1
|
Pekar K, Young RT, Sensale S. Optimizing Binding among Bimolecular Tethered Complexes. J Phys Chem B 2024; 128:5506-5512. [PMID: 38786364 DOI: 10.1021/acs.jpcb.4c01088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Tethered motion is ubiquitous in nature, offering controlled movement and spatial constraints to otherwise chaotic systems. The enhanced functionality and practical utility of tethers has been exploited in biotechnology, catalyzing the design of novel biosensors and molecular assembly techniques. While notable technological advances incorporating tethered motifs have been made, a theoretical gap persists within the paradigm, hindering a comprehensive understanding of tethered-based technologies. In this work, we focus on the characterization of the binding kinetics of two tethered molecules functionalized to a hard surface. Using a mean-field approximation, the binding time of such bimolecular system is determined analytically. Furthermore, estimates of the grafting site separation and polymer lengths which expedite binding are provided. These estimates, along with the analytical theories and frameworks established here, have the potential to improve efficacy in self-assembly methods in DNA nanotechnology and can be extended to more biologically specific endeavors including targeted drug-delivery and molecular sensing.
Collapse
Affiliation(s)
- Kyle Pekar
- Department of Mechanical Engineering, Cleveland State University, Cleveland, Ohio 44115-2214, United States
| | - Robert T Young
- Department of Physics, Cleveland State University, Cleveland, Ohio 44115-2214, United States
| | - Sebastian Sensale
- Department of Physics, Cleveland State University, Cleveland, Ohio 44115-2214, United States
| |
Collapse
|
2
|
Yu B, Chang BS, Loo WS, Dhuey S, O’Reilly P, Ashby PD, Connolly MD, Tikhomirov G, Zuckermann RN, Ruiz R. Nanopatterned Monolayers of Bioinspired, Sequence-Defined Polypeptoid Brushes for Semiconductor/Bio Interfaces. ACS NANO 2024; 18:7411-7423. [PMID: 38412617 PMCID: PMC10938923 DOI: 10.1021/acsnano.3c10204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 02/12/2024] [Accepted: 02/15/2024] [Indexed: 02/29/2024]
Abstract
The ability to control and manipulate semiconductor/bio interfaces is essential to enable biological nanofabrication pathways and bioelectronic devices. Traditional surface functionalization methods, such as self-assembled monolayers (SAMs), provide limited customization for these interfaces. Polymer brushes offer a wider range of chemistries, but choices that maintain compatibility with both lithographic patterning and biological systems are scarce. Here, we developed a class of bioinspired, sequence-defined polymers, i.e., polypeptoids, as tailored polymer brushes for surface modification of semiconductor substrates. Polypeptoids featuring a terminal hydroxyl (-OH) group are designed and synthesized for efficient melt grafting onto the native oxide layer of Si substrates, forming ultrathin (∼1 nm) monolayers. By programming monomer chemistry, our polypeptoid brush platform offers versatile surface modification, including adjustments to surface energy, passivation, preferential biomolecule attachment, and specific biomolecule binding. Importantly, the polypeptoid brush monolayers remain compatible with electron-beam lithographic patterning and retain their chemical characteristics even under harsh lithographic conditions. Electron-beam lithography is used over polypeptoid brushes to generate highly precise, binary nanoscale patterns with localized functionality for the selective immobilization (or passivation) of biomacromolecules, such as DNA origami or streptavidin, onto addressable arrays. This surface modification strategy with bioinspired, sequence-defined polypeptoid brushes enables monomer-level control over surface properties with a large parameter space of monomer chemistry and sequence and therefore is a highly versatile platform to precisely engineer semiconductor/bio interfaces for bioelectronics applications.
Collapse
Affiliation(s)
- Beihang Yu
- The
Molecular Foundry, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Boyce S. Chang
- The
Molecular Foundry, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Whitney S. Loo
- The
Molecular Foundry, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
- Prizker
School of Molecular Engineering, University
of Chicago, Chicago, Illinois 60637, United States
| | - Scott Dhuey
- The
Molecular Foundry, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | | | - Paul D. Ashby
- The
Molecular Foundry, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Michael D. Connolly
- The
Molecular Foundry, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Grigory Tikhomirov
- Department
of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, California 94709, United States
| | - Ronald N. Zuckermann
- The
Molecular Foundry, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Ricardo Ruiz
- The
Molecular Foundry, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| |
Collapse
|
3
|
Martynenko IV, Erber E, Ruider V, Dass M, Posnjak G, Yin X, Altpeter P, Liedl T. Site-directed placement of three-dimensional DNA origami. NATURE NANOTECHNOLOGY 2023; 18:1456-1462. [PMID: 37640908 PMCID: PMC7616159 DOI: 10.1038/s41565-023-01487-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 07/14/2023] [Indexed: 08/31/2023]
Abstract
The combination of lithographic methods with two-dimensional DNA origami self-assembly has led, among others, to the development of photonic crystal cavity arrays and the exploration of sensing nanoarrays where molecular devices are patterned on the sub-micrometre scale. Here we extend this concept to the third dimension by mounting three-dimensional DNA origami onto nanopatterned substrates, followed by silicification to provide hybrid DNA-silica structures exhibiting mechanical and chemical stability and achieving feature sizes in the sub-10-nm regime. Our versatile and scalable method relying on self-assembly at ambient temperatures offers the potential to three-dimensionally position any inorganic and organic components compatible with DNA origami nanoarchitecture, demonstrated here with gold nanoparticles. This way of nanotexturing could provide a route for the low-cost production of complex and three-dimensionally patterned surfaces and integrated devices designed on the molecular level and reaching macroscopic dimensions.
Collapse
Affiliation(s)
- Irina V Martynenko
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany.
| | - Elisabeth Erber
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany
| | - Veronika Ruider
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany
| | - Mihir Dass
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany
| | - Gregor Posnjak
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany
| | - Xin Yin
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany
| | - Philipp Altpeter
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany
| | - Tim Liedl
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany.
| |
Collapse
|
4
|
Luo L, Manda S, Park Y, Demir B, Sanchez J, Anantram MP, Oren EE, Gopinath A, Rolandi M. DNA nanopores as artificial membrane channels for bioprotonics. Nat Commun 2023; 14:5364. [PMID: 37666808 PMCID: PMC10477224 DOI: 10.1038/s41467-023-40870-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 08/14/2023] [Indexed: 09/06/2023] Open
Abstract
Biological membrane channels mediate information exchange between cells and facilitate molecular recognition. While tuning the shape and function of membrane channels for precision molecular sensing via de-novo routes is complex, an even more significant challenge is interfacing membrane channels with electronic devices for signal readout, which results in low efficiency of information transfer - one of the major barriers to the continued development of high-performance bioelectronic devices. To this end, we integrate membrane spanning DNA nanopores with bioprotonic contacts to create programmable, modular, and efficient artificial ion-channel interfaces. Here we show that cholesterol modified DNA nanopores spontaneously and with remarkable affinity span the lipid bilayer formed over the planar bio-protonic electrode surface and mediate proton transport across the bilayer. Using the ability to easily modify DNA nanostructures, we illustrate that this bioprotonic device can be programmed for electronic recognition of biomolecular signals such as presence of Streptavidin and the cardiac biomarker B-type natriuretic peptide, without modifying the biomolecules. We anticipate this robust interface will allow facile electronic measurement and quantification of biomolecules in a multiplexed manner.
Collapse
Affiliation(s)
- Le Luo
- Department of Electrical and Computer Engineering, Jack Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Swathi Manda
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Yunjeong Park
- Department of Electrical and Computer Engineering, Jack Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Busra Demir
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara, 06560, Turkey
- Department of Materials Science and Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara, 06560, Turkey
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Jesse Sanchez
- Department of Electrical and Computer Engineering, Jack Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
- School of Chemical, Biological, and Environmental Engineering, Oregon State University, Corvallis, OR, 97331, USA
| | - M P Anantram
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Ersin Emre Oren
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara, 06560, Turkey
- Department of Materials Science and Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara, 06560, Turkey
| | - Ashwin Gopinath
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Marco Rolandi
- Department of Electrical and Computer Engineering, Jack Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA.
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA.
- Institute for the Biology of Stem Cells, University of California Santa Cruz, Santa Cruz, CA, 95064, USA.
| |
Collapse
|
5
|
Pothineni BK, Grundmeier G, Keller A. Cation-dependent assembly of hexagonal DNA origami lattices on SiO 2 surfaces. NANOSCALE 2023; 15:12894-12906. [PMID: 37462427 DOI: 10.1039/d3nr02926c] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
DNA origami nanostructures have emerged as functional materials for applications in various areas of science and technology. In particular, the transfer of the DNA origami shape into inorganic materials using established silicon lithography methods holds great promise for the fabrication of nanostructured surfaces for nanoelectronics and nanophotonics. Using ordered DNA origami lattices directly assembled on the oxidized silicon surface instead of single nanostructures would enable the fabrication of functional nanopatterned surfaces with macroscopic dimensions. Here, we thus investigate the assembly of hexagonal DNA lattices from DNA origami triangles on RCA-cleaned silicon wafers with hydroxylated surface oxide by time-lapse atomic force microscopy (AFM). Lattice assembly on the SiO2 surface is achieved by a competition of monovalent and divalent cations at elevated temperatures. Ca2+ is found to be superior to Mg2+ in promoting the assembly of ordered lattices, while the presence of Mg2+ rather results in DNA origami aggregation and multilayer formation at the comparably high Na+ concentrations of 200 to 600 mM. Furthermore, Na+ concentration and temperature have a similar effect on lattice order, so that a reduction of temperature can be compensated to some extent by an increase in Na+ concentration. However, even under optimized conditions, the DNA origami lattices assembled on the SiO2 surface exhibit a lower degree of order than equivalent lattices assembled on mica, which is attributed to a higher desorption rate of the DNA origami nanostructures. Even though this high desorption rate also complicates any post-assembly treatment, the formed DNA origami lattices could successfully be transferred into the dry state, which is an important prerequisite for further processing steps.
Collapse
Affiliation(s)
- Bhanu Kiran Pothineni
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098 Paderborn, Germany.
| | - Guido Grundmeier
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098 Paderborn, Germany.
| | - Adrian Keller
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098 Paderborn, Germany.
| |
Collapse
|
6
|
Zhan P, Peil A, Jiang Q, Wang D, Mousavi S, Xiong Q, Shen Q, Shang Y, Ding B, Lin C, Ke Y, Liu N. Recent Advances in DNA Origami-Engineered Nanomaterials and Applications. Chem Rev 2023; 123:3976-4050. [PMID: 36990451 PMCID: PMC10103138 DOI: 10.1021/acs.chemrev.3c00028] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Indexed: 03/31/2023]
Abstract
DNA nanotechnology is a unique field, where physics, chemistry, biology, mathematics, engineering, and materials science can elegantly converge. Since the original proposal of Nadrian Seeman, significant advances have been achieved in the past four decades. During this glory time, the DNA origami technique developed by Paul Rothemund further pushed the field forward with a vigorous momentum, fostering a plethora of concepts, models, methodologies, and applications that were not thought of before. This review focuses on the recent progress in DNA origami-engineered nanomaterials in the past five years, outlining the exciting achievements as well as the unexplored research avenues. We believe that the spirit and assets that Seeman left for scientists will continue to bring interdisciplinary innovations and useful applications to this field in the next decade.
Collapse
Affiliation(s)
- Pengfei Zhan
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Andreas Peil
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Qiao Jiang
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Dongfang Wang
- School
of Biomedical Engineering and Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou 215123, China
| | - Shikufa Mousavi
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Qiancheng Xiong
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
| | - Qi Shen
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
- Department
of Molecular Biophysics and Biochemistry, Yale University, 266
Whitney Avenue, New Haven, Connecticut 06511, United States
| | - Yingxu Shang
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Baoquan Ding
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Chenxiang Lin
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
- Department
of Biomedical Engineering, Yale University, 17 Hillhouse Avenue, New Haven, Connecticut 06511, United States
| | - Yonggang Ke
- Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Na Liu
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
- Max Planck
Institute for Solid State Research, Heisenbergstrasse 1, 70569 Stuttgart, Germany
| |
Collapse
|
7
|
Díaz-Marín CD, Li D, Vázquez-Cosme FJ, Pajovic S, Cha H, Song Y, Kilpatrick C, Vaartstra G, Wilson CT, Boriskina S, Wang EN. Capillary Transfer of Self-Assembled Colloidal Crystals. NANO LETTERS 2023; 23:1888-1896. [PMID: 36802577 DOI: 10.1021/acs.nanolett.2c04896] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Colloidal self-assembly has attracted significant interest in numerous applications including optics, electrochemistry, thermofluidics, and biomolecule templating. To meet the requirements of these applications, numerous fabrication methods have been developed. However, these are limited to narrow ranges of feature sizes, are incompatible with many substrates, and/or have low scalability, significantly limiting the use of colloidal self-assembly. In this work, we study the capillary transfer of colloidal crystals and demonstrate that this approach overcomes these limitations. Enabled by capillary transfer, we fabricate 2D colloidal crystals with nano-to-micro feature sizes spanning 2 orders of magnitude and on typically challenging substrates including those that are hydrophobic, rough, curved, or structured with microchannels. We developed and systemically validated a capillary peeling model, elucidating the underlying transfer physics. Due to its high versatility, good quality, and simplicity, this approach can expand the possibilities of colloidal self-assembly and enhance the performance of applications using colloidal crystals.
Collapse
Affiliation(s)
- Carlos D Díaz-Marín
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Diane Li
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Fernando J Vázquez-Cosme
- Departamento de Ingeniería Mecánica, Universidad de Puerto Rico─Mayagüez, Mayagüez, 00681, Puerto Rico
| | - Simo Pajovic
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Hyeongyun Cha
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Youngsup Song
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Cameron Kilpatrick
- Department of Mechanical Engineering, Stanford University, Stanford, California, 94305, United States
| | - Geoffrey Vaartstra
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Chad T Wilson
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Svetlana Boriskina
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Evelyn N Wang
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
8
|
Ranasinghe DR, Doerk G, Aryal BR, Pang C, Davis RC, Harb JN, Woolley AT. Block copolymer self-assembly to pattern gold nanodots for site-specific placement of DNA origami and attachment of nanomaterials. NANOSCALE 2023; 15:2188-2196. [PMID: 36633155 DOI: 10.1039/d2nr05045e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Directed placement of DNA origami could play a key role in future integrated nanoelectronic devices. Here we demonstrated the site-selective attachment of DNA origami on gold dots formed using a pattern transfer method through block copolymer self-assembly. First, a random copolymer brush layer is grafted on the Si surface and then poly (styrene-b-methylmethacrylate) block copolymer is spin-coated to give a hexagonal nanoarray after annealing. UV irradiation followed by acetic acid etching is used to remove the PMMA, creating cylindrical holes and then oxygen plasma etching removes the random copolymer layer inside those holes. Next, metal evaporation, followed by lift-off creates a gold dot array. We evaluated different ligand functionalization of Au dots, as well as DNA hybridization to attach DNA origami to the nanodots. DNA-coated Au nanorods are assembled on the DNA origami as a step towards creating nanowires and to facilitate electron microscopy characterization of the attachment of DNA origami on these Au nanodots. The DNA hybridization approach showed better DNA attachment to Au nanodots than localization by electrostatic interaction. This work contributes to the understanding of DNA-templated assembly, nanomaterials, and block copolymer nanolithography. Furthermore, the work shows potential for creating DNA-templated nanodevices and their placement in ordered arrays in future nanoelectronics.
Collapse
Affiliation(s)
| | - Gregory Doerk
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, USA
| | - Basu R Aryal
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA.
| | - Chao Pang
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA.
| | - Robert C Davis
- Department of Physics and Astronomy, Brigham Young University, Provo, UT, USA
| | - John N Harb
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Adam T Woolley
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA.
| |
Collapse
|
9
|
Yang M, Bakker D, Raghu D, Li ITS. A single strand: A simplified approach to DNA origami. Front Chem 2023; 11:1126177. [PMID: 36891219 PMCID: PMC9986268 DOI: 10.3389/fchem.2023.1126177] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 01/30/2023] [Indexed: 02/22/2023] Open
Abstract
Just as a single polypeptide strand can self-fold into a complex 3D structure, a single strand of DNA can self-fold into DNA origami. Most DNA origami structures (i.e., the scaffold-staple and DNA tiling systems) utilize hundreds of short single-stranded DNA. As such, these structures come with challenges inherent to intermolecular construction. Many assembly challenges involving intermolecular interactions can be resolved if the origami structure is constructed from one DNA strand, where folding is not concentration dependent, the folded structure is more resistant to nuclease degradation, and the synthesis can be achieved at an industrial scale at a thousandth of the cost. This review discusses the design principles and considerations employed in single-stranded DNA origami and its potential benefits and drawbacks.
Collapse
Affiliation(s)
- Micah Yang
- Department of Chemistry, The University of British Columbia, Kelowna, BC, Canada
| | - David Bakker
- Department of Chemistry, The University of British Columbia, Kelowna, BC, Canada
| | - Dyuti Raghu
- Department of Chemistry, The University of British Columbia, Kelowna, BC, Canada
| | - Isaac T S Li
- Department of Chemistry, The University of British Columbia, Kelowna, BC, Canada
| |
Collapse
|
10
|
Lu B, Vecchioni S, Ohayon YP, Canary JW, Sha R. The wending rhombus: Self-assembling 3D DNA crystals. Biophys J 2022; 121:4759-4765. [PMID: 36004779 PMCID: PMC9808540 DOI: 10.1016/j.bpj.2022.08.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/11/2022] [Accepted: 08/16/2022] [Indexed: 01/07/2023] Open
Abstract
In this perspective, we provide a summary of recent developments in self-assembling three-dimensional (3D) DNA crystals. Starting from the inception of this subfield, we describe the various advancements in structure that have led to an increase in the diversity of macromolecular crystal motifs formed through self-assembly, and we further comment on the future directions of the field, which exploit noncanonical base pairing interactions beyond Watson-Crick. We then survey the current applications of self-assembling 3D DNA crystals in reversibly active nanodevices and materials engineering and provide an outlook on the direction researchers are taking these structures. Finally, we compare 3D DNA crystals with DNA origami and suggest how these distinct subfields might work together to enhance biomolecule structure solution, nanotechnological motifs, and their applications.
Collapse
Affiliation(s)
- Brandon Lu
- Department of Chemistry, New York University, New York, New York
| | - Simon Vecchioni
- Department of Chemistry, New York University, New York, New York
| | - Yoel P Ohayon
- Department of Chemistry, New York University, New York, New York
| | - James W Canary
- Department of Chemistry, New York University, New York, New York.
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, New York.
| |
Collapse
|
11
|
Domljanovic I, Loretan M, Kempter S, Acuna GP, Kocabey S, Ruegg C. DNA origami book biosensor for multiplex detection of cancer-associated nucleic acids. NANOSCALE 2022; 14:15432-15441. [PMID: 36219167 PMCID: PMC9612396 DOI: 10.1039/d2nr03985k] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/03/2022] [Indexed: 06/16/2023]
Abstract
DNA nanotechnology provides a promising approach for the development of biomedical point-of-care diagnostic nanoscale devices that are easy to use and cost-effective, highly sensitive and thus constitute an alternative to expensive, complex diagnostic devices. Moreover, DNA nanotechnology-based devices are particularly advantageous for applications in oncology, owing to being ideally suited for the detection of cancer-associated nucleic acids, including circulating tumor-derived DNA fragments (ctDNAs), circulating microRNAs (miRNAs) and other RNA species. Here, we present a dynamic DNA origami book biosensor that is precisely decorated with arrays of fluorophores acting as donors and acceptors and also fluorescence quenchers that produce a strong optical readout upon exposure to external stimuli for the single or dual detection of target oligonucleotides and miRNAs. This biosensor allowed the detection of target molecules either through the decrease of Förster resonance energy transfer (FRET) or an increase in the fluorescence intensity profile owing to a rotation of the constituent top layer of the structure. Single-DNA origami experiments showed that detection of two targets can be achieved simultaneously within 10 min with a limit of detection in the range of 1-10 pM. Overall, our DNA origami book biosensor design showed sensitive and specific detection of synthetic target oligonucleotides and natural miRNAs extracted from cancer cells. Based on these results, we foresee that our DNA origami biosensor may be developed into a cost-effective point-of-care diagnostic strategy for the specific and sensitive detection of a variety of DNAs and RNAs, such as ctDNAs, miRNAs, mRNAs, and viral DNA/RNAs in human samples.
Collapse
Affiliation(s)
- Ivana Domljanovic
- Laboratory of Experimental and Translational Oncology, Department of Oncology, Microbiology and Immunology, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 18, PER17, 1700 Fribourg, Switzerland.
| | - Morgane Loretan
- Photonic Nanosystems, Department of Physics, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 3, PER08, 1700 Fribourg, Switzerland.
| | - Susanne Kempter
- Department of Physics, Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539 Munich, Germany
| | - Guillermo P Acuna
- Photonic Nanosystems, Department of Physics, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 3, PER08, 1700 Fribourg, Switzerland.
| | - Samet Kocabey
- Laboratory of Experimental and Translational Oncology, Department of Oncology, Microbiology and Immunology, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 18, PER17, 1700 Fribourg, Switzerland.
| | - Curzio Ruegg
- Laboratory of Experimental and Translational Oncology, Department of Oncology, Microbiology and Immunology, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 18, PER17, 1700 Fribourg, Switzerland.
| |
Collapse
|
12
|
Dunn KE, Elfick A. Harnessing DNA Nanotechnology and Chemistry for Applications in Photonics and Electronics. Bioconjug Chem 2022; 34:97-104. [PMID: 36121896 PMCID: PMC9853499 DOI: 10.1021/acs.bioconjchem.2c00286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Many photonic and electronic devices rely on nanotechnology and nanofabrication, but DNA-based approaches have yet to make a significant commercial impact in these fields even though DNA molecules are now well-established as versatile building blocks for nanostructures. As we describe here, DNA molecules can be chemically modified with a wide variety of functional groups enabling nanocargoes to be attached at precisely determined locations. DNA nanostructures can also be used as templates for the growth of inorganic structures. Together, these factors enable the use of DNA nanotechnology for the construction of many novel devices and systems. In this topical review, we discuss four case studies of potential applications in photonics and electronics: carbon nanotube transistors, devices for quantum computing, artificial electromagnetic materials, and enzymatic fuel cells. We conclude by speculating about the barriers to the exploitation of these technologies in real-world settings.
Collapse
|
13
|
Cervantes-Salguero K, Freeley M, Gwyther REA, Jones DD, Chávez JL, Palma M. Single molecule DNA origami nanoarrays with controlled protein orientation. BIOPHYSICS REVIEWS 2022; 3:031401. [PMID: 38505279 PMCID: PMC10903486 DOI: 10.1063/5.0099294] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 07/20/2022] [Indexed: 03/21/2024]
Abstract
The nanoscale organization of functional (bio)molecules on solid substrates with nanoscale spatial resolution and single-molecule control-in both position and orientation-is of great interest for the development of next-generation (bio)molecular devices and assays. Herein, we report the fabrication of nanoarrays of individual proteins (and dyes) via the selective organization of DNA origami on nanopatterned surfaces and with controlled protein orientation. Nanoapertures in metal-coated glass substrates were patterned using focused ion beam lithography; 88% of the nanoapertures allowed immobilization of functionalized DNA origami structures. Photobleaching experiments of dye-functionalized DNA nanostructures indicated that 85% of the nanoapertures contain a single origami unit, with only 3% exhibiting double occupancy. Using a reprogrammed genetic code to engineer into a protein new chemistry to allow residue-specific linkage to an addressable ssDNA unit, we assembled orientation-controlled proteins functionalized to DNA origami structures; these were then organized in the arrays and exhibited single molecule traces. This strategy is of general applicability for the investigation of biomolecular events with single-molecule resolution in defined nanoarrays configurations and with orientational control of the (bio)molecule of interest.
Collapse
Affiliation(s)
- K. Cervantes-Salguero
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - M. Freeley
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - R. E. A. Gwyther
- Division of Molecular Biosciences, School of Biosciences, Main Building, Cardiff University, Cardiff, Wales, United Kingdom
| | - D. D. Jones
- Division of Molecular Biosciences, School of Biosciences, Main Building, Cardiff University, Cardiff, Wales, United Kingdom
| | - J. L. Chávez
- Air Force Research Laboratory, 711th Human Performance Wing, Wright Patterson Air Force Base, Dayton, Ohio 45433-7901, USA
| | - M. Palma
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| |
Collapse
|
14
|
Manuguri S, Nguyen MK, Loo J, Natarajan AK, Kuzyk A. Advancing the Utility of DNA Origami Technique through Enhanced Stability of DNA-Origami-Based Assemblies. Bioconjug Chem 2022; 34:6-17. [PMID: 35984467 PMCID: PMC9853507 DOI: 10.1021/acs.bioconjchem.2c00311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Since its discovery in 2006, the DNA origami technique has revolutionized bottom-up nanofabrication. This technique is simple yet versatile and enables the fabrication of nanostructures of almost arbitrary shapes. Furthermore, due to their intrinsic addressability, DNA origami structures can serve as templates for the arrangement of various nanoscale components (small molecules, proteins, nanoparticles, etc.) with controlled stoichiometry and nanometer-scale precision, which is often beyond the reach of other nanofabrication techniques. Despite the multiple benefits of the DNA origami technique, its applicability is often restricted by the limited stability in application-specific conditions. This Review provides an overview of the strategies that have been developed to improve the stability of DNA-origami-based assemblies for potential biomedical, nanofabrication, and other applications.
Collapse
Affiliation(s)
- Sesha Manuguri
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Minh-Kha Nguyen
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland,Faculty
of Chemical Engineering, Ho Chi Minh City
University of Technology (HCMUT), 268 Ly Thuong Kiet St., Dist. 10, Ho Chi Minh
City 70000, Vietnam,Vietnam
National University Ho Chi Minh City, Linh Trung Ward, Thu Duc Dist., Ho Chi Minh
City 756100, Vietnam
| | - Jacky Loo
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Ashwin Karthick Natarajan
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Anton Kuzyk
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland,
| |
Collapse
|
15
|
Kabusure KM, Piskunen P, Yang J, Kataja M, Chacha M, Ojasalo S, Shen B, Hakala TK, Linko V. Optical characterization of DNA origami-shaped silver nanoparticles created through biotemplated lithography. NANOSCALE 2022; 14:9648-9654. [PMID: 35718875 DOI: 10.1039/d1nr06256e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Here, we study optically resonant substrates fabricated using the previously reported BLIN (biotemplated lithography of inorganic nanostructures) technique with single triangle and bowtie DNA origami as templates. We present the first optical characterization of BLIN-fabricated origami-shaped silver nanoparticle patterns on glass surfaces, comprising optical transmission measurements and surface-enhanced Raman spectroscopy. The formed nanoparticle patterns are examined by optical transmission measurements and used for surface enhanced Raman spectroscopy (SERS) of Rhodamine 6G (R6G) dye molecules. Polarization-resolved simulations reveal that the higher SERS enhancement observed for the bowties is primarily due to spectral overlap of the optical resonances with the Raman transitions of R6G. The results manifest the applicability of the BLIN method and substantiate its potential in parallel and high-throughput substrate manufacturing with engineered optical properties. While the results demonstrate the crucial role of the formed nanogaps for SERS, the DNA origami may enable even more complex nanopatterns for various optical applications.
Collapse
Affiliation(s)
- Kabusure M Kabusure
- Department of Physics and Mathematics, University of Eastern Finland, Yliopistokatu 2, P.O Box 111, FI-80101, Joensuu, Finland.
| | - Petteri Piskunen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, FI-00076, Aalto, Finland.
| | - Jiaqi Yang
- Department of Physics and Mathematics, University of Eastern Finland, Yliopistokatu 2, P.O Box 111, FI-80101, Joensuu, Finland.
| | - Mikko Kataja
- Department of Physics and Mathematics, University of Eastern Finland, Yliopistokatu 2, P.O Box 111, FI-80101, Joensuu, Finland.
| | - Mwita Chacha
- Department of Physics and Mathematics, University of Eastern Finland, Yliopistokatu 2, P.O Box 111, FI-80101, Joensuu, Finland.
| | - Sofia Ojasalo
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, FI-00076, Aalto, Finland.
| | - Boxuan Shen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, FI-00076, Aalto, Finland.
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17165 Stockholm, Sweden
| | - Tommi K Hakala
- Department of Physics and Mathematics, University of Eastern Finland, Yliopistokatu 2, P.O Box 111, FI-80101, Joensuu, Finland.
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, FI-00076, Aalto, Finland.
- LIBER Center of Excellence, Aalto University, P.O. Box 16100, FI-00076, Aalto, Finland
| |
Collapse
|
16
|
Microarrays towards nanoarrays and the future Next Generation of Sequencing methodologies (NGS). SENSING AND BIO-SENSING RESEARCH 2022. [DOI: 10.1016/j.sbsr.2022.100503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
|
17
|
Vittala SK, Zhao Y, Han D. Programmed Assembly of DNA Templates by Silver Nanowires. Chempluschem 2022; 87:e202100478. [PMID: 35014201 DOI: 10.1002/cplu.202100478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/20/2021] [Indexed: 12/16/2022]
Abstract
DNA origami templates are known to exhibit many advantages to integrate functional components at desirable locations for nanoelectronic applications. In order to immobilize conducting or semiconducting species in a bottom-up approach, the programmed assembly of DNA templates is of utmost necessity. This report demonstrates the silver nanowires enabled bridging of two linear DNA origami (DO) nanostructures by utilizing the host-guest interaction of biotin-STV and sequence-specific silver metallization of poly(dG-dC) DNA nanowires (in 10 % yield) using (dA)10 coated AgNPs (15 nm). The enzymatic synthesis of 750 bp, 1500 bp and 3000 bp bis-biotinylated poly(dG-dC), facile synthesis of 1 : 1 biotin-STV and silver-nanowire bridged DNA templates were characterized by gel electrophoresis, atomic force microscope imaging techniques. The strategy utilized here provides a method that can precisely connect heterogeneous templates towards bottom-up fabrication of practical nanoelectronics.
Collapse
Affiliation(s)
- Sandeepa K Vittala
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
| | - Yumeng Zhao
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
| | - Da Han
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
| |
Collapse
|
18
|
Heuer-Jungemann A, Linko V. Engineering Inorganic Materials with DNA Nanostructures. ACS CENTRAL SCIENCE 2021; 7:1969-1979. [PMID: 34963890 PMCID: PMC8704036 DOI: 10.1021/acscentsci.1c01272] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Indexed: 05/25/2023]
Abstract
Nucleic acid nanotechnology lays a foundation for the user-friendly design and synthesis of DNA frameworks of any desirable shape with extreme accuracy and addressability. Undoubtedly, such features make these structures ideal modules for positioning and organizing molecules and molecular components into complex assemblies. One of the emerging concepts in the field is to create inorganic and hybrid materials through programmable DNA templates. Here, we discuss the challenges and perspectives of such DNA nanostructure-driven materials science engineering and provide insights into the subject by introducing various DNA-based fabrication techniques including metallization, mineralization, lithography, casting, and hierarchical self-assembly of metal nanoparticles.
Collapse
Affiliation(s)
- Amelie Heuer-Jungemann
- Max
Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
- Center
for Nanoscience, Ludwig-Maximilians University, 80539 Munich, Germany
| | - Veikko Linko
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
| |
Collapse
|
19
|
Díaz-Marín CD, Shetty RM, Cheung S, Vaartstra G, Gopinath A, Wang EN. Rational Fabrication of Nano-to-Microsphere Polycrystalline Opals Using Slope Self-Assembly. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:12568-12576. [PMID: 34672609 DOI: 10.1021/acs.langmuir.1c01857] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Self-assembly of artificial opals has garnered significant interest as a facile nanofabrication technique capable of producing highly ordered structures for optical, electrochemical, biomolecular, and thermal applications. In these applications, the optimum opal particle diameter can vary by several orders of magnitude because the properties of the resultant structures depend strongly on the feature size. However, current opal fabrication techniques only produce high-quality structures over a limited range of sphere sizes or require complex processes and equipment. In this work, the rational and simple fabrication of polycrystalline opals with diameters between 500 nm and 10 μm was demonstrated using slope self-assembly of colloids suspended in ethanol-water. The role of the various process parameters was elucidated through a scaling-based model that accurately captures the variations of opal substrate coverage for spheres of size 2 μm or smaller. For spheres of 10 μm and larger, capillary forces were shown to play a key role in the process dynamics. Based on these insights, millimeter-scale monolayered opals were successfully fabricated, while centimeter-scale opals were possible with sparse sphere stacking or small uncovered areas. These insights provide a guide for the simple and fast fabrication of opals that can be used as optical coatings, templates for high power density electrodes, molecule templates, and high-performance thermo-fluidic devices.
Collapse
Affiliation(s)
- Carlos D Díaz-Marín
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Rishabh M Shetty
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Samantha Cheung
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Geoffrey Vaartstra
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ashwin Gopinath
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Evelyn N Wang
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
20
|
Martynenko IV, Ruider V, Dass M, Liedl T, Nickels PC. DNA Origami Meets Bottom-Up Nanopatterning. ACS NANO 2021; 15:10769-10774. [PMID: 34255962 PMCID: PMC8320526 DOI: 10.1021/acsnano.1c04297] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
DNA origami has emerged as a powerful molecular breadboard with nanometer resolution that can integrate the world of bottom-up (bio)chemistry with large-scale, macroscopic devices created by top-down lithography. Substituting the top-down patterning with self-assembled colloidal nanoparticles now takes the manufacturing complexity of top-down lithography out of the equation. As a result, the deterministic positioning of single molecules or nanoscale objects on macroscopic arrays is benchtop ready and easily accessible.
Collapse
Affiliation(s)
- Irina V. Martynenko
- Faculty of Physics and Center for NanoScience (CeNS)
Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1,
80539 Munich, Germany
| | - Veronika Ruider
- Faculty of Physics and Center for NanoScience (CeNS)
Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1,
80539 Munich, Germany
| | - Mihir Dass
- Faculty of Physics and Center for NanoScience (CeNS)
Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1,
80539 Munich, Germany
| | - Tim Liedl
- Faculty of Physics and Center for NanoScience (CeNS)
Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1,
80539 Munich, Germany
| | - Philipp C. Nickels
- Faculty of Physics and Center for NanoScience (CeNS)
Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1,
80539 Munich, Germany
| |
Collapse
|