1
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Adams MC, Milam VT. Uncovering Molecular Quencher Effects on FRET Phenomena in Microsphere-Immobilized Probe Systems. Anal Chem 2023; 95:13796-13803. [PMID: 37651319 PMCID: PMC10515108 DOI: 10.1021/acs.analchem.3c01064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 08/10/2023] [Indexed: 09/02/2023]
Abstract
Double-stranded (ds) oligonucleotide probes composed of quencher-dye sequence pairs outperform analogous single-stranded (ss) probes due to their superior target sequence specificity without any prerequisite target labeling. Optimizing sequence combinations for dsprobe design requires promoting a fast, accurate response to a specific target sequence while minimizing spontaneous dsprobe dissociation events. Here, flow cytometry is used to rapidly interrogate the stability and selective responsiveness of 20 candidate LNA and DNA dsprobes to a 24 base-long segment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA and ∼243 degenerate RNA sequences serving as model variants. Importantly, in contrast to quantifying binding events of dye-labeled targets via flow cytometry, the current work employs the Förster resonance energy transfer (FRET)-based detection of unlabeled RNA targets. One DNA dsprobe with a 15-base-long hybridization partner containing a central abasic site emerged as very stable yet responsive only to the SARS-CoV-2 RNA segment. Separate displacement experiments, however, indicated that ∼12% of these quencher-capped hybridization partners remain bound, even in the presence of an excess SARS-CoV-2 RNA target. To examine their quenching range, additional titration studies varied the ratios and spatial placement of nonquencher and quencher-capped hybridization partners in the dsprobes. These titration studies indicate that these residual, bound quencher-capped partners, even at low percentages, act as nodes, enabling both static quenching effects within each residual dsprobe as well as longer-range quenching effects on neighboring FAM moieties. Overall, these studies provide insight into practical implications for rapid dsprobe screening and target detection by combining flow cytometry with FRET-based detection.
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Affiliation(s)
- Mary Catherine Adams
- School
of Materials Science and Engineering, Parker H. Petit Institute for Bioengineering, Bioscience Georgia Institute of Technology, 771 Ferst Drive NW, Atlanta, Georgia 30332-0245 United States
| | - Valeria T. Milam
- School
of Materials Science and Engineering, Parker H. Petit Institute for Bioengineering, Bioscience Georgia Institute of Technology, 771 Ferst Drive NW, Atlanta, Georgia 30332-0245 United States
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2
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Eze NA, Milam VT. Quantitative Analysis of In Situ Locked Nucleic Acid and DNA Competitive Displacement Events on Microspheres. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:6871-6881. [PMID: 35617467 DOI: 10.1021/acs.langmuir.2c00220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Synthetic analogues of natural oligonucleotides known as locked nucleic acids (LNAs) offer superior nuclease resistance and cytocompatibility for numerous scenarios ranging from in vitro detection to intracellular imaging of nucleic acids. While recognized as stronger hybridization partners than equivalent DNA residues, quantitative analysis of LNA hybridization activity is lacking, especially with respect to competitive displacement of the original hybridization partner by another oligonucleotide. In the current study, we perform in situ measurements of toehold-mediated competitive displacement of soluble, fluorescently labeled primary targets from probe strands immobilized on microspheres using high throughput flow cytometry. Both LNA-DNA hybrid sequences and pure DNA sequences are employed as the immobilized strands, as soluble, fluorescently labeled 9-base-long primary targets, and as unlabeled 15-base-long secondary or competitive targets. In addition to comparing chemically substituted and unsubstituted sequences, we explore the effects of mismatched primary targets and the location of the toehold segment within the primary duplexes on the resulting displacement profiles. The primary duplex or double-stranded probe (dsprobe) systems implemented here exhibited varying responses to unlabeled secondary targets ranging from surprisingly modest primary target displacement activity despite the presence of a six base-long nucleotide toehold segment at the dsprobe free end to distinctive displacement profiles sensitive to LNA substitutions and the placement of the toehold segment closer to the microsphere surface.
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3
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Yang X, Liang X, Nandi R, Tian Y, Zhang Y, Li Y, Zhou J, Dong Y, Liu D, Zhong Z, Yang Z. DNA-Modified Liquid Crystal Droplets. BIOSENSORS 2022; 12:275. [PMID: 35624576 PMCID: PMC9138460 DOI: 10.3390/bios12050275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/19/2022] [Accepted: 04/25/2022] [Indexed: 06/15/2023]
Abstract
In this work, we have combined the advantages of sequence programmability of DNA nanotechnology and optical birefringence of liquid crystals (LCs). Herein, DNA amphiphiles were adsorbed onto LC droplets. A unique phenomenon of LC droplet aggregation was demonstrated, using DNA-modified LC droplets, through complementary DNA hybridization. Further functionalization of DNA-modified LC droplets with a desired DNA sequence was used to detect a wide range of chemicals and biomolecules, such as Hg2+, thrombin, and enzymes, through LC droplet aggregation and vice versa, which can be seen through the naked eye. These DNA-modified LC droplets can be printed onto a desired patterned surface with temperature-induced responsiveness and reversibility. Overall, our work is the first to report DNA-modified LC droplet, which provides a general detection platform based on the development of DNA aptamers. Additionally, this work inspires the exploration of surface information visualization combined with microcontact printing.
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Affiliation(s)
- Xiuxiu Yang
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China; (X.Y.); (X.L.); (R.N.); (Y.T.); (Y.Z.); (Y.L.); (J.Z.); (Y.D.); (D.L.)
| | - Xiao Liang
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China; (X.Y.); (X.L.); (R.N.); (Y.T.); (Y.Z.); (Y.L.); (J.Z.); (Y.D.); (D.L.)
| | - Rajib Nandi
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China; (X.Y.); (X.L.); (R.N.); (Y.T.); (Y.Z.); (Y.L.); (J.Z.); (Y.D.); (D.L.)
| | - Yi Tian
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China; (X.Y.); (X.L.); (R.N.); (Y.T.); (Y.Z.); (Y.L.); (J.Z.); (Y.D.); (D.L.)
| | - Yiyang Zhang
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China; (X.Y.); (X.L.); (R.N.); (Y.T.); (Y.Z.); (Y.L.); (J.Z.); (Y.D.); (D.L.)
| | - Yan Li
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China; (X.Y.); (X.L.); (R.N.); (Y.T.); (Y.Z.); (Y.L.); (J.Z.); (Y.D.); (D.L.)
| | - Jingsheng Zhou
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China; (X.Y.); (X.L.); (R.N.); (Y.T.); (Y.Z.); (Y.L.); (J.Z.); (Y.D.); (D.L.)
| | - Yuanchen Dong
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China; (X.Y.); (X.L.); (R.N.); (Y.T.); (Y.Z.); (Y.L.); (J.Z.); (Y.D.); (D.L.)
| | - Dongsheng Liu
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China; (X.Y.); (X.L.); (R.N.); (Y.T.); (Y.Z.); (Y.L.); (J.Z.); (Y.D.); (D.L.)
| | - Zhengwei Zhong
- Department of Chemical Engineering, Hebei Petroleum University of Technology, Chengde 067000, China
| | - Zhongqiang Yang
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China; (X.Y.); (X.L.); (R.N.); (Y.T.); (Y.Z.); (Y.L.); (J.Z.); (Y.D.); (D.L.)
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4
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Sontakke VA, Yokobayashi Y. Programmable Macroscopic Self-Assembly of DNA-Decorated Hydrogels. J Am Chem Soc 2022; 144:2149-2155. [DOI: 10.1021/jacs.1c10308] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Vyankat A. Sontakke
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate School, Onna, Okinawa 904-0495, Japan
| | - Yohei Yokobayashi
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate School, Onna, Okinawa 904-0495, Japan
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5
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Brady RA, Brooks NJ, Foderà V, Cicuta P, Di Michele L. Amphiphilic-DNA Platform for the Design of Crystalline Frameworks with Programmable Structure and Functionality. J Am Chem Soc 2018; 140:15384-15392. [PMID: 30351920 DOI: 10.1021/jacs.8b09143] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The reliable preparation of functional, ordered, nanostructured frameworks would be a game changer for many emerging technologies, from energy storage to nanomedicine. Underpinned by the excellent molecular recognition of nucleic acids, along with their facile synthesis and breadth of available functionalizations, DNA nanotechnology is widely acknowledged as a prime route for the rational design of nanostructured materials. Yet, the preparation of crystalline DNA frameworks with programmable structure and functionality remains a challenge. Here we demonstrate the potential of simple amphiphilic DNA motifs, dubbed "C-stars", as a versatile platform for the design of programmable DNA crystals. In contrast to all-DNA materials, in which structure depends on the precise molecular details of individual building blocks, the self-assembly of C-stars is controlled uniquely by their topology and symmetry. Exploiting this robust self-assembly principle, we design a range of topologically identical, but structurally and chemically distinct C-stars that following a one-pot reaction self-assemble into highly porous, functional, crystalline frameworks. Simple design variations allow us to fine-tune the lattice parameter and thus control the partitioning of macromolecules within the frameworks, embed responsive motifs that can induce isothermal disassembly, and include chemical moieties to capture target proteins specifically and reversibly.
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Affiliation(s)
- Ryan A Brady
- Biological and Soft Systems, Cavendish Laboratory , University of Cambridge , Cambridge CB3 0HE , United Kingdom
| | - Nicholas J Brooks
- Department of Chemistry , Imperial College London , London SW7 2AZ , United Kingdom
| | - Vito Foderà
- Department of Pharmacy , University of Copenhagen , Universitetsparken 2 , 2100 Copenhagen , Denmark
| | - Pietro Cicuta
- Biological and Soft Systems, Cavendish Laboratory , University of Cambridge , Cambridge CB3 0HE , United Kingdom
| | - Lorenzo Di Michele
- Biological and Soft Systems, Cavendish Laboratory , University of Cambridge , Cambridge CB3 0HE , United Kingdom
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6
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Gehrels EW, Rogers WB, Manoharan VN. Using DNA strand displacement to control interactions in DNA-grafted colloids. SOFT MATTER 2018; 14:969-984. [PMID: 29323396 DOI: 10.1039/c7sm01722g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Grafting DNA oligonucleotides to colloidal particles leads to specific, reversible interactions between those particles. However, the interaction strength varies steeply and monotonically with temperature, hindering the use of DNA-mediated interactions in self-assembly. We show how the dependence on temperature can be modified in a controlled way by incorporating DNA strand-displacement reactions. The method allows us to make multicomponent systems that can self-assemble over a wide range of temperatures, invert the dependence on temperature to design colloidal systems that melt upon cooling, controllably transition between structures with different compositions, or design systems with multiple melting transitions. This wide range of behaviors can be realized simply by adding a small number of DNA strands to the solution, making the approach modular and straightforward to implement. We conclude with practical considerations for designing systems of DNA-mediated colloidal interactions.
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Affiliation(s)
- Emily W Gehrels
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
| | - W Benjamin Rogers
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA and Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Vinothan N Manoharan
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA and Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA.
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7
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Eze NA, Sullivan RS, Milam VT. Analysis of in Situ LNA and DNA Hybridization Events on Microspheres. Biomacromolecules 2017; 18:1086-1096. [PMID: 28233983 DOI: 10.1021/acs.biomac.6b01373] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The hybridization activity of single-stranded DNA and locked nucleic acid (LNA) sequences on microspheres is quantified in situ using flow cytometry. In contrast to conventional sample preparation for flow cytometry that involves several wash steps for posthybridization analysis, the current work entails directly monitoring hybridization events as they occur between oligonucleotide-functionalized microspheres and fluorescently tagged 9 or 15 base-long targets. We find that the extent of hybridization between single-stranded, immobilized probes and soluble targets generally increases with target sequence length or with the incorporation of LNA nucleotides in one or both oligonucleotide strands involved in duplex formation. The rate constants for duplex formation, on the other hand, remain nearly identical for all but one probe-target sequence combination. The exception to this trend involves the LNA probe and shortest perfectly matched DNA target, which exhibit a rate constant that is an order of magnitude lower than any other probe-target pair, including a mismatched duplex case. Separate studies entailing brief heat treatments to suspensions generally do not consistently yield appreciable differences in associated target densities to probe-functionalized microspheres.
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Affiliation(s)
- Ngozi A Eze
- School of Materials Science and Engineering, ‡Wallace H. Coulter Department of Biomedical Engineering, §Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology , 771 Ferst Drive NW, Atlanta, Georgia 30332-0245, United States
| | - Richard S Sullivan
- School of Materials Science and Engineering, ‡Wallace H. Coulter Department of Biomedical Engineering, §Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology , 771 Ferst Drive NW, Atlanta, Georgia 30332-0245, United States
| | - Valeria T Milam
- School of Materials Science and Engineering, ‡Wallace H. Coulter Department of Biomedical Engineering, §Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology , 771 Ferst Drive NW, Atlanta, Georgia 30332-0245, United States
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8
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Amjad OA, Mognetti BM, Cicuta P, Di Michele L. Membrane Adhesion through Bridging by Multimeric Ligands. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:1139-1146. [PMID: 28068766 DOI: 10.1021/acs.langmuir.6b03692] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Ligand/receptor multivalent interactions have been exploited to drive self-assembly of nanoparticles, hard colloids, and, more recently, compliant units including emulsion droplets and lipid vesicles. In deformable liposomes, formation of links between two membranes produces morphological changes depending on the amount of ligands in the environment. Here, we study a proof-of-concept biosensing system in which single lipid vesicles adhere to a flat supported lipid bilayer, both decorated with membrane-anchored biotinylated receptors. Adhesion is driven by multivalent streptavidin (SA) ligands forming bridges between the vesicles and the supported bilayer. Upon changing the concentration of ligands, we characterize the morphological and mechanical changes of the vesicles, including the formation of a stable adhesion patch, membrane tension, and the kinetics of bridge rupture/formation. We observe vesicle binding only within a specific range of ligand concentrations: adhesion does not occur if the amount of SA is either too low or too high. A theoretical model is presented, elucidating the mechanism underlying this observation, particularly, the role of SA multivalency in determining the onset of adhesion. We elaborate on how the behavior of membranes studied here could be exploited in next-generation (bio)molecular analytical devices.
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Affiliation(s)
- Omar A Amjad
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge , JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Bortolo M Mognetti
- Université libre de Bruxelles (ULB) , Interdisciplinary Center for Nonlinear Phenomena and Complex Systems, Campus Plaine, CP 231, Blvd. du Triomphe, B-1050 Brussels, Belgium
| | - Pietro Cicuta
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge , JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Lorenzo Di Michele
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge , JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
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9
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Shim TS, Estephan ZG, Qian Z, Prosser JH, Lee SY, Chenoweth DM, Lee D, Park SJ, Crocker JC. Shape changing thin films powered by DNA hybridization. NATURE NANOTECHNOLOGY 2017; 12:41-47. [PMID: 27775726 DOI: 10.1038/nnano.2016.192] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 08/30/2016] [Indexed: 06/06/2023]
Abstract
Active materials that respond to physical and chemical stimuli can be used to build dynamic micromachines that lie at the interface between biological systems and engineered devices. In principle, the specific hybridization of DNA can be used to form a library of independent, chemically driven actuators for use in such microrobotic applications and could lead to device capabilities that are not possible with polymer- or metal-layer-based approaches. Here, we report shape changing films that are powered by DNA strand exchange reactions with two different domains that can respond to distinct chemical signals. The films are formed from DNA-grafted gold nanoparticles using a layer-by-layer deposition process. Films consisting of an active and a passive layer show rapid, reversible curling in response to stimulus DNA strands added to solution. Films consisting of two independently addressable active layers display a complex suite of repeatable transformations, involving eight mechanochemical states and incorporating self-righting behaviour.
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Affiliation(s)
- Tae Soup Shim
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Chemical Engineering, Ajou University, Suwon 16499, Korea
- Department of Energy Systems Research, Ajou University, Suwon 16499, Korea
| | - Zaki G Estephan
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Zhaoxia Qian
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Jacob H Prosser
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Su Yeon Lee
- Division of Advanced Materials, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Korea
| | - David M Chenoweth
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Daeyeon Lee
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - So-Jung Park
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - John C Crocker
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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10
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Oligonucleotide-based recognition in colloidal systems - opportunities and challenges. Curr Opin Colloid Interface Sci 2016. [DOI: 10.1016/j.cocis.2016.09.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Sarma D, Gawlitza K, Rurack K. Polystyrene Core-Silica Shell Particles with Defined Nanoarchitectures as a Versatile Platform for Suspension Array Technology. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:3717-3727. [PMID: 27018430 DOI: 10.1021/acs.langmuir.6b00373] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The need for rapid and high-throughput screening in analytical laboratories has led to significant growth in interest in suspension array technologies (SATs), especially with regard to cytometric assays targeting a low to medium number of analytes. Such SAT or bead-based assays rely on spherical objects that constitute the analytical platform. Usually, functionalized polymer or silica (SiO2) microbeads are used which each have distinct advantages and drawbacks. In this paper, we present a straightforward synthetic route to highly monodisperse SiO2-coated polystyrene core-shell (CS) beads for SAT with controllable architectures from smooth to raspberry- and multilayer-like shells by varying the molecular weight of poly(vinylpyrrolidone) (PVP), which was used as the stabilizer of the cores. The combination of both organic polymer core and a structurally controlled inorganic SiO2 shell in one hybrid particle holds great promises for flexible next-generation design of the spherical platform. The particles were characterized by electron microscopy (SEM, T-SEM, and TEM), thermogravimetry, flow cytometry, and nitrogen adsorption/desorption, offering comprehensive information on the composition, size, structure, and surface area. All particles show ideal cytometric detection patterns and facile handling due to the hybrid structure. The beads are endowed with straightforward modification possibilities through the defined SiO2 shells. We successfully implemented the particles in fluorometric SAT model assays, illustrating the benefits of tailored surface area which is readily available for small-molecule anchoring. Very promising assay performance was shown for DNA hybridization assays with quantification limits down to 8 fmol.
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Affiliation(s)
- Dominik Sarma
- Chemical and Optical Sensing Division 1.9, Bundesanstalt für Materialforschung und -prüfung (BAM) , Richard-Willstätter-Str. 11, D-12489 Berlin, Germany
| | - Kornelia Gawlitza
- Chemical and Optical Sensing Division 1.9, Bundesanstalt für Materialforschung und -prüfung (BAM) , Richard-Willstätter-Str. 11, D-12489 Berlin, Germany
| | - Knut Rurack
- Chemical and Optical Sensing Division 1.9, Bundesanstalt für Materialforschung und -prüfung (BAM) , Richard-Willstätter-Str. 11, D-12489 Berlin, Germany
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12
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Parolini L, Kotar J, Di Michele L, Mognetti BM. Controlling Self-Assembly Kinetics of DNA-Functionalized Liposomes Using Toehold Exchange Mechanism. ACS NANO 2016; 10:2392-8. [PMID: 26845414 DOI: 10.1021/acsnano.5b07201] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The selectivity of Watson-Crick base pairing has allowed the design of DNA-based functional materials bearing an unprecedented level of accuracy. Examples include DNA origami, made of tiles assembling into arbitrarily complex shapes, and DNA coated particles featuring rich phase behaviors. Frequently, the realization of conceptual DNA-nanotechnology designs has been hampered by the lack of strategies for effectively controlling relaxations. In this article, we address the problem of kinetic control on DNA-mediated interactions between Brownian objects. We design a kinetic pathway based on toehold-exchange mechanisms that enables rearrangement of DNA bonds without the need for thermal denaturation, and test it on suspensions of DNA-functionalized liposomes, demonstrating tunability of aggregation rates over more than 1 order of magnitude. While the possibility to design complex phase behaviors using DNA as a glue is already well recognized, our results demonstrate control also over the kinetics of such systems.
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Affiliation(s)
- Lucia Parolini
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge , JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Jurij Kotar
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge , JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Lorenzo Di Michele
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge , JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Bortolo M Mognetti
- Interdisciplinary Center for Nonlinear Phenomena and Complex Systems & Service de Physique des Systémes Complexes et Mécanique Statistique, Université Libre de Bruxelles (ULB) , Campus Plaine, CP 231, Blvd du Triomphe, B-1050 Brussels, Belgium
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13
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McGinley JT, Wang Y, Jenkins IC, Sinno T, Crocker JC. Crystal-Templated Colloidal Clusters Exhibit Directional DNA Interactions. ACS NANO 2015; 9:10817-10825. [PMID: 26439813 DOI: 10.1021/acsnano.5b03272] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Spherical colloids covered with grafted DNA have been used in the directed self-assembly of a number of distinct crystal and gel structures. Simulation suggests that the use of anisotropic building blocks greatly augments the variety of potential colloidal assemblies that can be formed. Here, we form five distinct symmetries of colloidal clusters from DNA-functionalized spheres using a single type of colloidal crystal as a template. The crystals are formed by simple sedimentation of a binary mixture containing a majority "host" species that forms close-packed crystals with the minority "impurity" species occupying substitutional or interstitial defect sites. After the DNA strands between the two species are hybridized and enzymatically ligated, the results are colloidal clusters, one for each impurity particle, with a symmetry determined by the nearest neighbors in the original crystal template. By adjusting the size ratio of the two spheres and the timing of the ligation, we are able to generate clusters having the symmetry of tetrahedra, octahedra, cuboctahedra, triangular orthobicupola, and icosahedra, which can be readily separated from defective clusters and leftover spheres by centrifugation. We further demonstrate that these clusters, which are uniformly covered in DNA strands, display directional binding with spheres bearing complementary DNA strands, acting in a manner similar to patchy particles or proteins having multiple binding sites. The scalable nature of the fabrication process, along with the reprogrammability and directional nature of their resulting DNA interactions, makes these clusters suitable building blocks for use in further rounds of directed self-assembly.
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Affiliation(s)
- James T McGinley
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania , 220 South 33rd Street, Philadelphia, Pennsylvania 19104, United States
| | - Yifan Wang
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania , 220 South 33rd Street, Philadelphia, Pennsylvania 19104, United States
| | - Ian C Jenkins
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania , 220 South 33rd Street, Philadelphia, Pennsylvania 19104, United States
| | - Talid Sinno
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania , 220 South 33rd Street, Philadelphia, Pennsylvania 19104, United States
| | - John C Crocker
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania , 220 South 33rd Street, Philadelphia, Pennsylvania 19104, United States
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14
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Evaluating the dual target binding capabilities of immobilized aptamers using flow cytometry. Biointerphases 2015; 10:019015. [PMID: 25787142 DOI: 10.1116/1.4915107] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
In the current study, the authors quantify the binding activity of particle-immobilized DNA aptamers to their nucleotide and non-nucleotide targets. For the purposes of this work, DNA and vascular endothelial growth factor (VEGF) binding analysis was carried out for VEGF-binding aptamers and compared to that of an ampicillin-binding aptamer as well as a non-aptamer DNA probe. Binding analysis followed incubation of one target type, coincubation of both DNA and VEGF targets, and serial incubations of each target type. Moreover, recovery of aptamer binding activity following displacement of the DNA target from aptamer:DNA duplexes was also explored. Flow cytometry served as the quantitative tool to directly monitor binding events of both the DNA target and protein target to the various aptamer and non-aptamer functionalized particles. The current work demonstrates how processing steps such as annealing and binding history of particle-immobilized aptamers can affect subsequent binding activity. To this end, the authors demonstrate the ability to fully recover DNA target binding activity capabilities and to partially recover protein target binding activity.
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15
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Zhang X, Wang R, Xue G. Programming macro-materials from DNA-directed self-assembly. SOFT MATTER 2015; 11:1862-70. [PMID: 25687673 DOI: 10.1039/c4sm02649g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
DNA is a powerful tool that can be attached to nano- and micro-objects and direct the self-assembly through base pairing. Since the strategy of DNA programmable nanoparticle self-assembly was first introduced in 1996, it has remained challenging to use DNA to make powerful diagnostic tools and to make designed materials with novel properties and highly ordered crystal structures. In this review, we summarize recent experimental and theoretical developments of DNA-programmable self-assembly into three-dimensional (3D) materials. Various types of aggregates and 3D crystal structures obtained from an experimental DNA-driven assembly are introduced. Furthermore, theoretical calculations and simulations for DNA-mediated assembly systems are described and we highlight some typical theoretical models for Monte Carlo and Molecular Dynamics simulations.
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Affiliation(s)
- Xuena Zhang
- Department of Polymer Science and Engineering, Key Laboratory of High Performance Polymer Materials and Technology of Ministry of Education, State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China.
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16
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Rogers WB, Manoharan VN. DNA nanotechnology. Programming colloidal phase transitions with DNA strand displacement. Science 2015; 347:639-42. [PMID: 25657244 DOI: 10.1126/science.1259762] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
DNA-grafted nanoparticles have been called "programmable atom-equivalents": Like atoms, they form three-dimensional crystals, but unlike atoms, the particles themselves carry information (the sequences of the grafted strands) that can be used to "program" the equilibrium crystal structures. We show that the programmability of these colloids can be generalized to the full temperature-dependent phase diagram, not just the crystal structures themselves. We add information to the buffer in the form of soluble DNA strands designed to compete with the grafted strands through strand displacement. Using only two displacement reactions, we program phase behavior not found in atomic systems or other DNA-grafted colloids, including arbitrarily wide gas-solid coexistence, reentrant melting, and even reversible transitions between distinct crystal phases.
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Affiliation(s)
- W Benjamin Rogers
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Vinothan N Manoharan
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA. Department of Physics, Harvard University, Cambridge, MA 02138, USA.
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17
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Duncan GA, Bevan MA. Tunable aggregation by competing biomolecular interactions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:15253-15260. [PMID: 25458784 DOI: 10.1021/la503772g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Measurements and models are reported for Concanavalin A (ConA) mediated aggregation of dextran coated colloids that is tunable via a competing ConA-glucose interaction. Video and confocal scanning laser microscopy were used to characterize ConA adsorption to dextran colloids and quasi-2D dextran coated colloid aggregation kinetics vs [ConA] and [glucose]. ConA adsorption to, and aggregation rates of, dextran coated colloids increased from negligible values to high coverage and rapid rates for increasing [ConA] in the range 0.1-10 mM and decreasing [glucose] in the range 1-100 mM, consistent with dissociation constant estimates. Analysis of colloidal aggregation kinetics indicates ConA bridge formation is the rate-limiting step controlling the transition from slow to rapid aggregation. Our findings reveal a mechanism for tuning colloidal interactions and aggregation kinetics through specific, competitive biomolecular interactions, which lends insights into aggregation phenomena in mixed synthetic-biomaterial and biological systems.
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Affiliation(s)
- Gregg A Duncan
- Chemical & Biomolecular Engineering, Johns Hopkins University , Baltimore, Maryland 21218, United States
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18
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Hardin JO, Fernandez-Nieves A, Martinez CJ, Milam VT. Altering colloidal surface functionalization using DNA encapsulated inside monodisperse gelatin microsphere templates. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:5534-5539. [PMID: 23560747 DOI: 10.1021/la400280x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Soluble oligonucleotides are typically introduced to bulk solution to promote hybridization activity on DNA-functionalized surfaces. Here, an alternative approach is explored by encapsulating secondary target strands inside semipermeable colloidal satellite assemblies, then triggering their release at 37 °C for subsequent surface hybridization activity. To prepare DNA-loaded satellite assemblies, uniform gelatin microspheres are fabricated using microfluidics, loaded with 15 base-long secondary DNA targets, capped with a polyelectrolyte bilayer, and finally coated with a monolayer of polystyrene microspheres functionalized with duplexes comprised of immobilized probes and soluble, 13 base-long hybridization partner strands. Once warmed to 37 °C, secondary DNA targets are released from the gelatin template and then competitively displace the shorter, original hybridization partners on the polystyrene microspheres.
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Affiliation(s)
- James O Hardin
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30032-0245, United States
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19
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Hardin JO, Milam VT. Measuring in situ primary and competitive DNA hybridization activity on microspheres. Biomacromolecules 2013; 14:986-92. [PMID: 23402211 DOI: 10.1021/bm3017466] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Microspheres serve as convenient substrates for studying DNA activity on surfaces. Here, in addition to employing conventional sample preparation involving multiple wash and resuspension steps prior to flow cytometry measurements, we also directly sampled the reaction volume to acquire in situ measurements of primary and competitive hybridization events. Even in the absence of post hybridization wash steps, nonspecific binding events were negligible and thus allowed for direct, quantitative assessment of hybridization events as they occurred on colloidal surfaces. The in situ results indicate that primary duplex formation between immobilized probes and soluble targets on microsphere surfaces is less favorable than predicted by solution models. The kinetics of competitive displacement of primary hybridization partners by secondary targets measured in situ or post washing also deviate from expectations based on theoretical solution thermodynamics, but are consistent with predicted kinetic trends stemming from differences in either the toehold base length or branch migration.
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Affiliation(s)
- James O Hardin
- School of Materials Science and Engineering, Georgia Institute of Technology , 771 Ferst Drive NW, Atlanta, Georgia 30332-0245, USA
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20
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Baker BA, Mahmoudabadi G, Milam VT. Using double-stranded DNA probes to promote specificity in target capture. Colloids Surf B Biointerfaces 2013; 102:884-90. [DOI: 10.1016/j.colsurfb.2012.09.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Revised: 08/10/2012] [Accepted: 09/10/2012] [Indexed: 12/30/2022]
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21
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Zhou Z, Wei W, Zhang Y, Liu S. DNA-responsive disassembly of AuNP aggregates: influence of nonbase-paired regions and colorimetric DNA detection by exonuclease III aided amplification. J Mater Chem B 2013; 1:2851-2858. [DOI: 10.1039/c3tb20206b] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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22
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Specific and reversible DNA-directed self-assembly of oil-in-water emulsion droplets. Proc Natl Acad Sci U S A 2012; 109:20320-5. [PMID: 23175791 DOI: 10.1073/pnas.1214386109] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Higher-order structures that originate from the specific and reversible DNA-directed self-assembly of microscopic building blocks hold great promise for future technologies. Here, we functionalized biotinylated soft colloid oil-in-water emulsion droplets with biotinylated single-stranded DNA oligonucleotides using streptavidin as an intermediary linker. We show the components of this modular linking system to be stable and to induce sequence-specific aggregation of binary mixtures of emulsion droplets. Three length scales were thereby involved: nanoscale DNA base pairing linking microscopic building blocks resulted in macroscopic aggregates visible to the naked eye. The aggregation process was reversible by changing the temperature and electrolyte concentration and by the addition of competing oligonucleotides. The system was reset and reused by subsequent refunctionalization of the emulsion droplets. DNA-directed self-assembly of oil-in-water emulsion droplets, therefore, offers a solid basis for programmable and recyclable soft materials that undergo structural rearrangements on demand and that range in application from information technology to medicine.
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23
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Tang H, Deschner R, Allen P, Cho Y, Sermas P, Maurer A, Ellington AD, Willson CG. Analysis of DNA-guided self-assembly of microspheres using imaging flow cytometry. J Am Chem Soc 2012; 134:15245-8. [PMID: 22938015 PMCID: PMC3470448 DOI: 10.1021/ja3066896] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Imaging flow cytometry was used to analyze the self-assembly of DNA-conjugated polystyrene microspheres. This technique enables quantitative analysis of the assembly process and thereby enables detailed analysis of the effect of structural and process variables on the assembly yield. In a demonstration of the potential of this technique, the influence of DNA strand base pair (bp) length was examined, and it was found that 50 bp was sufficient to drive the assembly of microspheres efficiently, forming not only dimers but also chainlike structures. The effect of stoichiometry on the yield was also examined. The analysis demonstrated that self-assembly of 50 bp microspheres can be driven nearly to completion by stoichiometric excess in a manner similar to Le Chatelier's principle in common chemical equilibrium.
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Affiliation(s)
- Hao Tang
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712, United States
| | - Ryan Deschner
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712, United States
| | - Peter Allen
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, TX 78712, United States
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, United States
| | - Younjin Cho
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, TX 78712, United States
| | - Patrick Sermas
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712, United States
| | - Alejandro Maurer
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712, United States
| | - Andrew D. Ellington
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, TX 78712, United States
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, United States
| | - C. Grant Willson
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712, United States
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, TX 78712, United States
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24
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Direct measurements of DNA-mediated colloidal interactions and their quantitative modeling. Proc Natl Acad Sci U S A 2011; 108:15687-92. [PMID: 21896714 DOI: 10.1073/pnas.1109853108] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA bridging can be used to induce specific attractions between small particles, providing a highly versatile approach to creating unique particle-based materials having a variety of periodic structures. Surprisingly, given the fact that the thermodynamics of DNA strands in solution are completely understood, existing models for DNA-induced particle interactions are typically in error by more than an order of magnitude in strength and a factor of two in their temperature dependence. This discrepancy has stymied efforts to design the complex temperature, sequence and time-dependent interactions needed for the most interesting applications, such as materials having highly complex or multicomponent microstructures or the ability to reconfigure or self-replicate. Here we report high-spatial resolution measurements of DNA-induced interactions between pairs of polystyrene microspheres at binding strengths comparable to those used in self-assembly experiments, up to 6 k(B)T. We also describe a conceptually straightforward and numerically tractable model that quantitatively captures the separation dependence and temperature-dependent strength of these DNA-induced interactions, without empirical corrections. This model was equally successful when describing the more complex and practically relevant case of grafted DNA brushes with self-interactions that compete with interparticle bridge formation. Together, our findings motivate a nanomaterial design approach where unique functional structures can be found computationally and then reliably realized in experiment.
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25
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Baker BA, Milam VT. Hybridization kinetics between immobilized double-stranded DNA probes and targets containing embedded recognition segments. Nucleic Acids Res 2011; 39:e99. [PMID: 21613238 PMCID: PMC3159461 DOI: 10.1093/nar/gkr293] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2010] [Revised: 04/05/2011] [Accepted: 04/14/2011] [Indexed: 12/27/2022] Open
Abstract
We have investigated the time-dependent strand displacement activity of several targets with double-stranded DNA probes (dsProbes) of varying affinity. Here, the relative affinity of various dsProbes is altered through choices in hybridization length (11-15 bases) and the selective inclusion of center mismatches in the duplexes. While the dsProbes are immobilized on microspheres, the soluble, 15 base-long complementary sequence is presented either alone as a short target strand or as a recognition segment embedded within a longer target strand. Compared to the short target, strand displacement activity of the longer targets is slower, but still successful. Additionally, the longer targets exhibit modest differences in the observed displacement rates, depending on the location of recognition segment within the long target. Overall, our study demonstrates that the kinetics of strand displacement activity can be tuned through dsProbe sequence design parameters and is only modestly affected by the location of the complementary segment within a longer target strand.
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Affiliation(s)
- Bryan A. Baker
- School of Materials Science and Engineering, Wallace H. Coulter Department of Biomedical Engineering and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, 771 Ferst Dr. NW, Atlanta, GA 30332-0245, USA
| | - Valeria T. Milam
- School of Materials Science and Engineering, Wallace H. Coulter Department of Biomedical Engineering and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, 771 Ferst Dr. NW, Atlanta, GA 30332-0245, USA
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26
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Baker BA, Milam VT. DNA density-dependent assembly behavior of colloidal micelles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:9818-9826. [PMID: 20349914 DOI: 10.1021/la100077f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
A key advantage of DNA-mediated colloidal assembly is the ability to tune the strength of adhesion between particles based on sequence characteristics. In the current study, we have investigated DNA-mediated assembly of polystyrene colloidal particles as a function of sequence length, sequence fidelity, and probe density for DNA sequences patterned from the Salmonella genome. The results of our work indicate that the density of DNA probe strands heavily influences the ability of immobilized sequences to hybridize between surfaces of bidisperse colloidal particles. Incubating suspensions at higher temperatures (to minimize secondary structures that might otherwise compromise duplex formation) was also found to have less effect than duplex density on DNA-mediated particle assembly. We believe these results may add to the understanding and design considerations of directed particle assembly using DNA hybridization, especially in the submicrometer and micrometer size regime.
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Affiliation(s)
- Bryan A Baker
- School of Materials Science & Engineering, Georgia Institute of Technology, 771 Ferst Drive NW, Atlanta, Georgia 30332-0245, USA
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27
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Bi S, Yan Y, Hao S, Zhang S. Colorimetric Logic Gates Based on Supramolecular DNAzyme Structures. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201000840] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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28
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29
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Zhang Z, Cheng Q, Feng P. Selective removal of DNA-labeled nanoparticles from planar substrates by DNA displacement reactions. Angew Chem Int Ed Engl 2009; 48:118-22. [PMID: 19035368 DOI: 10.1002/anie.200803840] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Zhenyu Zhang
- Department of Chemistry, University of California, Riverside, CA 92521, USA
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30
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Zhang Z, Cheng Q, Feng P. Selective Removal of DNA-Labeled Nanoparticles from Planar Substrates by DNA Displacement Reactions. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200803840] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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31
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Tison CK, Milam VT. Manipulating DNA probe presentation via enzymatic cleavage of diluent strands. Biomacromolecules 2008; 9:2468-76. [PMID: 18715032 DOI: 10.1021/bm800497g] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We previously reported a system for the controlled redispersion of DNA-linked aggregates using secondary, competitive hybridization events and found that complete redispersion is contingent upon dilution of the active 20 base-long probe strands with 20 base-long nonhybridizing strands. Here, to reduce the steric interference of nonhybridizing or diluent strands on probe activity, we investigate the effect of shorter diluent strands on the hybridization activity of immobilized probes using the following two approaches: (1) simultaneously coupling shorter diluent strands and longer probe strands to microspheres and (2) simultaneously coupling diluent and probe strands of the same base length to microspheres and then clipping diluent strands with the restriction endonuclease AluI. Results indicate that one can reduce the duplex density down by 50-70% of its initial value, depending on the location of the recognition motif along the hybridization segment. In addition, tighter control over the number of probe-target duplexes is achieved with the enzyme-based approach.
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Affiliation(s)
- Christopher K Tison
- School of Materials Science and Engineering, Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, 771 Ferst Drive NW, Atlanta, Georgia 30332-0245, USA
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32
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Shyr MHS, Wernette DP, Wiltzius P, Lu Y, Braun PV. DNA and DNAzyme-Mediated 2D Colloidal Assembly. J Am Chem Soc 2008; 130:8234-40. [DOI: 10.1021/ja711026r] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Margaret H. S. Shyr
- Beckman Institute, Department of Materials Science and Engineering, and Department of Chemistry, University of Illinois at Urbana−Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801
| | - Daryl P. Wernette
- Beckman Institute, Department of Materials Science and Engineering, and Department of Chemistry, University of Illinois at Urbana−Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801
| | - Pierre Wiltzius
- Beckman Institute, Department of Materials Science and Engineering, and Department of Chemistry, University of Illinois at Urbana−Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801
| | - Yi Lu
- Beckman Institute, Department of Materials Science and Engineering, and Department of Chemistry, University of Illinois at Urbana−Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801
| | - Paul V. Braun
- Beckman Institute, Department of Materials Science and Engineering, and Department of Chemistry, University of Illinois at Urbana−Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801
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