121 research outputs found
Applications of DNA self-assembled structures in nanoelectronics and plasmonics
No full textIn this thesis, the potential applications of DNA self-assembled structures were
explored in both nanoelectronics and plasmonics. The works can be divided into
two parts: electrical characterization of unmodified multilayered DNA origami and
DNA-gold-nanoparticle conjugates after they were trapped between gold nanoelectrodes by dielectrophoresis, and the development of a novel fabrication method using DNA origami as a template for smooth, high resolution metallic nanostructures
as well as optical characterization of them.
One of the biggest challenges in self-assembled nanoelectronic devices is to
connect them to macroscopic circuits. Dielectrophoretic (DEP) trapping has been
used extensively in manipulation of micro- and nanoscale objects in solution. We
have demonstrated this technique by trapping four structurally distinct multilayered DNA origami between gold nanoelectrodes by DEP and electrically characterized some of the trapped structures at high relative humidity. Most of the samples
showed insulating behavior in both DC I-V measurement and AC impedance spectroscopy. In the other experiment, an assembly of three gold nanoparticles (AuNPs)
conjugated with a triple-cross-over-tile (TX-tile) structure were designed, synthesized, and trapped by DEP. At the beginning no current was observed, but after
a few chemical gold growth steps, Coulomb blockade behavior was observed from
the liquid helium temperature up to the room temperature. Although no gated measurement was carried out, the random switching at low temperature measurements
highly resembled a similar behavior of single electron transistor (SET).
The second half of this thesis is focused on the development of a DNA-assisted
lithography (DALI) method, in which DNA origami was used to mask the growth
of SiO2 on Si chips in order to generate a stencil mask with openings of the DNA
origami shape. Then the stencil was used in conventional microfabrication processes
to deposit metallic nanostructures with almost the same shape as DNA origami
on different substrates. Three different DNA origami were used to fabricate metallic structures with various optical properties on sapphire substrates. The localized
surface plasmon resonance (LSPR) of Seeman tile and a bowtie antenna was characterized by a dark-field microscope. The surface enhanced Raman spectroscopy
(SERS) of two different marker molecules on gold bowtie antennas was characterized too. Finally, the chiral double-L samples landed on a surface with different orientation combinations showed distinct circular dichroism (CD) spectra. In addition,
a method to deposit DNA origami on unmodified surface with large area by spray
coating technique was reported.unknown accessibilityei tietoa saavutettavuudest
Disruption of outdoor activities caused by wildfire smoke shapes circulation of respiratory pathogens
No full textAs climate change accelerates, the frequency and severity of extreme weather events, such as wildfires, are increasing, with profound impacts on human health. While much attention has been paid to the direct health consequences of these events, such as chronic diseases from poor air quality, less is known about how behavioral shifts induced by such events can influence the transmission of infectious diseases. This study investigates how wildfire-induced changes in human behavior during the U.S. West Coast wildfires of 2020 may affect the spread of airborne diseases. Using a mobility data-driven indoor activity index, we find that the wildfire-induced deterioration of air quality led to a substantial increase in indoor activities, fostering conditions conducive to airborne disease transmission. Specifically, counties in Oregon and Washington experienced an average 10.8% and 14.3% increase in indoor activity, respectively, during the wildfire events, with major cities like Portland and Seattle experiencing increases of 11% and 16%, respectively. We quantify these behavioral changes and integrate them into an SIR epidemic model to characterize the increased indoor activity and disease dynamics. The model predicts the greatest impact on diseases with shorter generation times, such as RSV and influenza. Our results show that even a modest increase in indoor mask-wearing (as low as 10%) could significantly reduce the risk of disease spread in these settings, with higher compliance needed for more substantial reductions. As wildfires and other climate-related events become more frequent, integrating behavioral responses into public health policies will be crucial to mitigate the compounded risks of climate change and its secondary health impacts.[Author summary] The effects of climate change on human health are becoming more evident, but we often overlook one crucial factor: how extreme weather events influence our behaviors and, in turn, the spread of infectious diseases. In this study, we explore the role of wildfire-induced behavioral changes on the transmission of airborne diseases, focusing on the U.S. West Coast wildfires of September 2020. Our findings show that wildfires led to a dramatic increase in indoor activities, creating the ideal conditions for respiratory diseases such as influenza to spread. But—by incorporating simple measures like indoor mask-wearing, we can reduce this risk. This research underscores the importance of considering human behavior responses when tackling health risks associated with climate change. As we face more frequent extreme events, public health strategies must evolve to address not just the environmental impact, but also the ways we adapt, react to the emergency. By understanding and planning for this behavioral response, we can better protect public health in a warming world.Research reported in this publication was supported by the Fritz-Family fellowship program to SB and GP.Peer reviewe
DNA Origami Nanophotonics and Plasmonics at Interfaces
No full textDNA nanotechnology provides a versatile toolbox for creating custom and accurate shapes that can serve as versatile templates for nanopatterning. These DNA templates can be used as molecular-scale precision tools in, for example, biosensing, nanometrology, and super-resolution imaging, and biocompatible scaffolds for arranging other nano-objects, for example, for drug delivery applications and molecular electronics. Recently, increasing attention has been paid to their potent use in nanophotonics since these modular templates allow a wide range of plasmonic and photonic ensembles ranging from DNA-directed nanoparticle and fluorophore arrays to entirely metallic nanostructures. This Feature Article focuses on the DNA-origami-based nanophotonics and plasmonics - especially on the methods that take advantage of various substrates and interfaces for the foreseen applications.Peer reviewe
DNA-Origamit Biosensorien ja Nanovalmistuksen Työkaluina
No full textSelf-assembling DNA (deoxyribonucleic acid) origami nanostructures provide an approachable pathway for making a wide array of programmable, precise and highly addressable platforms at the nanometer-scale. These custom nanoshapes can be employed as versatile tools for applications in e.g. medicine, sensing, and solid-state nanofabrication, but the integration of these DNA-based structures to the various demanding application-specific environments is not always straightforward. Therefore methods for improving the stability of DNA origami or using them as templates for materials with more desirable physical properties are often required.
Thus, in publication I of this thesis, the structural dependence of the environmental stability of DNA origami was investigated by comparing two DNA origami designs with identical superstructures but different internal structures. It was shown how the structures behave very differently in buffers with low electrostatic screening and under endonuclease digestion.
In publication II, DNA origami were used as new components for amplifying the sensitivity of an electrochemical DNA biosensor by up to two orders of magnitude via manipulation of the effective size of an analyte.
Then, in publications III and IV, lithographic pathways for transforming DNA origami shapes into fully solid-state nano-objects are shown. Of these, III presents an optimized workflow for DNA-assisted lithography (DALI), while publication IV develops the method much further into the more versatile biotemplated lithography of inorganic nanostructures (BLIN) technique, that makes the process compatible with a greatly expanded range of materials.
Finally, publications V and VI use the techniques presented in III and IV for fabricating nanopatterned substrates for SERS measurements and then characterize their properties using practical measurements and simulations. In V, solely particle-patterned substrates as natively fabricated with BLIN are discussed, while in VI, also more complex architectures based on coupled particle-aperture features are introduced.
Overall, the works shown in this thesis provide important insights into the behavior of DNA origami in various environments and demonstrate how their structural properties can be leveraged in promising tools for optical and electrochemical biosensing. Additionally, by enabling the use of DNA origami in solid-state nanofabrication, the methods developed herein could also facilitate the efficient manufacturing of otherwise demanding multifunctional and intricate nanopatterned surfaces for a variety of uses.Itsejärjestyvät DNA (deoksiribonukleiinihappo)-origami-nanorakenteet tarjoavat helposti lähestyttävän tavan valmistaa ohjelmoitavia ja tarkkaan muokattavia alustoja nanomittakaavassa. Näitä mukautettavia alustoja voidaan käyttää monipuolisina työkaluina esimerkiksi lääketieteen, havainnoinnin ja kiinteän aineen nanovalmistusmenetelmien sovelluksissa. DNA:han pohjautuvien rakenteiden integroiminen erilaisiin vaativiin sovellusympäristöihin ei kuitenkaan yleensä ole suoraviivaista, joten uusia menetelmiä DNA-origamien stabiilisuuden parantamiseksi tarvitaan. Vaihtoehtoisesti origameja voidaan myös käyttää muiden ominaisuuksiltaan mielekkäämpien materiaalien muokkaamiseen.
Tämän väitöskirjan julkaisussa I perehdytään DNA-origamien rakenteellisista yksityiskohdista riippuvaan stabiilisuuteen vertailemalla kahta ulkoisesti identtistä mutta sisäisiltä ominaisuuksiltaan erilaista DNA-origamia. Tutkimuksessa osoitetaan, että nämä rakenteet käyttäytyvät hyvin eri tavoin matalan sähköstaattisen varjostuksen puskuriliuoksissa ja endonukleaasi-entsyymejä sisältävissä ympäristöissä.
Julkaisussa II DNA-origameja hyödynnetään sähkökemiallisen DNA-biosensorin komponentteina. DNA-origamin avulla kohdeanalyytin efektiivistä kokoa voidaan kasvattaa, jolloin sensorin herkkyyttä voidaan parantaa jopa kahdella kertaluokalla perinteisiin menetelmiin nähden.Julkaisuissa III ja IV kehitetään litografisia keinoja muuttaa DNA-origamien tarkat muodot täysin kiinteän aineen nanokuvioiksi. III esittelee optimoidun prosessiketjun DALI-tekniikalle (DNA-avusteinen litografia). IV vastaavasti kehittää DALI-menetelmää paljon pidemmälle ns. BLIN-tekniikaksi tehden siitä yhteensopivan huomattavasti aiempaa laajemman materiaalivalikoiman kanssa.
Lopuksi julkaisut V ja VI hyödyntävät III- ja IV-julkaisuissa kehitettyjä nanovalmistusmenetelmiä pintavahvisteisessa Raman-spektroskopiassa (SERS) käytettävien mittausalustojen kuvioimiseen. Näin valmistettujen alustojen suorituskykyä karakterisoidaan sekä käytännön mittauksilla että simulaatioiden avulla. V:ssa keskitytään pelkästään partikkeleilla kuvioituihin pintoihin, joita BLIN-tekniikalla voidaan lähtökohtaisesti valmistaa. VI:ssa esitellään näiden pintojen lisäksi monipuolisempia rakenteita, jotka pohjautuvat kytkeytyneisiin partikkeli-apertuuri -kuvioihin.
Tässä väitöskirjassa esitetyt työt tarjoavat tärkeitä näkökulmia DNA-origamien stabiilisuuteen ja demonstroivat, miten origameja voidaan hyödyntää lupaavina työkaluina optisissa ja sähkökemiallisissa biosensoreissa. DNA-origamien käyttö kiinteän aineen nanovalmistuksessa voi lisäksi mahdollistaa muutoin vaativien monitoiminnalisten ja monimutkaisten nanokuvioitujen pintojen valmistamisen erilaisiin käyttökohteisiin
Spatial control of protein binding with DNA nanostructures
No full textThe physical and chemical properties of DNA, including its structure predictability thanks to Watson-Crick base pairing, make it into an obvious polymer of choice to use as a biomaterial for the fabrication of complex three dimensional nanostructures. These nanostructures are produced by the technique of DNA origami, where a long single stranded circular DNA, called scaffold, is folded into a pre-designed shape by the hybridization of partially complementary oligonucleotides, the staples. The programmability of DNA origami, i.e. the specific control, by design, of the location of every DNA sequence within the structure, can be harnessed for the positioning of molecules with nanoscale precision. In the present thesis, we have explored different branches of the DNA origami technology, from its functionalization with proteins, its structural characterization and its application for method development, targeted treatment and study of molecular processes taking place at the nanoscale.In Paper I, we develop an approach to quantify the incorporation of proteins in DNA origami using DNA-PAINT, a multiplexed super-resolution imaging method that allows the characterization of structures with single-molecule resolution and high reliability. Even as protein-decorated DNA nanostructures become increasingly important tools for biomedical sciences, the existing strategies to study and maximize protein incorporation provide limited insight into functionalization. With DNA-PAINT, we were able to explore factors influencing incorporation rate such as oligonucleotide quality, protein size, or purification method, rank their impact, and model their combined effects. Thus, we were able to offer a comprehensive view of functionalization efficiency and precise parameters for yield optimization, which can have significant implications for the application of DNA origami in fields beyond academia.In Paper II, we introduce the new method PLASTIQ for assessing DNA origami structural integrity in vivo with a detection sensitivity of 0.01 femtomolar. Despite the potential of DNA origami in therapeutics, the lack of structural assessment methods for in vivo use hampers its clinical initiation. Sampling only 1 ul of blood, PLASTIQ allowed us to monitor the degradation patterns of nanostructures over time. We examined the protective effects of PEGylation and obtained the pharmacokinetic profiles of different origamis. Additionally, we were able to observe differential degradation of structural regions depending on how exposed they were to the environment. Altogether, PLASTIQ is an accurate tool for assessing structural stability, offering valuable insights for advancing DNA origami-based drug development.In Paper III, we present PANMAP, a method based on antigen patterning on DNA nanostructures to measure antibody affinity while taking multivalency into account. Multivalency is fundamental in many biological systems, especially in antibody-antigen interactions where multiple binding sites improve affinity and specificity. However, conventional affinity assays such as ELISA provide only a limited perspective on binding characterization and do not address multivalency. With PANMAP overcoming these limitations, we found that antibody binding equilibrium is influenced by antigen spacing, leading to competitive exclusion at close distances, optimal bivalent binding at intermediate distances, and a monovalent regime at longer distances. Thus, PANMAP enabled a complete profile of multivalency and the binding states that constitute it, potentially providing useful insights into biological processes and engineering applications.In Paper IV, we apply DNA origami displaying Jag1 ligands to stimulate neuroepithelial stem-like cells to study the molecular mechanism leading to Notch receptor activation. The Notch pathway is a highly evolutionarily conserved signaling system that plays a key role in embryonic and nervous system development. However, it is unclear how the activation unravels, with the leading hypothesis being force-driven conformational changes. Here, we demonstrate that Notch triggering can occur without pulling forces and that it instead proceeds upon extended binding. These findings suggest an alternative molecular mechanism for receptor activation, suggesting potential for the design of soluble agonists.In Paper V, we engineer a pH-responsive DNA robotic switch that selectively displays death receptor ligands only in acidic tumor microenvironments to induce apoptosis of cancer cells. As these receptors are responsible for initiating cell death but are ubiquitously expressed on the membranes of most cells, a targeted approach for their use in tumor therapies is desired. The DNA robotic switch hides the ligands, arranged in a hexagonal pattern inside a cavity while at neutral pH, until encountering pH 6.5 where the ligands are revealed, leading to clustering of DR and triggering apoptosis of breast cancer cells. Our results probe the functionality of the nanodevice in vitro and shows the significant tumor volume reduction in mice with human breast cancer xenografts. Overall, this work highlights the potential for targeted cancer treatment using DNA origami.List of scientific papers1. Iris Rocamonde-Lago, Ferenc Fördös, Cagla Sahin, Ian T. Hoffecker & Björn Högberg. Exploring DNA origami protein functionalization using super resolution imaging. [Manuscript]II. Yang Wang*, Iris Rocamonde-Lago*, Janine Waldvogel, Shuya Zang, Igor Baars, Alexander Kloosterman, Boxuan Shen, Ian T. Hoffecker, Qin He & Björn Högberg. DNA origami structural integrity tracked in vivo using proximity ligation. [Manuscript]III. Iris Rocamonde-Lago, Ieva Berzina, Ian T. Hoffecker & Björn Högberg. Profiling of multivalent binding with DNA origami reveals spatial determinants of antigen-antibody interactions. [Manuscript]IV. Ioanna Smyrlaki, Ferenc Fördös, Iris Rocamonde-Lago, Yang Wang, Boxuan Shen, Antonio Lentini, Vincent C. Luca, Björn Reinius, Ana I. Teixeira & Björn Högberg. Soluble and multivalent Jag1 DNA origami nanopatterns activate Notch without pulling force. Nature Communications, 15(1), 465. https://doi.org/10.1038/s41467-023-44059-4V. Yang Wang, Igor Baars, Ieva Berzina, Iris Rocamonde-Lago, Boxuan Shen, Yunshi Yang, Marco Lolaico, Janine Waldvogel, Ioanna Smyrlaki, Keying Zhu, Robert A. Harris & Björn Högberg. A DNA robotic switch with regulated autonomous display of cytotoxic ligand nanopatterns. Nature Nanotechnology, 19(9), 1366-1374. https://doi.org/10.1038/s41565-024-01676-4*Shared first authorship</p
Dielectrophoretic trapping of multilayer DNA origami nanostructures and DNA origami-induced local destruction of silicon dioxide
No full textPeer reviewe
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