Veikko Linko | Aalto University (original) (raw)
Papers by Veikko Linko
The Journal of Physical Chemistry C, 2011
... Antila†, Mikko J. Heikkila , Ville Ma kinen‡, Niko Humalama ki†, Mikko Laitinen§, Veikko Link... more ... Antila†, Mikko J. Heikkila , Ville Ma kinen‡, Niko Humalama ki†, Mikko Laitinen§, Veikko Linko‡, Pasi Jalkanen‡, Jussi Toppari‡, Viivi Aumanen†, Marianna Kemell , Pasi Myllyperkio †, Karoliina Honkala†, Hannu Ha kkinen†‡, Markku Leskela , and Jouko EI Korppi-Tommola*†. ...
Trends in Biotechnology, 2015
DNA molecules can be assembled into custom predesigned shapes via hybridization of sequence-compl... more DNA molecules can be assembled into custom predesigned shapes via hybridization of sequence-complementary domains. The folded structures have high spatial addressability and a tremendous potential to serve as platforms and active components in a plethora of bionanotechnological applications. DNA is a truly programmable material, and its nanoscale engineering thus opens up numerous attractive possibilities to develop novel methods for therapeutics. The tailored molecular devices could be used in targeting cells and triggering the cellular actions in the biological environment. In this review we focus on the DNA-based assemblies - primarily DNA origami nanostructures - that could perform complex tasks in cells and serve as smart drug-delivery vehicles in, for example, cancer therapy, prodrug medication, and enzyme replacement therapy.
Biophysical Journal, 2014
Chem. Commun., 2015
In this communication, we present a nanoscale reactor assembled from tuneable and spatially addre... more In this communication, we present a nanoscale reactor assembled from tuneable and spatially addressable tubular DNA origami units. We can controllably combine separate origami units equipped with glucose oxidase (GOx) and horseradish peroxidase (HRP), and demonstrate efficient GOx/HRP enzyme cascade reaction inside the tube. The reactor could be utilized as a nanoscale diagnostic tool, and modularity of the proposed system would further enable more complex reactions.
Current Opinion in Biotechnology, 2013
It is notoriously difficult to observe, let alone control, the position and orientation of molecu... more It is notoriously difficult to observe, let alone control, the position and orientation of molecules due to their small size and the constant thermal fluctuations that they experience in solution. Molecular self-assembly with DNA enables building custom-shaped nanometer-scale objects with molecular weights up to the megadalton regime. It provides a viable route for placing molecules and constraining their fluctuations in user-defined ways, thereby opening up completely new avenues for scientific and technological exploration. Here, we review progress that has been made in recent years toward the state of an enabled DNA nanotechnology.
Scientific reports, 2015
DNA origami nanostructures have tremendous potential to serve as versatile platforms in self-asse... more DNA origami nanostructures have tremendous potential to serve as versatile platforms in self-assembly -based nanofabrication and in highly parallel nanoscale patterning. However, uniform deposition and reliable anchoring of DNA nanostructures often requires specific conditions, such as pre-treatment of the chosen substrate or a fine-tuned salt concentration for the deposition buffer. In addition, currently available deposition techniques are suitable merely for small scales. In this article, we exploit a spray-coating technique in order to resolve the aforementioned issues in the deposition of different 2D and 3D DNA origami nanostructures. We show that purified DNA origamis can be controllably deposited on silicon and glass substrates by the proposed method. The results are verified using either atomic force microscopy or fluorescence microscopy depending on the shape of the DNA origami. DNA origamis are successfully deposited onto untreated substrates with surface coverage of abou...
Journal of Self-Assembly and Molecular Electronics, 2013
Recent developments in structural DNA nanotechnology have made complex and spatially exactly cont... more Recent developments in structural DNA nanotechnology have made complex and spatially exactly controlled self-assembled DNA nanoarchitectures widely accessible. The available methods enable large variety of different possible shapes combined with the possibility of using DNA structures as templates for high-resolution patterning of nano-objects, thus opening up various opportunities for diverse nanotechnological applications. These DNA motifs possess enormous possibilities to be exploited in realization of molecular scale sensors and electronic devices, and thus, could enable further miniaturization of electronics. However, there are arguably two main issues on making use of DNA-based electronics: (1) incorporation of individual DNA designs into larger extrinsic systems is rather challenging, and (2) electrical properties of DNA molecules and the utilizable DNA templates themselves, are not yet fully understood. This review focuses on the above mentioned issues and also briefly summarizes the potential applications of DNA-based electronic devices.
Nanoscale, 2015
The DNA origami technique provides an intriguing possibility to develop customized nanostructures... more The DNA origami technique provides an intriguing possibility to develop customized nanostructures for various bionanotechnological purposes. One target is to create tailored bottom-up-based plasmonic devices and metamaterials based on DNA metallization or controlled attachment of nanoparticles to the DNA designs. In this article, we demonstrate an alternative approach: DNA origami nanoshapes can be utilized in creating accurate, uniform and entirely metallic (e.g. gold, silver and copper) nanostructures on silicon substrates. The technique is based on developing silhouettes of the origamis in the grown silicon dioxide layer, and subsequently using this layer as a mask for further patterning. The proposed method has a high spatial resolution, and the fabrication yields can approach 90%. The approach allows a cost-effective, parallel, large-scale patterning on a chip with fully tailored metallic nanostructures; the DNA origami shape and the applied metal can be specifically chosen for each conceivable implementation.
ELECTROPHORESIS, 2015
DNA origami is a widely used method for fabrication of custom-shaped nanostructures. However, to ... more DNA origami is a widely used method for fabrication of custom-shaped nanostructures. However, to utilize such structures, one needs to controllably position them on nanoscale. Here we demonstrate how different types of 3D scaffolded multilayer origamis can be accurately anchored to lithographically fabricated nanoelectrodes on a silicon dioxide substrate by DEP. Straight brick-like origami structures, constructed both in square (SQL) and honeycomb lattices, as well as curved "C"-shaped and angular "L"-shaped origamis were trapped with nanoscale precision and single-structure accuracy. We show that the positioning and immobilization of all these structures can be realized with or without thiol-linkers. In general, structural deformations of the origami during the DEP trapping are highly dependent on the shape and the construction of the structure. The SQL brick turned out to be the most robust structure under the high DEP forces, and accordingly, its single-structure trapping yield was also highest. In addition, the electrical conductivity of single immobilized plain brick-like structures was characterized. The electrical measurements revealed that the conductivity is negligible (insulating behavior). However, we observed that the trapping process of the SQL brick equipped with thiol-linkers tended to induce an etched "nanocanyon" in the silicon dioxide substrate. The nanocanyon was formed exactly between the electrodes, that is, at the location of the DEP-trapped origami. The results show that the demonstrated DEP-trapping technique can be readily exploited in assembling and arranging complex multilayered origami geometries. In addition, DNA origamis could be utilized in DEP-assisted deformation of the substrates onto which they are attached.
Small, 2008
wing to its exceptional self-assembly properties, DNA could become a key player in bottom-up fabr... more wing to its exceptional self-assembly properties, DNA could become a key player in bottom-up fabrication of nanoscale systems. A striking example of a DNA self-assembly technique is ''DNA origami'' which involves folding long single-stranded DNA with the help of short oligonucleotides. Each short oligonucleotide can serve as a pixel. Therefore, origami structures can be decorated with complex patterns with 6-nm resolution to form a ''nanobreadboard'', that is, a planar template for attachment of various materials (proteins, carbon nanotubes, metal nanoparticles). Controlled positioning of DNA origami structures on the chip is a crucial open challenge for the realization of the ''nanobreadboard'' idea. Here we present a fully developed dielectrophoresis-based method for trapping DNA origami structures. The method gives a high yield of single-structure trapping between nanoelectrodes and controlled positioning of origami structures on a chip. The method provides a means of bridging bottom-up and top-down fabrication approaches in nanotechnology.
Nanotechnology, 2011
We present a novel, defined-size, small and rigid DNA template, a so-called B-A-B complex, based ... more We present a novel, defined-size, small and rigid DNA template, a so-called B-A-B complex, based on DNA triple crossover motifs (TX tiles), which can be utilized in molecular scale patterning for nanoelectronics, plasmonics and sensing applications. The feasibility of the designed construct is demonstrated by functionalizing the TX tiles with one biotin-triethylene glycol (TEG) and efficiently decorating them with streptavidin, and furthermore by positioning and anchoring single thiol-modified B-A-B complexes to certain locations on a chip via dielectrophoretic trapping. Finally, we characterize the conductance properties of the non-functionalized construct, first by measuring DC conductivity and second by utilizing AC impedance spectroscopy in order to describe the conductivity mechanism of a single B-A-B complex using a detailed equivalent circuit model. This analysis also reveals further information about the conductivity of DNA structures in general.
Nanoscale, 2011
We present a method for controlled connection of gold electrodes with dsDNA molecules (locally on... more We present a method for controlled connection of gold electrodes with dsDNA molecules (locally on a 10 chip) by utilizing polymerase to elongate single-stranded DNA primers attached to the electrodes. Thiolmodified oligonucleotides are directed and immobilized to nanoscale electrodes by means of dielectrophoretic trapping, and extended in a procedure mimicking PCR, finally forming a complete dsDNA molecule bridging the gap between the electrodes. The technique opens up opportunities for building from the bottom-up, for detection and sensing applications, and also for molecular electronics.
Nano Letters, 2014
DNA origami structures can be programmed into arbitrary shapes with nanometer scale precision, wh... more DNA origami structures can be programmed into arbitrary shapes with nanometer scale precision, which opens up numerous attractive opportunities to engineer novel functional materials. One intriguing possibility is to use DNA origamis for fully tunable, targeted, and triggered drug delivery. In this work, we demonstrate the coating of DNA origami nanostructures with virus capsid proteins for enhancing cellular delivery. Our approach utilizes purified cowpea chlorotic mottle virus capsid proteins that can bind and self-assemble on the origami surface through electrostatic interactions and further pack the origami nanostructures inside the viral capsid. Confocal microscopy imaging and transfection studies with a human HEK293 cell line indicate that protein coating improves cellular attachment and delivery of origamis into the cells by 13-fold compared to bare DNA origamis. The presented method could readily find applications not only in sophisticated drug delivery applications but also in organizing intracellular reactions by origami-based templates.
The Journal of Physical Chemistry C, 2011
... Antila†, Mikko J. Heikkila , Ville Ma kinen‡, Niko Humalama ki†, Mikko Laitinen§, Veikko Link... more ... Antila†, Mikko J. Heikkila , Ville Ma kinen‡, Niko Humalama ki†, Mikko Laitinen§, Veikko Linko‡, Pasi Jalkanen‡, Jussi Toppari‡, Viivi Aumanen†, Marianna Kemell , Pasi Myllyperkio †, Karoliina Honkala†, Hannu Ha kkinen†‡, Markku Leskela , and Jouko EI Korppi-Tommola*†. ...
Trends in Biotechnology, 2015
DNA molecules can be assembled into custom predesigned shapes via hybridization of sequence-compl... more DNA molecules can be assembled into custom predesigned shapes via hybridization of sequence-complementary domains. The folded structures have high spatial addressability and a tremendous potential to serve as platforms and active components in a plethora of bionanotechnological applications. DNA is a truly programmable material, and its nanoscale engineering thus opens up numerous attractive possibilities to develop novel methods for therapeutics. The tailored molecular devices could be used in targeting cells and triggering the cellular actions in the biological environment. In this review we focus on the DNA-based assemblies - primarily DNA origami nanostructures - that could perform complex tasks in cells and serve as smart drug-delivery vehicles in, for example, cancer therapy, prodrug medication, and enzyme replacement therapy.
Biophysical Journal, 2014
Chem. Commun., 2015
In this communication, we present a nanoscale reactor assembled from tuneable and spatially addre... more In this communication, we present a nanoscale reactor assembled from tuneable and spatially addressable tubular DNA origami units. We can controllably combine separate origami units equipped with glucose oxidase (GOx) and horseradish peroxidase (HRP), and demonstrate efficient GOx/HRP enzyme cascade reaction inside the tube. The reactor could be utilized as a nanoscale diagnostic tool, and modularity of the proposed system would further enable more complex reactions.
Current Opinion in Biotechnology, 2013
It is notoriously difficult to observe, let alone control, the position and orientation of molecu... more It is notoriously difficult to observe, let alone control, the position and orientation of molecules due to their small size and the constant thermal fluctuations that they experience in solution. Molecular self-assembly with DNA enables building custom-shaped nanometer-scale objects with molecular weights up to the megadalton regime. It provides a viable route for placing molecules and constraining their fluctuations in user-defined ways, thereby opening up completely new avenues for scientific and technological exploration. Here, we review progress that has been made in recent years toward the state of an enabled DNA nanotechnology.
Scientific reports, 2015
DNA origami nanostructures have tremendous potential to serve as versatile platforms in self-asse... more DNA origami nanostructures have tremendous potential to serve as versatile platforms in self-assembly -based nanofabrication and in highly parallel nanoscale patterning. However, uniform deposition and reliable anchoring of DNA nanostructures often requires specific conditions, such as pre-treatment of the chosen substrate or a fine-tuned salt concentration for the deposition buffer. In addition, currently available deposition techniques are suitable merely for small scales. In this article, we exploit a spray-coating technique in order to resolve the aforementioned issues in the deposition of different 2D and 3D DNA origami nanostructures. We show that purified DNA origamis can be controllably deposited on silicon and glass substrates by the proposed method. The results are verified using either atomic force microscopy or fluorescence microscopy depending on the shape of the DNA origami. DNA origamis are successfully deposited onto untreated substrates with surface coverage of abou...
Journal of Self-Assembly and Molecular Electronics, 2013
Recent developments in structural DNA nanotechnology have made complex and spatially exactly cont... more Recent developments in structural DNA nanotechnology have made complex and spatially exactly controlled self-assembled DNA nanoarchitectures widely accessible. The available methods enable large variety of different possible shapes combined with the possibility of using DNA structures as templates for high-resolution patterning of nano-objects, thus opening up various opportunities for diverse nanotechnological applications. These DNA motifs possess enormous possibilities to be exploited in realization of molecular scale sensors and electronic devices, and thus, could enable further miniaturization of electronics. However, there are arguably two main issues on making use of DNA-based electronics: (1) incorporation of individual DNA designs into larger extrinsic systems is rather challenging, and (2) electrical properties of DNA molecules and the utilizable DNA templates themselves, are not yet fully understood. This review focuses on the above mentioned issues and also briefly summarizes the potential applications of DNA-based electronic devices.
Nanoscale, 2015
The DNA origami technique provides an intriguing possibility to develop customized nanostructures... more The DNA origami technique provides an intriguing possibility to develop customized nanostructures for various bionanotechnological purposes. One target is to create tailored bottom-up-based plasmonic devices and metamaterials based on DNA metallization or controlled attachment of nanoparticles to the DNA designs. In this article, we demonstrate an alternative approach: DNA origami nanoshapes can be utilized in creating accurate, uniform and entirely metallic (e.g. gold, silver and copper) nanostructures on silicon substrates. The technique is based on developing silhouettes of the origamis in the grown silicon dioxide layer, and subsequently using this layer as a mask for further patterning. The proposed method has a high spatial resolution, and the fabrication yields can approach 90%. The approach allows a cost-effective, parallel, large-scale patterning on a chip with fully tailored metallic nanostructures; the DNA origami shape and the applied metal can be specifically chosen for each conceivable implementation.
ELECTROPHORESIS, 2015
DNA origami is a widely used method for fabrication of custom-shaped nanostructures. However, to ... more DNA origami is a widely used method for fabrication of custom-shaped nanostructures. However, to utilize such structures, one needs to controllably position them on nanoscale. Here we demonstrate how different types of 3D scaffolded multilayer origamis can be accurately anchored to lithographically fabricated nanoelectrodes on a silicon dioxide substrate by DEP. Straight brick-like origami structures, constructed both in square (SQL) and honeycomb lattices, as well as curved "C"-shaped and angular "L"-shaped origamis were trapped with nanoscale precision and single-structure accuracy. We show that the positioning and immobilization of all these structures can be realized with or without thiol-linkers. In general, structural deformations of the origami during the DEP trapping are highly dependent on the shape and the construction of the structure. The SQL brick turned out to be the most robust structure under the high DEP forces, and accordingly, its single-structure trapping yield was also highest. In addition, the electrical conductivity of single immobilized plain brick-like structures was characterized. The electrical measurements revealed that the conductivity is negligible (insulating behavior). However, we observed that the trapping process of the SQL brick equipped with thiol-linkers tended to induce an etched "nanocanyon" in the silicon dioxide substrate. The nanocanyon was formed exactly between the electrodes, that is, at the location of the DEP-trapped origami. The results show that the demonstrated DEP-trapping technique can be readily exploited in assembling and arranging complex multilayered origami geometries. In addition, DNA origamis could be utilized in DEP-assisted deformation of the substrates onto which they are attached.
Small, 2008
wing to its exceptional self-assembly properties, DNA could become a key player in bottom-up fabr... more wing to its exceptional self-assembly properties, DNA could become a key player in bottom-up fabrication of nanoscale systems. A striking example of a DNA self-assembly technique is ''DNA origami'' which involves folding long single-stranded DNA with the help of short oligonucleotides. Each short oligonucleotide can serve as a pixel. Therefore, origami structures can be decorated with complex patterns with 6-nm resolution to form a ''nanobreadboard'', that is, a planar template for attachment of various materials (proteins, carbon nanotubes, metal nanoparticles). Controlled positioning of DNA origami structures on the chip is a crucial open challenge for the realization of the ''nanobreadboard'' idea. Here we present a fully developed dielectrophoresis-based method for trapping DNA origami structures. The method gives a high yield of single-structure trapping between nanoelectrodes and controlled positioning of origami structures on a chip. The method provides a means of bridging bottom-up and top-down fabrication approaches in nanotechnology.
Nanotechnology, 2011
We present a novel, defined-size, small and rigid DNA template, a so-called B-A-B complex, based ... more We present a novel, defined-size, small and rigid DNA template, a so-called B-A-B complex, based on DNA triple crossover motifs (TX tiles), which can be utilized in molecular scale patterning for nanoelectronics, plasmonics and sensing applications. The feasibility of the designed construct is demonstrated by functionalizing the TX tiles with one biotin-triethylene glycol (TEG) and efficiently decorating them with streptavidin, and furthermore by positioning and anchoring single thiol-modified B-A-B complexes to certain locations on a chip via dielectrophoretic trapping. Finally, we characterize the conductance properties of the non-functionalized construct, first by measuring DC conductivity and second by utilizing AC impedance spectroscopy in order to describe the conductivity mechanism of a single B-A-B complex using a detailed equivalent circuit model. This analysis also reveals further information about the conductivity of DNA structures in general.
Nanoscale, 2011
We present a method for controlled connection of gold electrodes with dsDNA molecules (locally on... more We present a method for controlled connection of gold electrodes with dsDNA molecules (locally on a 10 chip) by utilizing polymerase to elongate single-stranded DNA primers attached to the electrodes. Thiolmodified oligonucleotides are directed and immobilized to nanoscale electrodes by means of dielectrophoretic trapping, and extended in a procedure mimicking PCR, finally forming a complete dsDNA molecule bridging the gap between the electrodes. The technique opens up opportunities for building from the bottom-up, for detection and sensing applications, and also for molecular electronics.
Nano Letters, 2014
DNA origami structures can be programmed into arbitrary shapes with nanometer scale precision, wh... more DNA origami structures can be programmed into arbitrary shapes with nanometer scale precision, which opens up numerous attractive opportunities to engineer novel functional materials. One intriguing possibility is to use DNA origamis for fully tunable, targeted, and triggered drug delivery. In this work, we demonstrate the coating of DNA origami nanostructures with virus capsid proteins for enhancing cellular delivery. Our approach utilizes purified cowpea chlorotic mottle virus capsid proteins that can bind and self-assemble on the origami surface through electrostatic interactions and further pack the origami nanostructures inside the viral capsid. Confocal microscopy imaging and transfection studies with a human HEK293 cell line indicate that protein coating improves cellular attachment and delivery of origamis into the cells by 13-fold compared to bare DNA origamis. The presented method could readily find applications not only in sophisticated drug delivery applications but also in organizing intracellular reactions by origami-based templates.