1
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Sun C, Li M, Wang F. Programming and monitoring surface-confined DNA computing. Bioorg Chem 2024; 143:107080. [PMID: 38183684 DOI: 10.1016/j.bioorg.2023.107080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/19/2023] [Accepted: 12/28/2023] [Indexed: 01/08/2024]
Abstract
DNA-based molecular computing has evolved to encompass a diverse range of functions, demonstrating substantial promise for both highly parallel computing and various biomedical applications. Recent advances in DNA computing systems based on surface reactions have demonstrated improved levels of specificity and computational speed compared to their solution-based counterparts that depend on three-dimensional molecular collisions. Herein, computational biomolecular interactions confined by various surfaces such as DNA origamis, nanoparticles, lipid membranes and chips are systematically reviewed, along with their manipulation methodologies. Monitoring techniques and applications for these surface-based computing systems are also described. The advantages and challenges of surface-confined DNA computing are discussed.
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Affiliation(s)
- Chenyun Sun
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mingqiang Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Fei Wang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China.
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2
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Qiao YP, Ren CL. Correlated Hybrid DNA Structures Explored by the oxDNA Model. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:109-117. [PMID: 38154122 DOI: 10.1021/acs.langmuir.3c02231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2023]
Abstract
Thermodynamically, perfect DNA hybridization can be formed between probes and their corresponding targets due to the favorable energy. However, this is not the case dynamically. Here, we use molecular dynamics (MD) simulations based on the oxDNA model to investigate the process of DNA microarray hybridization. In general, correlated hybrid DNA structures are formed, including one probe associated with several targets as well as one target hybrid with multiple probes leading to the target-mediated hybridization. The formation of these two types of correlated structures largely depends on the surface coverage of the DNA microarray. Moreover, DNA sequence, DNA length, and spacer length have an impact on the structural formation. Our findings shed light on the dynamics of DNA hybridization, which is important for the application of DNA microarray.
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Affiliation(s)
- Ye-Peng Qiao
- National Laboratory of Solid State Microstructures and Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Chun-Lai Ren
- National Laboratory of Solid State Microstructures and Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
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3
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Suh S, Xing Y, Rottensteiner A, Zhu R, Oh YJ, Howorka S, Hinterdorfer P. Molecular Recognition in Confined Space Elucidated with DNA Nanopores and Single-Molecule Force Microscopy. NANO LETTERS 2023; 23:4439-4447. [PMID: 37166380 PMCID: PMC10214486 DOI: 10.1021/acs.nanolett.3c00743] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/24/2023] [Indexed: 05/12/2023]
Abstract
The binding of ligands to receptors within a nanoscale small space is relevant in biology, biosensing, and affinity filtration. Binding in confinement can be studied with biological systems but under the limitation that essential parameters cannot be easily controlled including receptor type and position within the confinement and its dimensions. Here we study molecular recognition with a synthetic confined nanopore with controllable pore dimension and molecular DNA receptors at different depth positions within the channel. Binding of a complementary DNA strand is studied at the single-molecule level with atomic force microscopy. Following the analysis, kinetic association rates are lower for receptors positioned deeper inside the pore lumen while dissociation is faster and requires less force. The phenomena are explained by the steric constraints on molecular interactions in confinement. Our study is the first to explore recognition in DNA nanostructures with atomic force microscopy and lays out new tools to further quantify the effect of nanoconfinement on molecular interactions.
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Affiliation(s)
- Saanfor
Hubert Suh
- Department
of Applied Experimental Biophysics, Johannes
Kepler University Linz, Institute of Biophysics, Gruberstr. 40, 4020 Linz, Austria
| | - Yongzheng Xing
- Department
of Chemistry, University College London,
Institute of Structural and Molecular Biology, 20 Gordon Street, London WC1H OAJ, United Kingdom
| | - Alexia Rottensteiner
- Department
of Chemistry, University College London,
Institute of Structural and Molecular Biology, 20 Gordon Street, London WC1H OAJ, United Kingdom
| | - Rong Zhu
- Department
of Applied Experimental Biophysics, Johannes
Kepler University Linz, Institute of Biophysics, Gruberstr. 40, 4020 Linz, Austria
| | - Yoo Jin Oh
- Department
of Applied Experimental Biophysics, Johannes
Kepler University Linz, Institute of Biophysics, Gruberstr. 40, 4020 Linz, Austria
| | - Stefan Howorka
- Department
of Chemistry, University College London,
Institute of Structural and Molecular Biology, 20 Gordon Street, London WC1H OAJ, United Kingdom
| | - Peter Hinterdorfer
- Department
of Applied Experimental Biophysics, Johannes
Kepler University Linz, Institute of Biophysics, Gruberstr. 40, 4020 Linz, Austria
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4
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Pal N, Walter NG. Using Single-Molecule FRET to Evaluate DNA Nanodevices at Work. Methods Mol Biol 2023; 2639:157-172. [PMID: 37166717 DOI: 10.1007/978-1-0716-3028-0_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The observation of DNA nanodevices at a single molecule (i.e., device) level and in real time provides rich information that is typically masked in ensemble measurements. Single-molecule fluorescence resonance energy transfer (smFRET) offers a means to directly follow dynamic conformational or compositional changes that DNA nanodevices undergo while operating, thereby retrieving insights critical for refining them toward optimal function. To be successful, smFRET measurements require careful execution and meticulous data analysis for robust statistics. Here we outline the elemental steps for smFRET experiments on DNA nanodevices, starting from microscope slide preparation for single-molecule observation to data acquisition and analysis.
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Affiliation(s)
- Nibedita Pal
- Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, Andhra Pradesh, India.
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
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5
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6
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Pal N. Single-Molecule FRET: A Tool to Characterize DNA Nanostructures. Front Mol Biosci 2022; 9:835617. [PMID: 35330798 PMCID: PMC8940195 DOI: 10.3389/fmolb.2022.835617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/14/2022] [Indexed: 11/17/2022] Open
Abstract
DNA nanostructures often involve temporally evolving spatial features. Tracking these temporal behaviors in real time requires sophisticated experimental methods with sufficiently high spatial and temporal resolution. Among the several strategies developed for this purpose, single-molecule FRET (smFRET) offers avenues to observe the structural rearrangement or locomotion of DNA nanostructures in real time and quantitatively measure the kinetics as well at the single nanostructure level. In this mini review, we discuss a few applications of smFRET-based techniques to study DNA nanostructures. These examples exemplify how smFRET signals not only have played an important role in the characterization of the nanostructures but also often have helped to improve the design and overall performance of the nanostructures and the devices designed from those structures. Overall, this review consolidates the potential of smFRET in providing crucial quantitative information on structure–function relations in DNA nanostructures.
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7
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DNA hybridisation kinetics using single-molecule fluorescence imaging. Essays Biochem 2021; 65:27-36. [PMID: 33491734 PMCID: PMC8056036 DOI: 10.1042/ebc20200040] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/17/2020] [Accepted: 12/21/2020] [Indexed: 01/05/2023]
Abstract
Deoxyribonucleic acid (DNA) hybridisation plays a key role in many biological processes and nucleic acid biotechnologies, yet surprisingly there are many aspects about the process which are still unknown. Prior to the invention of single-molecule microscopy, DNA hybridisation experiments were conducted at the ensemble level, and thus it was impossible to directly observe individual hybridisation events and understand fully the kinetics of DNA hybridisation. In this mini-review, recent single-molecule fluorescence-based studies of DNA hybridisation are discussed, particularly for short nucleic acids, to gain more insight into the kinetics of DNA hybridisation. As well as looking at single-molecule studies of intrinsic and extrinsic factors affecting DNA hybridisation kinetics, the influence of the methods used to detect hybridisation of single DNAs is considered. Understanding the kinetics of DNA hybridisation not only gives insight into an important biological process but also allows for further advancements in the growing field of nucleic acid biotechnology.
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8
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Mann VR, Manea F, Borys NJ, Ajo-Franklin CM, Cohen BE. Controlled and Stable Patterning of Diverse Inorganic Nanocrystals on Crystalline Two-Dimensional Protein Arrays. Biochemistry 2021; 60:1063-1074. [PMID: 33691067 DOI: 10.1021/acs.biochem.1c00032] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Controlled patterning of nanoparticles on bioassemblies enables synthesis of complex materials for applications in optics, nanoelectronics, and sensing. Biomolecular self-assembly offers molecular control for engineering patterned nanomaterials, but current approaches have been limited in their ability to combine high nanoparticle coverage with generality that enables incorporation of multiple nanoparticle types. Here, we synthesize photonic materials on crystalline two-dimensional (2D) protein sheets using orthogonal bioconjugation reactions, organizing quantum dots (QDs), gold nanoparticles (AuNPs), and upconverting nanoparticles along the surface-layer (S-layer) protein SbsB from the extremophile Geobacillus stearothermophilus. We use electron and optical microscopy to show that isopeptide bond-forming SpyCatcher and SnoopCatcher systems enable the simultaneous and controlled conjugation of multiple types of nanoparticles (NPs) at high densities along the SbsB sheets. These NP conjugation reactions are orthogonal to each other and to Au-thiol bond formation, allowing tailorable nanoparticle combinations at sufficient labeling efficiencies to permit optical interactions between nanoparticles. Fluorescence lifetime imaging of SbsB sheets conjugated to QDs and AuNPs at distinct attachment sites shows spatially heterogeneous QD emission, with shorter radiative decays and brighter fluorescence arising from plasmonic enhancement at short interparticle distances. This specific, stable, and efficient conjugation of NPs to 2D protein sheets enables the exploration of interactions between pairs of nanoparticles at defined distances for the engineering of protein-based photonic nanomaterials.
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9
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Toward a Quantitative Relationship between Nanoscale Spatial Organization and Hybridization Kinetics of Surface Immobilized Hairpin DNA Probes. ACS Sens 2021; 6:371-379. [PMID: 32945167 DOI: 10.1021/acssensors.0c01278] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Hybridization of DNA probes immobilized on a solid support is a key process for DNA biosensors and microarrays. Although the surface environment is known to influence the kinetics of DNA hybridization, so far it has not been possible to quantitatively predict how hybridization kinetics is influenced by the complex interactions of the surface environment. Using spatial statistical analysis of probes and hybridized target molecules on a few electrochemical DNA (E-DNA) sensors, functioning through hybridization-induced conformational change of redox-tagged hairpin probes, we developed a phenomenological model that describes how the hybridization rates for single probe molecules are determined by the local environment. The predicted single-molecule rate constants, upon incorporation into numerical simulation, reproduced the overall kinetics of E-DNA sensor surfaces at different probe densities and different degrees of probe clustering. Our study showed that the nanoscale spatial organization is a major factor behind the counterintuitive trends in hybridization kinetics. It also highlights the importance of models that can account for heterogeneity in surface hybridization. The molecular level understanding of hybridization at surfaces and accurate prediction of hybridization kinetics may lead to new opportunities in development of more sensitive and reproducible DNA biosensors and microarrays.
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10
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Auer A, Strauss MT, Strauss S, Jungmann R. nanoTRON: a Picasso module for MLP-based classification of super-resolution data. Bioinformatics 2020; 36:3620-3622. [PMID: 32145010 PMCID: PMC7267816 DOI: 10.1093/bioinformatics/btaa154] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/13/2020] [Accepted: 03/03/2020] [Indexed: 01/01/2023] Open
Abstract
Motivation Classification of images is an essential task in higher-level analysis of biological data. By bypassing the diffraction limit of light, super-resolution microscopy opened up a new way to look at molecular details using light microscopy, producing large amounts of data with exquisite spatial detail. Statistical exploration of data usually needs initial classification, which is up to now often performed manually. Results We introduce nanoTRON, an interactive open-source tool, which allows super-resolution data classification based on image recognition. It extends the software package Picasso with the first deep learning tool with a graphic user interface. Availability and implementation nanoTRON is written in Python and freely available under the MIT license as a part of the software collection Picasso on GitHub (http://www.github.com/jungmannlab/picasso). All raw data can be obtained from the authors upon reasonable request. Contact jungmann@biochem.mpg.de Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Alexander Auer
- Department of Physics and Center for Nanoscience, Ludwig Maximilian University, 80539 Munich, Germany.,Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | | | - Sebastian Strauss
- Department of Physics and Center for Nanoscience, Ludwig Maximilian University, 80539 Munich, Germany.,Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Ralf Jungmann
- Department of Physics and Center for Nanoscience, Ludwig Maximilian University, 80539 Munich, Germany.,Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
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11
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Cai S, Deng Y, Fu S, Li J, Yu C, Su X. Single-molecule dynamic DNA junctions for engineering robust molecular switches. Chem Sci 2019; 10:9922-9927. [PMID: 32110309 PMCID: PMC7006622 DOI: 10.1039/c9sc03389k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 10/04/2019] [Indexed: 12/23/2022] Open
Abstract
DNA molecular switches have emerged as a versatile and highly programmable toolbox and are extensively used in sensing, diagnosis, and therapeutics. Toehold mediated strand displacement serves as the core reaction for signal transduction and amplification. However, the severe leakage of this reaction limits the development of scalable and robust circuits. We engineered single-molecule dynamic DNA junctions for developing 'zero-leakage' molecular switches which are responsive to various inputs. Input binding enhances dynamic junctions' stability allowing for the transient binding of fluorescent probes as the output signal. Unlike the conventional intensity-based output, this molecular switch provides remarkably distinguishable kinetics-based outputs permitting ruling out leakage signals at the single-molecule level. The inputs are detected with significant sensitivity without using any amplification step. It is also revealed that the output signal is sensitive to the binding affinity of inputs and their recognition elements making the molecular switch a potential affinity meter. Considering these features, we anticipate that it would find broad applications in large-scale DNA circuits, responsive materials, and biomolecule interaction study.
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Affiliation(s)
- Shuang Cai
- College of Life Science and Technology , Beijing University of Chemical Technology , Beijing 100029 , China .
| | - Yingnan Deng
- College of Life Science and Technology , Beijing University of Chemical Technology , Beijing 100029 , China .
| | - Shengnan Fu
- College of Life Science and Technology , Beijing University of Chemical Technology , Beijing 100029 , China .
| | - Junjie Li
- College of Life Science and Technology , Beijing University of Chemical Technology , Beijing 100029 , China .
| | - Changyuan Yu
- College of Life Science and Technology , Beijing University of Chemical Technology , Beijing 100029 , China .
| | - Xin Su
- College of Life Science and Technology , Beijing University of Chemical Technology , Beijing 100029 , China .
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12
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Traeger JC, Lamberty Z, Schwartz DK. Influence of Oligonucleotide Grafting Density on Surface-Mediated DNA Transport and Hybridization. ACS NANO 2019; 13:7850-7859. [PMID: 31244029 DOI: 10.1021/acsnano.9b02157] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Adsorption of soluble DNA to surfaces decorated with complementary DNA plays an important role in many bionanotechnology applications, and previous studies have reported complex dependencies of the surface density of immobilized DNA on hybridization. While these effects have been speculatively ascribed to steric or electrostatic effects, the influence of surface-mediated molecular transport (i.e., intermittent "hopping diffusion") has not been fully appreciated. Here, single-molecule tracking and Förster resonance energy transfer (FRET) were employed to characterize the mobility and the hybridization efficiency of adsorbed ssDNA oligonucleotides ("target") at solid-liquid interfaces exhibiting surface-immobilized ssDNA ("probe") over a wide range of surface grafting densities. Two distinct regimes were observed, with qualitatively different transport and hybridization behaviors. At dilute grafting density, only 1-3% of target molecules were observed to associate with probes (i.e., to hybridize). Adsorbing target molecules often searched unsuccessfully and "flew", via desorption-mediated diffusion, to secondary locations before hybridizing. In contrast, at high probe grafting density, approximately 20% of target DNA hybridized to immobilized probes, and almost always in the vicinity of initial adsorption. Moreover, following a dehybridization event, target molecules rehybridized at high probe density, but rehybridization was infrequent in the dilute density regime. Interestingly, the intermittent interfacial transport of mobile target molecules was suppressed by the presence of immobilized probe DNA, presumably due to an increased probability of readsorption following each "hop". Together, these findings suggested that many salient effects of grafting density on surface-mediated DNA hybridization can be directly related to the mechanisms of surface-mediated intermittent diffusion.
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Affiliation(s)
- Jeremiah C Traeger
- Department of Chemical and Biological Engineering , University of Colorado Boulder , Boulder , Colorado 80309 , United States
| | - Zachary Lamberty
- Department of Chemical and Biological Engineering , University of Colorado Boulder , Boulder , Colorado 80309 , United States
| | - Daniel K Schwartz
- Department of Chemical and Biological Engineering , University of Colorado Boulder , Boulder , Colorado 80309 , United States
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13
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Zhang Y, Deng Y, Wang C, Li L, Xu L, Yu Y, Su X. Probing and regulating the activity of cellular enzymes by using DNA tetrahedron nanostructures. Chem Sci 2019; 10:5959-5966. [PMID: 31360402 PMCID: PMC6566069 DOI: 10.1039/c9sc01912j] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 05/03/2019] [Indexed: 01/14/2023] Open
Abstract
Given the essential role of apurinic/apyrimidinic endonuclease (APE1) in gene repair and cancer progression, we report a novel approach for probing and regulating cellular APE1 activity by using DNA tetrahedrons.
Given the essential role of apurinic/apyrimidinic endonuclease (APE1) in gene repair and cancer progression, we report a novel approach for probing and regulating cellular APE1 activity by using DNA tetrahedrons. The tetrahedron with an AP site-containing antenna exhibits high sensitivity and specificity to APE1. It is suitable for APE1 in vitro detection (detection limit 5 pM) and cellular fluorescence imaging without any auxiliary transfection reagents, which discriminates the APE1 expression level of cancer cells and normal cells. In contrast, the tetrahedron with an AP site on its scaffold exhibits high binding affinity to APE1 but limits enzymatic catalysis making this nanostructure an APE1 inhibitor with an IC50 of 14.8 nM. It suppresses the APE1 activity in living cells and sensitizes cancer cells to anticancer drugs. We also demonstrate that the APE1 probe and inhibitor can be switched allosterically via stand displacement, which holds potential for reversible inhibition of APE1. Our approach provides a new way for fabricating enzyme probes and regulators and new insights into enzyme–substrate interactions, and it can be expanded to regulate other nucleic acid related enzymes.
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Affiliation(s)
- Yi Zhang
- College of Life Science and Technology , Beijing University of Chemical Technology , Beijing 100029 , China .
| | - Yingnan Deng
- College of Life Science and Technology , Beijing University of Chemical Technology , Beijing 100029 , China .
| | - Congshan Wang
- College of Life Science and Technology , Beijing University of Chemical Technology , Beijing 100029 , China .
| | - Lidan Li
- College of Life Science and Technology , Beijing University of Chemical Technology , Beijing 100029 , China .
| | - Lida Xu
- College of Life Science and Technology , Beijing University of Chemical Technology , Beijing 100029 , China .
| | - Yingjie Yu
- Department of Biomedical Engineering , Tufts University , Medford , MA 02155 , USA .
| | - Xin Su
- College of Life Science and Technology , Beijing University of Chemical Technology , Beijing 100029 , China .
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14
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Choi Y, Schmidt C, Tinnefeld P, Bald I, Rödiger S. A new reporter design based on DNA origami nanostructures for quantification of short oligonucleotides using microbeads. Sci Rep 2019; 9:4769. [PMID: 30886341 PMCID: PMC6423227 DOI: 10.1038/s41598-019-41136-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 02/28/2019] [Indexed: 01/05/2023] Open
Abstract
The DNA origami technique has great potential for the development of brighter and more sensitive reporters for fluorescence based detection schemes such as a microbead-based assay in diagnostic applications. The nanostructures can be programmed to include multiple dye molecules to enhance the measured signal as well as multiple probe strands to increase the binding strength of the target oligonucleotide to these nanostructures. Here we present a proof-of-concept study to quantify short oligonucleotides by developing a novel DNA origami based reporter system, combined with planar microbead assays. Analysis of the assays using the VideoScan digital imaging platform showed DNA origami to be a more suitable reporter candidate for quantification of the target oligonucleotides at lower concentrations than a conventional reporter that consists of one dye molecule attached to a single stranded DNA. Efforts have been made to conduct multiplexed analysis of different targets as well as to enhance fluorescence signals obtained from the reporters. We therefore believe that the quantification of short oligonucleotides that exist in low copy numbers is achieved in a better way with the DNA origami nanostructures as reporters.
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Affiliation(s)
- Youngeun Choi
- University of Potsdam, Department of Chemistry, Physical Chemistry, 14476, Potsdam, Germany.,BAM Federal Institute for Materials Research and Testing, 12489, Berlin, Germany
| | - Carsten Schmidt
- Brandenbrug University of Technology Cottbus-Senftenberg, Institute of Biotechnology, 01968, Senftenberg, Germany
| | - Philip Tinnefeld
- Department Chemie and Center for NanoScience, Ludwig-Maximilians-Universitaet Muenchen, Butenandtstr, 5-13 Haus E, 81377, Muenchen, Germany
| | - Ilko Bald
- University of Potsdam, Department of Chemistry, Physical Chemistry, 14476, Potsdam, Germany. .,BAM Federal Institute for Materials Research and Testing, 12489, Berlin, Germany.
| | - Stefan Rödiger
- Brandenbrug University of Technology Cottbus-Senftenberg, Institute of Biotechnology, 01968, Senftenberg, Germany.
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15
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Kempter S, Khmelinskaia A, Strauss MT, Schwille P, Jungmann R, Liedl T, Bae W. Single Particle Tracking and Super-Resolution Imaging of Membrane-Assisted Stop-and-Go Diffusion and Lattice Assembly of DNA Origami. ACS NANO 2019; 13:996-1002. [PMID: 30588792 DOI: 10.1021/acsnano.8b04631] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
DNA nanostructures offer the possibility to mimic functional biological membrane components due to their nanometer-precise shape configurability and versatile biochemical functionality. Here we show that the diffusional behavior of DNA nanostructures and their assembly into higher order membrane-bound lattices can be controlled in a stop-and-go manner and that the process can be monitored with super-resolution imaging. The DNA structures are transiently immobilized on glass-supported lipid bilayers by changing the mono- and divalent cation concentrations of the surrounding buffer. Using DNA points accumulation for imaging in nanoscale topography (DNA-PAINT) super-resolution microscopy, we confirm the fixation of DNA origami structures with different shapes. On mica-supported lipid bilayers, in contrast, we observe residual movement. By increasing the concentration of NaCl and depleting MgCl2, a large fraction of DNA structures restarts to diffuse freely on both substrates. After addition of a set of oligonucleotides that enables three Y-shaped monomers to assemble into a three-legged shape (triskelion), the triskelions can be stopped and super-resolved. Exchanging buffer and adding another set of oligonucleotides triggers the triskelions to diffuse and assemble into hexagonal 2D lattices. This stop-and-go imaging technique provides a way to control and observe the diffusional behavior of DNA nanostructures on lipid membranes that could also lead to control of membrane-associated cargos.
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Affiliation(s)
- Susanne Kempter
- Faculty of Physics and Center for NanoScience , Ludwig-Maximilians-Universität , München 80539 , Germany
| | | | - Maximilian T Strauss
- Faculty of Physics and Center for NanoScience , Ludwig-Maximilians-Universität , München 80539 , Germany
- Max Planck Institute of Biochemistry , Martinsried 82152 , Germany
| | - Petra Schwille
- Max Planck Institute of Biochemistry , Martinsried 82152 , Germany
| | - Ralf Jungmann
- Faculty of Physics and Center for NanoScience , Ludwig-Maximilians-Universität , München 80539 , Germany
- Max Planck Institute of Biochemistry , Martinsried 82152 , Germany
| | - Tim Liedl
- Faculty of Physics and Center for NanoScience , Ludwig-Maximilians-Universität , München 80539 , Germany
| | - Wooli Bae
- Faculty of Physics and Center for NanoScience , Ludwig-Maximilians-Universität , München 80539 , Germany
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16
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Shen W, Liu Q, Ding B, Shen Z, Zhu C, Mao C. The study of the paranemic crossover (PX) motif in the context of self-assembly of DNA 2D crystals. Org Biomol Chem 2018; 14:7187-90. [PMID: 27404049 DOI: 10.1039/c6ob01146b] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
This manuscript systematically studies the self-assembly behavior of the paranemic crossover (PX) motif in the context of DNA 2D crystallization. The PX structure is a class of DNA nanomotifs that has been suggested as a model for DNA homologous recognition in cells and, more importantly, used as a cohesion mechanism/building block (tile) for DNA nanoconstruction. However, there is no vigorous examination on the relationship between structural variation and assembly behavior. The lack of this essential information prevents us from applying the PX motif to complex nanoconstruction. In this study, we have devised a system that allows us to systematically examine this relationship and found the best PX motif that best suits the assembly of 2D crystals.
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Affiliation(s)
- Weili Shen
- College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, China.
| | - Qing Liu
- National Center for NanoScience and Technology, ZhongGuanCun, Beijing 100190, China
| | - Baoquan Ding
- National Center for NanoScience and Technology, ZhongGuanCun, Beijing 100190, China
| | - Zhiyong Shen
- College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, China.
| | - Changqing Zhu
- College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, China.
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA.
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17
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Choi Y, Kotthoff L, Olejko L, Resch-Genger U, Bald I. DNA Origami-Based Förster Resonance Energy-Transfer Nanoarrays and Their Application as Ratiometric Sensors. ACS APPLIED MATERIALS & INTERFACES 2018; 10:23295-23302. [PMID: 29916243 DOI: 10.1021/acsami.8b03585] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
DNA origami nanostructures provide a platform where dye molecules can be arranged with nanoscale accuracy allowing to assemble multiple fluorophores without dye-dye aggregation. Aiming to develop a bright and sensitive ratiometric sensor system, we systematically studied the optical properties of nanoarrays of dyes built on DNA origami platforms using a DNA template that provides a high versatility of label choice at minimum cost. The dyes are arranged at distances, at which they efficiently interact by Förster resonance energy transfer (FRET). To optimize array brightness, the FRET efficiencies between the donor fluorescein (FAM) and the acceptor cyanine 3 were determined for different sizes of the array and for different arrangements of the dye molecules within the array. By utilizing nanoarrays providing optimum FRET efficiency and brightness, we subsequently designed a ratiometric pH nanosensor using coumarin 343 as a pH-inert FRET donor and FAM as a pH-responsive acceptor. Our results indicate that the sensitivity of a ratiometric sensor can be improved simply by arranging the dyes into a well-defined array. The dyes used here can be easily replaced by other analyte-responsive dyes, demonstrating the huge potential of DNA nanotechnology for light harvesting, signal enhancement, and sensing schemes in life sciences.
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Affiliation(s)
- Youngeun Choi
- Department of Chemistry, Physical Chemistry , University of Potsdam , 14476 Potsdam , Germany
- BAM Federal Institute for Materials Research and Testing , 12489 Berlin , Germany
- School of Analytical Sciences Adlershof , Humboldt-Universität zu Berlin , 10099 Berlin , Germany
| | - Lisa Kotthoff
- Department of Chemistry, Physical Chemistry , University of Potsdam , 14476 Potsdam , Germany
- BAM Federal Institute for Materials Research and Testing , 12489 Berlin , Germany
| | - Lydia Olejko
- Department of Chemistry, Physical Chemistry , University of Potsdam , 14476 Potsdam , Germany
| | - Ute Resch-Genger
- BAM Federal Institute for Materials Research and Testing , 12489 Berlin , Germany
- School of Analytical Sciences Adlershof , Humboldt-Universität zu Berlin , 10099 Berlin , Germany
| | - Ilko Bald
- Department of Chemistry, Physical Chemistry , University of Potsdam , 14476 Potsdam , Germany
- BAM Federal Institute for Materials Research and Testing , 12489 Berlin , Germany
- School of Analytical Sciences Adlershof , Humboldt-Universität zu Berlin , 10099 Berlin , Germany
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18
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Kuzyk A, Jungmann R, Acuna GP, Liu N. DNA Origami Route for Nanophotonics. ACS PHOTONICS 2018; 5:1151-1163. [PMID: 30271812 PMCID: PMC6156112 DOI: 10.1021/acsphotonics.7b01580] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 02/06/2018] [Accepted: 02/11/2018] [Indexed: 05/21/2023]
Abstract
The specificity and simplicity of the Watson-Crick base pair interactions make DNA one of the most versatile construction materials for creating nanoscale structures and devices. Among several DNA-based approaches, the DNA origami technique excels in programmable self-assembly of complex, arbitrary shaped structures with dimensions of hundreds of nanometers. Importantly, DNA origami can be used as templates for assembly of functional nanoscale components into three-dimensional structures with high precision and controlled stoichiometry. This is often beyond the reach of other nanofabrication techniques. In this Perspective, we highlight the capability of the DNA origami technique for realization of novel nanophotonic systems. First, we introduce the basic principles of designing and fabrication of DNA origami structures. Subsequently, we review recent advances of the DNA origami applications in nanoplasmonics, single-molecule and super-resolution fluorescent imaging, as well as hybrid photonic systems. We conclude by outlining the future prospects of the DNA origami technique for advanced nanophotonic systems with tailored functionalities.
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Affiliation(s)
- Anton Kuzyk
- Max
Planck Institute for Intelligent Systems, Heisenbergstrasse 3, D-70569 Stuttgart, Germany
- Department
of Neuroscience and Biomedical Engineering, Aalto University School of Science, P.O. Box 12200, FI-00076 Aalto, Finland
| | - Ralf Jungmann
- Department
of Physics and Center for Nanoscience, Ludwig
Maximilian University, 80539 Munich, Germany
- Max
Planck Institute of Biochemistry, 82152 Martinsried near Munich, Germany
| | - Guillermo P. Acuna
- Institute
for Physical & Theoretical Chemistry, and Braunschweig Integrated
Centre of Systems Biology (BRICS), and Laboratory for Emerging Nanometrology
(LENA), Braunschweig University of Technology, Rebenring 56, 38106 Braunschweig, Germany
| | - Na Liu
- Max
Planck Institute for Intelligent Systems, Heisenbergstrasse 3, D-70569 Stuttgart, Germany
- Kirchhoff
Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, D-69120 Heidelberg, Germany
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19
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Thubagere AJ, Li W, Johnson RF, Chen Z, Doroudi S, Lee YL, Izatt G, Wittman S, Srinivas N, Woods D, Winfree E, Qian L. A cargo-sorting DNA robot. Science 2018; 357:357/6356/eaan6558. [PMID: 28912216 DOI: 10.1126/science.aan6558] [Citation(s) in RCA: 319] [Impact Index Per Article: 53.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 08/07/2017] [Indexed: 12/31/2022]
Abstract
Two critical challenges in the design and synthesis of molecular robots are modularity and algorithm simplicity. We demonstrate three modular building blocks for a DNA robot that performs cargo sorting at the molecular level. A simple algorithm encoding recognition between cargos and their destinations allows for a simple robot design: a single-stranded DNA with one leg and two foot domains for walking, and one arm and one hand domain for picking up and dropping off cargos. The robot explores a two-dimensional testing ground on the surface of DNA origami, picks up multiple cargos of two types that are initially at unordered locations, and delivers them to specified destinations until all molecules are sorted into two distinct piles. The robot is designed to perform a random walk without any energy supply. Exploiting this feature, a single robot can repeatedly sort multiple cargos. Localization on DNA origami allows for distinct cargo-sorting tasks to take place simultaneously in one test tube or for multiple robots to collectively perform the same task.
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Affiliation(s)
| | - Wei Li
- Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Robert F Johnson
- Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Zibo Chen
- Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Shayan Doroudi
- Computer Science, California Institute of Technology, Pasadena, CA 91125, USA
| | - Yae Lim Lee
- Electrical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Gregory Izatt
- Computer Science, California Institute of Technology, Pasadena, CA 91125, USA.,Computation and Neural Systems, California Institute of Technology, Pasadena, CA 91125, USA
| | - Sarah Wittman
- Computer Science, California Institute of Technology, Pasadena, CA 91125, USA
| | - Niranjan Srinivas
- Computation and Neural Systems, California Institute of Technology, Pasadena, CA 91125, USA
| | - Damien Woods
- Computer Science, California Institute of Technology, Pasadena, CA 91125, USA.
| | - Erik Winfree
- Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA.,Computer Science, California Institute of Technology, Pasadena, CA 91125, USA.,Computation and Neural Systems, California Institute of Technology, Pasadena, CA 91125, USA
| | - Lulu Qian
- Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA. .,Computer Science, California Institute of Technology, Pasadena, CA 91125, USA
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20
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Abstract
Far-field super-resolution fluorescence microscopy has allowed observation of biomolecular and synthetic nanoscale systems with features on the nanometre scale, with chemical specificity and multiplexing capability. DNA-PAINT (DNA-based point accumulation for imaging in nanoscale topography) is a super-resolution method that exploits programmable transient hybridization between short oligonucleotide strands, and allows multiplexed, single-molecule, single-label visualization with down to ~5-10 nm resolution. DNA-PAINT provides a method for structural characterisation of nucleic acid nanostructures with high spatial resolution and single-strand visibility.
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Affiliation(s)
- Mingjie Dai
- Wyss Institute for Biologically Inspired Engineering, Harvard University, CLSB 5th Floor, Blackfan Circle, Boston, MA, 02115, USA. .,Program in Biophysics, Harvard University, Boston, MA, 02115, USA.
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21
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Hong F, Zhang F, Liu Y, Yan H. DNA Origami: Scaffolds for Creating Higher Order Structures. Chem Rev 2017; 117:12584-12640. [DOI: 10.1021/acs.chemrev.6b00825] [Citation(s) in RCA: 645] [Impact Index Per Article: 92.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Fan Hong
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Fei Zhang
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Yan Liu
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Hao Yan
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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22
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Qiao C, Wu J, Huang Z, Cao X, Liu J, Xiong B, He Y, Yeung ES. Sequence-Modulated Interactions between Single Multivalent DNA-Conjugated Gold Nanoparticles. Anal Chem 2017; 89:5592-5597. [DOI: 10.1021/acs.analchem.7b00763] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chunyan Qiao
- State
Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry
and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Jia Wu
- State
Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry
and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Zhenrong Huang
- State
Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry
and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Xuan Cao
- State
Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry
and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Jiayu Liu
- State
Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry
and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Bin Xiong
- State
Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry
and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Yan He
- State
Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry
and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
- Department
of Chemistry, Tsinghua University, Beijing, 100084, P. R. China
| | - Edward S. Yeung
- State
Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry
and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
- Department
of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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23
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Real-time reliable determination of binding kinetics of DNA hybridization using a multi-channel graphene biosensor. Nat Commun 2017; 8:14902. [PMID: 28322227 PMCID: PMC5364407 DOI: 10.1038/ncomms14902] [Citation(s) in RCA: 183] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 02/10/2017] [Indexed: 12/12/2022] Open
Abstract
Reliable determination of binding kinetics and affinity of DNA hybridization and single-base mismatches plays an essential role in systems biology, personalized and precision medicine. The standard tools are optical-based sensors that are difficult to operate in low cost and to miniaturize for high-throughput measurement. Biosensors based on nanowire field-effect transistors have been developed, but reliable and cost-effective fabrication remains a challenge. Here, we demonstrate that a graphene single-crystal domain patterned into multiple channels can measure time- and concentration-dependent DNA hybridization kinetics and affinity reliably and sensitively, with a detection limit of 10 pM for DNA. It can distinguish single-base mutations quantitatively in real time. An analytical model is developed to estimate probe density, efficiency of hybridization and the maximum sensor response. The results suggest a promising future for cost-effective, high-throughput screening of drug candidates, genetic variations and disease biomarkers by using an integrated, miniaturized, all-electrical multiplexed, graphene-based DNA array. Monitoring DNA binding and single-base mismatches accurately in real time is difficult, especially for miniaturized devices. Here the authors report a graphene field-effect transistor array capable of reliably measuring DNA hybridization kinetics and affinity at the picomolar level.
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24
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Schlichthaerle T, Strauss MT, Schueder F, Woehrstein JB, Jungmann R. DNA nanotechnology and fluorescence applications. Curr Opin Biotechnol 2016; 39:41-47. [DOI: 10.1016/j.copbio.2015.12.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 12/19/2015] [Indexed: 12/30/2022]
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25
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Saoji M, Zhang D, Paukstelis PJ. Probing the role of sequence in the assembly of three-dimensional DNA crystals. Biopolymers 2016; 103:618-26. [PMID: 26015367 DOI: 10.1002/bip.22688] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 05/21/2015] [Accepted: 05/21/2015] [Indexed: 11/10/2022]
Abstract
DNA is a widely used biopolymer for the construction of nanometer-scale objects due to its programmability and structural predictability. One long-standing goal of the DNA nanotechnology field has been the construction of three-dimensional DNA crystals. We previously determined the X-ray crystal structure of a DNA 13-mer that forms a continuously hydrogen bonded three-dimensional lattice through Watson-Crick and non-canonical base pairs. Our current study sets out to understand how the sequence of the Watson-Crick duplex region influences crystallization of this 13-mer. We screened all possible self-complementary sequences in the hexameric duplex region and found 21 oligonucleotides that crystallized. Sequence analysis showed that one specific Watson-Crick pair influenced the crystallization propensity and the speed of crystal self-assembly. We determined X-ray crystal structures for 13 of these oligonucleotides and found sequence-specific structural changes that suggests that this base pair may serve as a structural anchor during crystal assembly. Finally, we explored the crystal self-assembly and nucleation process. Solution studies indicated that these oligonucleotides do not form base pairs in the absence of cations, but that the addition of divalent cations leads to rapid self-assembly to higher molecular weight complexes. We further demonstrate that crystals grown from mixtures of two different oligonucleotide sequences contain both oligonucleotides. These results suggest that crystal self-assembly is nucleated by the formation of the Watson-Crick duplexes initiated by a simple chemical trigger. This study provides new insight into the role of sequence for the assembly of periodic DNA structures.
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Affiliation(s)
- Maithili Saoji
- Department of Chemistry & Biochemistry, University of Maryland, College Park, MD, 20742
| | - Daoning Zhang
- Department of Chemistry & Biochemistry, University of Maryland, College Park, MD, 20742.,Biomolecular NMR Facility, College Park, MD, 20742
| | - Paul J Paukstelis
- Department of Chemistry & Biochemistry, University of Maryland, College Park, MD, 20742.,Center for Biomolecular Structure & Organization, College Park, MD, 20742.,Maryland Nanocenter, College Park, MD, 20742
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26
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Superresolution microscopy with transient binding. Curr Opin Biotechnol 2016; 39:8-16. [PMID: 26773299 DOI: 10.1016/j.copbio.2015.12.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 12/12/2015] [Accepted: 12/16/2015] [Indexed: 01/05/2023]
Abstract
For single-molecule localization based superresolution, the concentration of fluorescent labels has to be thinned out. This is commonly achieved by photophysically or photochemically deactivating subsets of molecules. Alternatively, apparent switching of molecules can be achieved by transient binding of fluorescent labels. Here, a diffusing dye yields bright fluorescent spots when binding to the structure of interest. As the binding interaction is weak, the labeling is reversible and the dye ligand construct diffuses back into solution. This approach of achieving superresolution by transient binding (STB) is reviewed in this manuscript. Different realizations of STB are discussed and compared to other localization-based superresolution modalities. We propose the development of labeling strategies that will make STB a highly versatile tool for superresolution microscopy at highest resolution.
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27
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Rahbani JF, Hariri AA, Cosa G, Sleiman HF. Dynamic DNA Nanotubes: Reversible Switching between Single and Double-Stranded Forms, and Effect of Base Deletions. ACS NANO 2015; 9:11898-11908. [PMID: 26556531 DOI: 10.1021/acsnano.5b04387] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
DNA nanotubes hold great potential as drug delivery vehicles and as programmable templates for the organization of materials and biomolecules. Existing methods for their construction produce assemblies that are entirely double-stranded and rigid, and thus have limited intrinsic dynamic character, or they rely on chemically modified and ligated DNA structures. Here, we report a simple and efficient synthesis of DNA nanotubes from 11 short unmodified strands, and the study of their dynamic behavior by atomic force microscopy and in situ single molecule fluorescence microscopy. This method allows the programmable introduction of DNA structural changes within the repeat units of the tubes. We generate and study fully double-stranded nanotubes, and convert them to nanotubes with one, two and three single-stranded sides, using strand displacement strategies. The nanotubes can be reversibly switched between these forms without compromising their stability and micron-scale lengths. We then site-specifically introduce DNA strands that shorten two sides of the nanotubes, while keeping the length of the third side. The nanotubes undergo bending with increased length mismatch between their sides, until the distortion is significant enough to shorten them, as measured by AFM and single-molecule fluorescence photobleaching experiments. The method presented here produces dynamic and robust nanotubes that can potentially behave as actuators, and allows their site-specific addressability while using a minimal number of component strands.
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Affiliation(s)
- Janane F Rahbani
- Department of Chemistry and Centre for Self-Assembled Chemical Structures, McGill University , 801 Sherbrooke Street West, Montreal, H3A 0B8, Canada
| | - Amani A Hariri
- Department of Chemistry and Centre for Self-Assembled Chemical Structures, McGill University , 801 Sherbrooke Street West, Montreal, H3A 0B8, Canada
| | - Gonzalo Cosa
- Department of Chemistry and Centre for Self-Assembled Chemical Structures, McGill University , 801 Sherbrooke Street West, Montreal, H3A 0B8, Canada
| | - Hanadi F Sleiman
- Department of Chemistry and Centre for Self-Assembled Chemical Structures, McGill University , 801 Sherbrooke Street West, Montreal, H3A 0B8, Canada
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28
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Pedersen RO, Kong J, Achim C, LaBean TH. Comparative Incorporation of PNA into DNA Nanostructures. Molecules 2015; 20:17645-58. [PMID: 26404232 PMCID: PMC6331967 DOI: 10.3390/molecules200917645] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 09/13/2015] [Accepted: 09/21/2015] [Indexed: 11/16/2022] Open
Abstract
DNA has shown great promise as a building material for self-assembling nanoscale structures. To further develop the potential of this technology, more methods are needed for functionalizing DNA-based nanostructures to increase their chemical diversity. Peptide nucleic acid (PNA) holds great promise for realizing this goal, as it conveniently allows for inclusion of both amino acids and peptides in nucleic acid-based structures. In this work, we explored incorporation of a positively charged PNA within DNA nanostructures. We investigated the efficiency of annealing a lysine-containing PNA probe with complementary, single-stranded DNA sequences within nanostructures, as well as the efficiency of duplex invasion and its dependence on salt concentration. Our results show that PNA allows for toehold-free strand displacement and that incorporation yield depends critically on binding site geometry. These results provide guidance for the design of PNA binding sites on nucleic acid nanostructures with an eye towards optimizing fabrication yield.
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Affiliation(s)
- Ronnie O Pedersen
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708-0354, USA.
| | - Jing Kong
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
| | - Catalina Achim
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
| | - Thomas H LaBean
- Department of Materials Science and Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC 27695-7907, USA.
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29
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Krainer G, Hartmann A, Schlierf M. farFRET: Extending the Range in Single-Molecule FRET Experiments beyond 10 nm. NANO LETTERS 2015; 15:5826-5829. [PMID: 26104104 DOI: 10.1021/acs.nanolett.5b01878] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Single-molecule Förster resonance energy transfer (smFRET) has become a powerful nanoscopic tool in studies of biomolecular structures and nanoscale objects; however, conventional smFRET measurements are generally blind to distances above 10 nm thus impeding the study of long-distance phenomena. Here, we report the development of farFRET, a technique that extends the range in smFRET measurements beyond the 10 nm line by enhanced energy transfer using multiple acceptors. We demonstrate that farFRET can be readily employed to quantify FRET efficiencies and conformational dynamics using double-stranded DNA molecules, RecA-filament formation on single-stranded DNA and Holliday junction dynamics. farFRET allows quantitative measurements of large biomolecular complexes and nanostructures thus bridging the remaining gap to superresolution microscopy.
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Affiliation(s)
- Georg Krainer
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden , Arnoldstraße 18, 01307 Dresden, Germany
- Molecular Biophysics, University of Kaiserslautern , Erwin-Schrödinger-Straße 13, 67663 Kaiserslautern, Germany
| | - Andreas Hartmann
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden , Arnoldstraße 18, 01307 Dresden, Germany
| | - Michael Schlierf
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden , Arnoldstraße 18, 01307 Dresden, Germany
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30
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Mallik L, Dhakal S, Nichols J, Mahoney J, Dosey AM, Jiang S, Sunahara RK, Skiniotis G, Walter NG. Electron Microscopic Visualization of Protein Assemblies on Flattened DNA Origami. ACS NANO 2015; 9:7133-41. [PMID: 26149412 PMCID: PMC5835357 DOI: 10.1021/acsnano.5b01841] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
DNA provides an ideal substrate for the engineering of versatile nanostructures due to its reliable Watson-Crick base pairing and well-characterized conformation. One of the most promising applications of DNA nanostructures arises from the site-directed spatial arrangement with nanometer precision of guest components such as proteins, metal nanoparticles, and small molecules. Two-dimensional DNA origami architectures, in particular, offer a simple design, high yield of assembly, and large surface area for use as a nanoplatform. However, such single-layer DNA origami were recently found to be structurally polymorphous due to their high flexibility, leading to the development of conformationally restrained multilayered origami that lack some of the advantages of the single-layer designs. Here we monitored single-layer DNA origami by transmission electron microscopy (EM) and discovered that their conformational heterogeneity is dramatically reduced in the presence of a low concentration of dimethyl sulfoxide, allowing for an efficient flattening onto the carbon support of an EM grid. We further demonstrated that streptavidin and a biotinylated target protein (cocaine esterase, CocE) can be captured at predesignated sites on these flattened origami while maintaining their functional integrity. Our demonstration that protein assemblies can be constructed with high spatial precision (within ∼2 nm of their predicted position on the platforms) by using strategically flattened single-layer origami paves the way for exploiting well-defined guest molecule assemblies for biochemistry and nanotechnology applications.
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Affiliation(s)
- Leena Mallik
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Soma Dhakal
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Joseph Nichols
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jacob Mahoney
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Anne M. Dosey
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Shuoxing Jiang
- The Biodesign Institute and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Roger K. Sunahara
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Georgios Skiniotis
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Nils G. Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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31
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32
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Fu J, Yang YR, Johnson-Buck A, Liu M, Liu Y, Walter NG, Woodbury NW, Yan H. Multi-enzyme complexes on DNA scaffolds capable of substrate channelling with an artificial swinging arm. NATURE NANOTECHNOLOGY 2014; 9:531-6. [PMID: 24859813 DOI: 10.1038/nnano.2014.100] [Citation(s) in RCA: 341] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 04/14/2014] [Indexed: 05/20/2023]
Abstract
Swinging arms are a key functional component of multistep catalytic transformations in many naturally occurring multi-enzyme complexes. This arm is typically a prosthetic chemical group that is covalently attached to the enzyme complex via a flexible linker, allowing the direct transfer of substrate molecules between multiple active sites within the complex. Mimicking this method of substrate channelling outside the cellular environment requires precise control over the spatial parameters of the individual components within the assembled complex. DNA nanostructures can be used to organize functional molecules with nanoscale precision and can also provide nanomechanical control. Until now, protein-DNA assemblies have been used to organize cascades of enzymatic reactions by controlling the relative distance and orientation of enzymatic components or by facilitating the interface between enzymes/cofactors and electrode surfaces. Here, we show that a DNA nanostructure can be used to create a multi-enzyme complex in which an artificial swinging arm facilitates hydride transfer between two coupled dehydrogenases. By exploiting the programmability of DNA nanostructures, key parameters including position, stoichiometry and inter-enzyme distance can be manipulated for optimal activity.
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Affiliation(s)
- Jinglin Fu
- 1] Center for Molecular Design and Biomimicry, Biodesign Institute at Arizona State University, Tempe, Arizona 85287, USA [2] Center for Innovations in Medicine, Biodesign Institute at Arizona State University, Tempe, Arizona 85287, USA [3] [4]
| | - Yuhe Renee Yang
- 1] Center for Molecular Design and Biomimicry, Biodesign Institute at Arizona State University, Tempe, Arizona 85287, USA [2] Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA [3]
| | - Alexander Johnson-Buck
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan at Ann Arbor, Ann Arbor, Michigan 48109, USA
| | - Minghui Liu
- 1] Center for Molecular Design and Biomimicry, Biodesign Institute at Arizona State University, Tempe, Arizona 85287, USA [2] Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA
| | - Yan Liu
- 1] Center for Molecular Design and Biomimicry, Biodesign Institute at Arizona State University, Tempe, Arizona 85287, USA [2] Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan at Ann Arbor, Ann Arbor, Michigan 48109, USA
| | - Neal W Woodbury
- 1] Center for Innovations in Medicine, Biodesign Institute at Arizona State University, Tempe, Arizona 85287, USA [2] Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA
| | - Hao Yan
- 1] Center for Molecular Design and Biomimicry, Biodesign Institute at Arizona State University, Tempe, Arizona 85287, USA [2] Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA
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Jiang S, Yan H, Liu Y. Kinetics of DNA tile dimerization. ACS NANO 2014; 8:5826-5832. [PMID: 24794259 PMCID: PMC4072410 DOI: 10.1021/nn500721n] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 05/03/2014] [Indexed: 06/03/2023]
Abstract
Investigating how individual molecular components interact with one another within DNA nanoarchitectures, both in terms of their spatial and temporal interactions, is fundamentally important for a better understanding of their physical behaviors. This will provide researchers with valuable insight for designing more complex higher-order structures that can be assembled more efficiently. In this report, we examined several spatial factors that affect the kinetics of bivalent, double-helical (DH) tile dimerization, including the orientation and number of sticky ends (SEs), the flexibility of the double helical domains, and the size of the tiles. The rate constants we obtained confirm our hypothesis that increased nucleation opportunities and well-aligned SEs accelerate tile-tile dimerization. Increased flexibility in the tiles causes slower dimerization rates, an effect that can be reversed by introducing restrictions to the tile flexibility. The higher dimerization rates of more rigid tiles results from the opposing effects of higher activation energies and higher pre-exponential factors from the Arrhenius equation, where the pre-exponential factor dominates. We believe that the results presented here will assist in improved implementation of DNA tile based algorithmic self-assembly, DNA based molecular robotics, and other specific nucleic acid systems, and will provide guidance to design and assembly processes to improve overall yield and efficiency.
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Johnson-Buck A, Jiang S, Yan H, Walter NG. DNA-cholesterol barges as programmable membrane-exploring agents. ACS NANO 2014; 8:5641-9. [PMID: 24833515 DOI: 10.1021/nn500108k] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
DNA nanotechnology enables the precise construction of nanoscale devices that mimic aspects of natural biomolecular systems yet exhibit robustly programmable behavior. While many important biological processes involve dynamic interactions between components associated with phospholipid membranes, little progress has been made toward creating synthetic mimics of such interfacial systems. We report the assembly and characterization of cholesterol-labeled DNA origami "barges" capable of reversible association with and lateral diffusion on supported lipid bilayers. Using single-particle fluorescence microscopy, we show that these DNA barges rapidly and stably embed in lipid bilayers and exhibit Brownian diffusion in a manner dependent on both cholesterol labeling and bilayer composition. Tracking of individual barges rapidly generates super-resolution maps of the contiguous regions of a membrane. Addition of appropriate command oligonucleotides enables membrane-associated barges to reversibly exchange fluorescent cargo with bulk solution, dissociate from the membrane, or form oligomers within the membrane, opening up new possibilities for programmable membrane-bound molecular devices.
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Affiliation(s)
- Alexander Johnson-Buck
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
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Chen N, Li J, Song H, Chao J, Huang Q, Fan C. Physical and biochemical insights on DNA structures in artificial and living systems. Acc Chem Res 2014; 47:1720-30. [PMID: 24588263 DOI: 10.1021/ar400324n] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
CONSPECTUS: Highly specific DNA base-pairing is the basis for both fulfilling its genetic role and constructing novel nanostructures and hybrid conjugates with inorganic nanomaterials (NMs). There exist many remarkable differences in the physical properties of single-stranded (ss) and double-stranded (ds) DNA, which play important roles in regulation of biological processes in nature. Rapid advances in nanoscience and nanotechnology pose new questions on how DNA and DNA structures interact with inorganic nanomaterials or cells and animals, which should be important for their biological and biomedical applications. In this Account, we intend to provide an overview on many facets of DNA and DNA structures in artificial and living systems, with the focus on their properties and functions at the interfaces of inorganic nanomaterials and biological systems. ssDNA, dsDNA, and DNA nanostructures interact with NMs in different ways. In particular, gold nanoparticles and graphene oxide exhibit strikingly different affinity toward ssDNA and dsDNA. Such binding differences can be coupled with optical properties of NMs. For example, DNA hybridization can effectively modulate the plasmonic and catalytic properties of gold nanoparticles. By exploitation of these interactions, there have been many ways for sensitive transduction of biomolecular recognition for various sensing applications. Alternatively, modulation of the properties of DNA and DNA structures with NMs has led to new tools for genetic analysis including genotyping and haplotyping. Self-assembled DNA nanostructures have emerged as a new type of NMs with pure biomolecules. These nanostructures can be designed in one, two, or three dimensions with various sizes, shapes, and geometries. They also have characteristics of uniform size, precise addressability, excellent water solubility, and biocompatibility. These nanostructures provide a new toolbox for biophysical studies with unparalleled advantages, for example, NMR-based protein structure determination and single-molecule studies. Also importantly, DNA nanostructures have proven highly useful in various applications including biological detection, bioreactors, and nanomedicine. In particular, DNA nanostructures exhibit high cellular permeability, a property that is not available for ssDNA and dsDNA, which is required for their drug delivery applications. DNA and DNA structures can also form hybrids with inorganic NMs. Notably, DNA anchored at the interface of inorganic NMs behaves differently from that at the macroscopic interface. Several types of DNA-NM conjugates have exerted beneficial effects for bioassays and in vitro translation of proteins. Even more interestingly, hybrid nanoconjugates demonstrate distinct properties under the context of biological systems such as cultured cells or animal models. These unprecedented properties not only arouse great interest in studying such interfaces but also open new opportunities for numerous applications in artificial and living systems.
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Affiliation(s)
- Nan Chen
- Division of Physical Biology & Bioimaging Center, Shanghai Sychrotron Radiation Facility (SSRF), CAS Key Laboratory of Microscale Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Jiang Li
- Division of Physical Biology & Bioimaging Center, Shanghai Sychrotron Radiation Facility (SSRF), CAS Key Laboratory of Microscale Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Haiyun Song
- Key
Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jie Chao
- Division of Physical Biology & Bioimaging Center, Shanghai Sychrotron Radiation Facility (SSRF), CAS Key Laboratory of Microscale Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Qing Huang
- Division of Physical Biology & Bioimaging Center, Shanghai Sychrotron Radiation Facility (SSRF), CAS Key Laboratory of Microscale Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Sychrotron Radiation Facility (SSRF), CAS Key Laboratory of Microscale Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
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Tsukanov R, Tomov TE, Liber M, Berger Y, Nir E. Developing DNA nanotechnology using single-molecule fluorescence. Acc Chem Res 2014; 47:1789-98. [PMID: 24828396 DOI: 10.1021/ar500027d] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
CONSPECTUS: An important effort in the DNA nanotechnology field is focused on the rational design and manufacture of molecular structures and dynamic devices made of DNA. As is the case for other technologies that deal with manipulation of matter, rational development requires high quality and informative feedback on the building blocks and final products. For DNA nanotechnology such feedback is typically provided by gel electrophoresis, atomic force microscopy (AFM), and transmission electron microscopy (TEM). These analytical tools provide excellent structural information; however, usually they do not provide high-resolution dynamic information. For the development of DNA-made dynamic devices such as machines, motors, robots, and computers this constitutes a major problem. Bulk-fluorescence techniques are capable of providing dynamic information, but because only ensemble averaged information is obtained, the technique may not adequately describe the dynamics in the context of complex DNA devices. The single-molecule fluorescence (SMF) technique offers a unique combination of capabilities that make it an excellent tool for guiding the development of DNA-made devices. The technique has been increasingly used in DNA nanotechnology, especially for the analysis of structure, dynamics, integrity, and operation of DNA-made devices; however, its capabilities are not yet sufficiently familiar to the community. The purpose of this Account is to demonstrate how different SMF tools can be utilized for the development of DNA devices and for structural dynamic investigation of biomolecules in general and DNA molecules in particular. Single-molecule diffusion-based Förster resonance energy transfer and alternating laser excitation (sm-FRET/ALEX) and immobilization-based total internal reflection fluorescence (TIRF) techniques are briefly described and demonstrated. To illustrate the many applications of SMF to DNA nanotechnology, examples of SMF studies of DNA hairpins and Holliday junctions and of the interactions of DNA strands with DNA origami and origami-related devices such as a DNA bipedal motor are provided. These examples demonstrate how SMF can be utilized for measurement of distances and conformational distributions and equilibrium and nonequilibrium kinetics, to monitor structural integrity and operation of DNA devices, and for isolation and investigation of minor subpopulations including malfunctioning and nonreactive devices. Utilization of a flow-cell to achieve measurements of dynamics with increased time resolution and for convenient and efficient operation of DNA devices is discussed briefly. We conclude by summarizing the various benefits provided by SMF for the development of DNA nanotechnology and suggest that the method can significantly assist in the design and manufacture and evaluation of operation of DNA devices.
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Affiliation(s)
- Roman Tsukanov
- Department of Chemistry and the
Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Toma E. Tomov
- Department of Chemistry and the
Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Miran Liber
- Department of Chemistry and the
Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Yaron Berger
- Department of Chemistry and the
Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Eyal Nir
- Department of Chemistry and the
Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
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37
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Hildebrandt LL, Preus S, Zhang Z, Voigt NV, Gothelf KV, Birkedal V. Single Molecule FRET Analysis of the 11 Discrete Steps of a DNA Actuator. J Am Chem Soc 2014; 136:8957-62. [DOI: 10.1021/ja502580t] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Lasse L. Hildebrandt
- Interdisciplinary
Nanoscience center (iNANO) and Centre for DNA Nanotechnology (CDNA), Aarhus University, Gustav Wieds vej 14, 8000 Aarhus, Denmark
| | - Søren Preus
- Interdisciplinary
Nanoscience center (iNANO) and Centre for DNA Nanotechnology (CDNA), Aarhus University, Gustav Wieds vej 14, 8000 Aarhus, Denmark
| | - Zhao Zhang
- Interdisciplinary
Nanoscience center (iNANO) and Centre for DNA Nanotechnology (CDNA), Aarhus University, Gustav Wieds vej 14, 8000 Aarhus, Denmark
- Department
of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus, Denmark
| | - Niels V. Voigt
- Interdisciplinary
Nanoscience center (iNANO) and Centre for DNA Nanotechnology (CDNA), Aarhus University, Gustav Wieds vej 14, 8000 Aarhus, Denmark
- Department
of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus, Denmark
| | - Kurt V. Gothelf
- Interdisciplinary
Nanoscience center (iNANO) and Centre for DNA Nanotechnology (CDNA), Aarhus University, Gustav Wieds vej 14, 8000 Aarhus, Denmark
- Department
of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus, Denmark
| | - Victoria Birkedal
- Interdisciplinary
Nanoscience center (iNANO) and Centre for DNA Nanotechnology (CDNA), Aarhus University, Gustav Wieds vej 14, 8000 Aarhus, Denmark
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38
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Discovering anomalous hybridization kinetics on DNA nanostructures using single-molecule fluorescence microscopy. Methods 2014; 67:177-84. [DOI: 10.1016/j.ymeth.2014.02.032] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 02/04/2014] [Accepted: 02/21/2014] [Indexed: 11/21/2022] Open
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