bowtie-shaped antenna structures on silicon nitride or sapphire substrates. The method relies on the selective growth of a silicon oxide layer on top of the origami deposition substrate, thus resulting in a patterning mask for following lithographic steps. These nanostructure-equipped surfaces can be further used as molecular sensors (e.g., surface-enhanced Raman spectroscopy (SERS)) and in various other optical applications at the visible wavelength range owing to the small feature sizes (sub-10 nm). The technique can be extended to other materials through methodological modifications; therefore, the resulting optically active surfaces may find use in development of metamaterials and metasurfaces. - Dynamics of DNA Origami Lattices
A2 Katsausartikkeli tieteellisessä aikakauslehdessä(2023-01-18) Julin, Sofia; Keller, Adrian; Linko, VeikkoHierarchical assembly of programmable DNA frameworks-such as DNA origami-paves the way for versatile nanometer-precise parallel nanopatterning up to macroscopic scales. As of now, the rapid evolution of the DNA nanostructure design techniques and the accessibility of these methods provide a feasible platform for building highly ordered DNA-based assemblies for various purposes. So far, a plethora of different building blocks based on DNA tiles and DNA origami have been introduced, but the dynamics of the large-scale lattice assembly of such modules is still poorly understood. Here, we focus on the dynamics of two-dimensional surface-assisted DNA origami lattice assembly at mica and lipid substrates and the techniques for prospective three-dimensional assemblies, and finally, we summarize the potential applications of such systems. - Electrostatic self-assembly of DNA origami and gold nanoparticles
Kemian tekniikan korkeakoulu | Master's thesis(2018-05-14) Julin, SofiaSpatially well-ordered structures of gold nanoparticles(AuNPs) and other metal nanoparticles have unique electronic, magnetic and optical properties, and hence there is ever-increasing interest towards these kinds of nanomaterials. DNA and DNA nanostructures have successfully been used to direct the higher-ordered arrangement of AuNPs, but the programmable arrangement of them into larger, well-defined structures is still challenging. The objective of this thesis is to establish a self-assembly method based on electrostatic interactions in which DNA origami nanostructures can be used to guide the higher ordered arrangement of cationic AuNPs in a controlled and programmable manner. The AuNP binding properties of different DNA origami structures was studied with UV/Vis spectroscopy and agarose gel electrophoretic mobility shift assay. DNA origami-AuNP assemblies were formed during dialysis against decreasing ionic strength, and the formed assemblies were characterized using small-angle X-ray scattering, transmission electron microscopy and cryogenic electron tomography. Electrostatic self-assembly of DNA origami 6HB nanostructures and small AuNPs (D_core = 2.5 nm, D_hydrodynamic_diameter = 8.5 nm) yielded highly ordered superlattice structures with a 3D tetragonal lattice structure, whereas other studied combinations of DNA origami structures and AuNPs resulted in amorphous aggregates. These results suggest that both shape and charge complementarity between the building blocks are needed for well-ordered structures to be formed through electrostatic self-assembly. According to the results, electrostatic self-assembly guided by DNA origami structures seems promising for construction of novel, well-ordered structures with unique properties, such as lattice geometry, designed specifically for the chosen application. - Phthalocyanine–DNA origami complexes with enhanced stability and optical properties
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä(2020-07-07) Shaukat, Ahmed; Anaya-Plaza, Eduardo; Julin, Sofia; Linko, Veikko; Torres, Tomas; Escosura, Andrés de la; Kostiainen, Mauri A.In this communication, electrostatically assembled phthalocyanine (Pc)-DNA origami (DO) complexes are formed and their optical properties are demonstrated. The formation of the complex prevents the Pc aggregation, thus yielding an enhanced optical response and photooxidative resilience towards aggregation in biologically relevant media. Simultaneously, the Pc protects the DO against enzymatic digestion. Both features solve previous drawbacks associated with phthalocyanine photosensitizers and DNA nanocarriers. The studied complexes may find use in technologies related to the photogeneration of singlet oxygen, e.g., photocatalysis, diagnositic arrays and photodynamic therapy. - Pitkien yksijuosteisten DNA-molekyylien suunnittelu ja valmistus DNA-origamirakenteiden käyttöön
Kemiantekniikan korkeakoulu | Bachelor's thesis(2024-05-30) Alapappila, NeaDNA on nykyään yksi laajimmin käytetyistä molekyylirakenteista itsekokoavien materiaalien suunnittelussa. Näitä nanomittakaavan DNA:lla valmistettuja materiaaleja käytetään yhä enemmän erilaisissa sovelluksissa kuten syövän immuunihoidossa ja lääkkeiden annostelujärjestelmissä. DNA-origamitekniikka on menetelmä, jossa kootaan näitä kaksi- ja kolmiulotteisia DNA-origamirakenteita taittamalla pitkä yksijuosteinen DNA-molekyyli lyhyillä komplementaarisilla oligonukleotideillä haluttuun muotoon. Yleisin käytetty runkojuoste DNA-origamirakenteiden valmistuksessa on virusperäinen pyöreä yksijuosteinen M13mp18-genomi, jolla on rajalliset mahdollisuudet lopullisten sekvenssin ja rakenteiden koon kannalta. Valmiiden rakenteiden koot ovat riippuvaisia runkojuosteen pituudesta ja siksi rakenteiden valmistuksessa räätälöityjen runkojuosteiden suunnittelu- ja valmistusmenetelmistä on tullut ratkaisevia. Tämä kandidaatintyö perehtyy erilaisiin niin perinteiseen kuin räätälöityjen runkojuosteiden suunnittelu- ja valmistusmenetelmiin, joita ovat bakteriofagipohjaiset menetelmät, PCR-pohjaiset menetelmät sekä entsymaattiset menetelmät. Yleisin tapa valmistaa runkojuosteita on yhä perinteinen bakteriofagipohjainen menetelmä sen yksinkertaisuuden sekä hyvän tuotantosaantonsa vuoksi. Muilla menetelmillä voidaan vaikuttaa runkojuosteiden sekvensseihin ja pituuksiin ja siten valmistaa räätälöityjä runkojuosteita. Näiden menetelmien laajempi käyttö kuitenkin rajoittuu vielä muun muassa huonoihin tuotantosaantoihin sekä monet menetelmistä ovat liian kalliita tai monimutkaisia. - Polymerpreparat med aktiv substans för oral läkemedelsadministrering
Sähkötekniikan korkeakoulu | Bachelor's thesis(2015-11-30) Julin, Sofia - Reconfigurable pH-Responsive DNA Origami Lattices
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä(2023-06-13) Julin, Sofia; Linko, Veikko; Kostiainen, Mauri A.DNA nanotechnology enables straightforward fabrication of user-defined and nanometer-precise templates for a cornucopia of different uses. To date, most of these DNA assemblies have been static, but dynamic structures are increasingly coming into view. The programmability of DNA not only allows for encoding of the DNA object shape but also it may be equally used in defining the mechanism of action and the type of stimuli-responsiveness of the dynamic structures. However, these “robotic” features of DNA nanostructures are usually demonstrated for only small, discrete, and device-like objects rather than for collectively behaving higher-order systems. Here, we show how a large-scale, two-dimensional (2D) and pH-responsive DNA origami-based lattice can be assembled into two different configurations (“open” and “closed” states) on a mica substrate and further switched from one to the other distinct state upon a pH change of the surrounding solution. The control over these two configurations is achieved by equipping the arms of the lattice-forming DNA origami units with “pH-latches” that form Hoogsteen-type triplexes at low pH. In short, we demonstrate how the electrostatic control over the adhesion and mobility of the DNA origami units on the surface can be used both in the large lattice formation (with the help of directed polymerization) and in the conformational switching of the whole lattice. To further emphasize the feasibility of the method, we also demonstrate the formation of pH-responsive 2D gold nanoparticle lattices. We believe this work can bridge the nanometer-precise DNA origami templates and higher-order large-scale systems with the stimuli-induced dynamicity. - Självorganiserade lipid-DNA-komplex
Kemiantekniikan korkeakoulu | Bachelor's thesis(2018-12-11) Småros, Fiona - Structural stability of DNA origami in organic solvents
Kemian tekniikan korkeakoulu | Master's thesis(2023-05-16) Ogunyemi, Olajide - Structural stability of DNA origami nanostructures in organic solvents
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä(2024-07-28) Enlund, Eeva; Julin, Sofia; Linko, Veikko; Kostiainen, Mauri A.DNA origami nanostructures have attracted significant attention as an innovative tool in a variety of research areas, spanning from nanophotonics to bottom-up nanofabrication. However, the use of DNA origami is often restricted by their rather limited structural stability in application-specific conditions. The structural integrity of DNA origami is known to be superstructure-dependent, and the integrity is influenced by various external factors, for example cation concentration, temperature, and presence of nucleases. Given the necessity to functionalize DNA origami also with non-water-soluble entities, it is important to acquire knowledge of the structural stability of DNA origami in various organic solvents. Therefore, we herein systematically investigate the post-folding DNA origami stability in a variety of polar, water-miscible solvents, including acetone, ethanol, DMF, and DMSO. Our results suggest that the structural integrity of DNA origami in organic solvents is both superstructure-dependent and dependent on the properties of the organic solvent. In addition, DNA origami are generally more resistant to added organic solvents in folding buffer compared to that in deionized water. DNA origami stability can be maintained in up to 25–40% DMF or DMSO and up to 70–90% acetone or ethanol, with the highest overall stability observed in acetone. By rationally selecting both the DNA origami design and the solvent, the DNA origami stability can be maintained in high concentrations of organic solvents, which paves the way for more extensive use of non-water-soluble compounds for DNA origami functionalization and complexation.