Co-reporter:Shuoxing Jiang, Fan Hong, Huiyu Hu, Hao Yan, and Yan Liu
ACS Nano September 26, 2017 Volume 11(Issue 9) pp:9370-9370
Publication Date(Web):August 16, 2017
DOI:10.1021/acsnano.7b04845
Although many models have been developed to guide the design and implementation of DNA tile-based self-assembly systems with increasing complexity, the fundamental assumptions of the models have not been thoroughly tested. To expand the quantitative understanding of DNA tile-based self-assembly and to test the fundamental assumptions of self-assembly models, we investigated DNA tile attachment to preformed “multi-tile” arrays in real time and obtained the thermodynamic and kinetic parameters of single tile attachment in various sticky end association scenarios. With more sticky ends, tile attachment becomes more thermostable with an approximately linear decrease in the free energy change (more negative). The total binding free energy of sticky ends is partially compromised by a sequence-independent energy penalty when tile attachment forms a constrained configuration: “loop”. The minimal loop is a 2 × 2 tetramer (Loop4). The energy penalty of loops of 4, 6, and 8 tiles was analyzed with the independent loop model assuming no interloop tension, which is generalizable to arbitrary tile configurations. More sticky ends also contribute to a faster on-rate under isothermal conditions when nucleation is the rate-limiting step. Incorrect sticky end contributes to neither the thermostability nor the kinetics. The thermodynamic and kinetic parameters of DNA tile attachment elucidated here will contribute to the future improvement and optimization of tile assembly modeling, precise control of experimental conditions, and structural design for error-free self-assembly.Keywords: DNA nanotechnology; double-crossover tile; kinetics; self-assembly; thermodynamics;
Co-reporter:Fan Hong, Fei Zhang, Yan Liu, and Hao Yan
Chemical Reviews October 25, 2017 Volume 117(Issue 20) pp:12584-12584
Publication Date(Web):June 12, 2017
DOI:10.1021/acs.chemrev.6b00825
DNA has become one of the most extensively used molecular building blocks for engineering self-assembling materials. DNA origami is a technique that uses hundreds of short DNA oligonucleotides, called staple strands, to fold a long single-stranded DNA, which is called a scaffold strand, into various designer nanoscale architectures. DNA origami has dramatically improved the complexity and scalability of DNA nanostructures. Due to its high degree of customization and spatial addressability, DNA origami provides a versatile platform with which to engineer nanoscale structures and devices that can sense, compute, and actuate. These capabilities open up opportunities for a broad range of applications in chemistry, biology, physics, material science, and computer science that have often required programmed spatial control of molecules and atoms in three-dimensional (3D) space. This review provides a comprehensive survey of recent developments in DNA origami structure, design, assembly, and directed self-assembly, as well as its broad applications.
Co-reporter:Chad R. Simmons, Fei Zhang, Tara MacCulloch, Noureddine Fahmi, Nicholas Stephanopoulos, Yan Liu, Nadrian C. Seeman, and Hao Yan
Journal of the American Chemical Society August 16, 2017 Volume 139(Issue 32) pp:11254-11254
Publication Date(Web):July 21, 2017
DOI:10.1021/jacs.7b06485
The foundational goal of structural DNA nanotechnology—the field that uses oligonucleotides as a molecular building block for the programmable self-assembly of nanostructured systems—was to use DNA to construct three-dimensional (3D) lattices for solving macromolecular structures. The programmable nature of DNA makes it an ideal system for rationally constructing self-assembled crystals and immobilizing guest molecules in a repeating 3D array through their specific stereospatial interactions with the scaffold. In this work, we have extended a previously described motif (4 × 5) by expanding the structure to a system that links four double-helical layers; we use a central weaving oligonucleotide containing a sequence of four six-base repeats (4 × 6), forming a matrix of layers that are organized and dictated by a series of Holliday junctions. In addition, we have assembled mirror image crystals (l-DNA) with the identical sequence that are completely resistant to nucleases. Bromine and selenium derivatives were obtained for the l- and d-DNA forms, respectively, allowing phase determination for both forms and solution of the resulting structures to 3.0 and 3.05 Å resolution. Both right- and left-handed forms crystallized in the trigonal space groups with mirror image 3-fold helical screw axes P32 and P31 for each motif, respectively. The structures reveal a highly organized array of discrete and well-defined cavities that are suitable for hosting guest molecules and allow us to dictate a priori the assembly of guest–DNA conjugates with a specified crystalline hand.
Co-reporter:Cheng Zhang, Jing Yang, Shuoxing Jiang, Yan Liu, and Hao Yan
Nano Letters 2016 Volume 16(Issue 1) pp:736-741
Publication Date(Web):December 9, 2015
DOI:10.1021/acs.nanolett.5b04608
Controlling DNA self-assembly processes using rationally designed logic gates is a major goal of DNA-based nanotechnology and programming. Such controls could facilitate the hierarchical engineering of complex nanopatterns responding to various molecular triggers or inputs. Here, we demonstrate the use of a series of DNAzyme-based logic gates to control DNA tile self-assembly onto a prescribed DNA origami frame. Logic systems such as “YES,” “OR,” “AND,” and “logic switch” are implemented based on DNAzyme-mediated tile recognition with the DNA origami frame. DNAzyme is designed to play two roles: (1) as an intermediate messenger to motivate downstream reactions and (2) as a final trigger to report fluorescent signals, enabling information relay between the DNA origami-framed tile assembly and fluorescent signaling. The results of this study demonstrate the plausibility of DNAzyme-mediated hierarchical self-assembly and provide new tools for generating dynamic and responsive self-assembly systems.
Co-reporter:Dr. Minghui Liu;Dr. Jinglin Fu;Dr. Xiaodong Qi;Shaun Wootten;Dr. Neal W. Woodbury;Dr. Yan Liu;Dr. Hao Yan
ChemBioChem 2016 Volume 17( Issue 12) pp:1097-1101
Publication Date(Web):
DOI:10.1002/cbic.201600103
Abstract
Cascade reactions drive and regulate a variety of metabolic activities. Efficient coupling of substrate transport between enzymes is important for overall pathway activity and also controls the depletion of intermediate molecules that drive the reaction forward. Here, we assembled a three-enzyme pathway on a series of DNA nanoscaffolds to investigate the dependence of their activities on spatial arrangement. Unlike previous studies, the overall activity of the three-enzyme pathway relied less on inter-enzyme distance and more on the geometric patterns that arranged them within a relatively small range of 10–30 nm. Pathway intermediate detection demonstrated that the assembled enzyme systems quickly depleted the intermediate molecules through efficient reaction coupling.
Co-reporter:Dr. Minghui Liu;Dr. Jinglin Fu;Dr. Xiaodong Qi;Shaun Wootten;Dr. Neal W. Woodbury;Dr. Yan Liu;Dr. Hao Yan
ChemBioChem 2016 Volume 17( Issue 12) pp:
Publication Date(Web):
DOI:10.1002/cbic.201600308
Co-reporter:Guoliang Ke;Dr. Minghui Liu;Shuoxing Jiang;Dr. Xiaodong Qi;Yuhe Renee Yang;Shaun Wootten;Dr. Fei Zhang; Zhi Zhu; Yan Liu; Chaoyong James Yang; Hao Yan
Angewandte Chemie International Edition 2016 Volume 55( Issue 26) pp:7483-7486
Publication Date(Web):
DOI:10.1002/anie.201603183
Abstract
Artificial multi-enzyme systems with precise and dynamic control over the enzyme pathway activity are of great significance in bionanotechnology and synthetic biology. Herein, we exploit a spatially addressable DNA nanoplatform for the directional regulation of two enzyme pathways (G6pDH–MDH and G6pDH–LDH) through the control of NAD+ substrate channeling by specifically shifting NAD+ between the two enzyme pairs. We believe that this concept will be useful for the design of regulatory biological circuits for synthetic biology and biomedicine.
Co-reporter:Guoliang Ke;Dr. Minghui Liu;Shuoxing Jiang;Dr. Xiaodong Qi;Yuhe Renee Yang;Shaun Wootten;Dr. Fei Zhang; Zhi Zhu; Yan Liu; Chaoyong James Yang; Hao Yan
Angewandte Chemie 2016 Volume 128( Issue 26) pp:7609-7612
Publication Date(Web):
DOI:10.1002/ange.201603183
Abstract
Artificial multi-enzyme systems with precise and dynamic control over the enzyme pathway activity are of great significance in bionanotechnology and synthetic biology. Herein, we exploit a spatially addressable DNA nanoplatform for the directional regulation of two enzyme pathways (G6pDH–MDH and G6pDH–LDH) through the control of NAD+ substrate channeling by specifically shifting NAD+ between the two enzyme pairs. We believe that this concept will be useful for the design of regulatory biological circuits for synthetic biology and biomedicine.
Co-reporter:Yuhe R. Yang, Yan Liu, and Hao Yan
Bioconjugate Chemistry 2015 Volume 26(Issue 8) pp:1381
Publication Date(Web):May 11, 2015
DOI:10.1021/acs.bioconjchem.5b00194
This Review focuses on how to use DNA nanostructures as scaffolds to organize biological molecules. First, we introduce the use of structural DNA nanotechnology to engineer rationally designed nanostructures. Second, we survey approaches used to generate protein–DNA conjugates. Third, we discuss studies exploring DNA scaffolds to create DNA nanodevices to analyze protein structures, to engineer enzyme pathways, to create artificial light-harvesting systems, and to generate nanomachines in vitro and in vivo. Future challenges and perspectives of using DNA nanostructures as programmable biomolecular scaffolds are addressed at the end.
Co-reporter:Palash K. Dutta ; Su Lin ; Andrey Loskutov ; Symon Levenberg ; Daniel Jun ; Rafael Saer ; J. Thomas Beatty ; Yan Liu ; Hao Yan ;Neal W. Woodbury
Journal of the American Chemical Society 2014 Volume 136(Issue 12) pp:4599-4604
Publication Date(Web):February 25, 2014
DOI:10.1021/ja411843k
Engineered cysteine residues near the primary electron donor (P) of the reaction center from the purple photosynthetic bacterium Rhodobacter sphaeroides were covalently conjugated to each of several dye molecules in order to explore the geometric design and spectral requirements for energy transfer between an artificial antenna system and the reaction center. An average of 2.5 fluorescent dye molecules were attached at specific locations near P. The enhanced absorbance cross-section afforded by conjugation of Alexa Fluor 660 dyes resulted in a 2.2-fold increase in the formation of reaction center charge-separated state upon intensity-limited excitation at 650 nm. The effective increase in absorbance cross-section resulting from the conjugation of two other dyes, Alexa Fluor 647 and Alexa Fluor 750, was also investigated. The key parameters that dictate the efficiency of dye-to-reaction center energy transfer and subsequent charge separation were examined using both steady-state and time-resolved fluorescence spectroscopy as well as transient absorbance spectroscopy techniques. An understanding of these parameters is an important first step toward developing more complex model light-harvesting systems integrated with reaction centers.
Co-reporter:Fei Zhang ; Jeanette Nangreave ; Yan Liu
Journal of the American Chemical Society 2014 Volume 136(Issue 32) pp:11198-11211
Publication Date(Web):July 16, 2014
DOI:10.1021/ja505101a
Over the past three decades DNA has emerged as an exceptional molecular building block for nanoconstruction due to its predictable conformation and programmable intra- and intermolecular Watson–Crick base-pairing interactions. A variety of convenient design rules and reliable assembly methods have been developed to engineer DNA nanostructures of increasing complexity. The ability to create designer DNA architectures with accurate spatial control has allowed researchers to explore novel applications in many directions, such as directed material assembly, structural biology, biocatalysis, DNA computing, nanorobotics, disease diagnosis, and drug delivery. This Perspective discusses the state of the art in the field of structural DNA nanotechnology and presents some of the challenges and opportunities that exist in DNA-based molecular design and programming.
Co-reporter:Palash K. Dutta ; Symon Levenberg ; Andrey Loskutov ; Daniel Jun ; Rafael Saer ; J. Thomas Beatty ; Su Lin ; Yan Liu ; Neal W. Woodbury
Journal of the American Chemical Society 2014 Volume 136(Issue 47) pp:16618-16625
Publication Date(Web):October 23, 2014
DOI:10.1021/ja509018g
A structurally and compositionally well-defined and spectrally tunable artificial light-harvesting system has been constructed in which multiple organic dyes attached to a three-arm-DNA nanostructure serve as an antenna conjugated to a photosynthetic reaction center isolated from Rhodobacter sphaeroides 2.4.1. The light energy absorbed by the dye molecules is transferred to the reaction center, where charge separation takes place. The average number of DNA three-arm junctions per reaction center was tuned from 0.75 to 2.35. This DNA-templated multichromophore system serves as a modular light-harvesting antenna that is capable of being optimized for its spectral properties, energy transfer efficiency, and photostability, allowing one to adjust both the size and spectrum of the resulting structures. This may serve as a useful test bed for developing nanostructured photonic systems.
Co-reporter:Yang Yang, Zhao Zhao, Fei Zhang, Jeanette Nangreave, Yan Liu, and Hao Yan
Nano Letters 2013 Volume 13(Issue 4) pp:1862-1866
Publication Date(Web):March 27, 2013
DOI:10.1021/nl400859d
We report a scaffold-free approach in which four- and six-helix DNA bundle units, assembled from a small number of single stranded DNA oligonucleotides precisely arranged in networks of contiguous and semicrossover strands, are connected into DNA nano rings. Nearly uniform structures with well-defined diameters of 53 ± 7, 81 ± 9, 85 ± 8, and 166 ± 13 nm were achieved by introducing uniform, in-plane curvature to the repeating units. We demonstrate that precise higher order assemblies can be achieved by fine tuning the particular features of the individual building blocks.
Co-reporter:Fei Zhang ; Yan Liu
Journal of the American Chemical Society 2013 Volume 135(Issue 20) pp:7458-7461
Publication Date(Web):May 7, 2013
DOI:10.1021/ja4035957
Archimedean tilings are periodic polygonal tessellations that are created by placing regular polygons edge-to-edge around a vertex to fill the plane. Here we show that three- and four-arm DNA junction tiles with specifically designed arm lengths and intertile sticky-end interactions can be used to form sophisticated two-dimensional (2D) and three-dimensional (3D) tessellation patterns. We demonstrate two different complex Archimedean patterns, (33.42) and (32.4.3.4), and the formation of 2D lattices, 3D tubes, and sealed polygon-shaped pockets from the tessellations. The successful growth of hybrid DNA tile motif arrays suggests that it maybe possible to generate 2D quasi-crystals from DNA building blocks.
Co-reporter:Zhao Zhao, Yan Liu and Hao Yan
Organic & Biomolecular Chemistry 2013 vol. 11(Issue 4) pp:596-598
Publication Date(Web):03 Dec 2012
DOI:10.1039/C2OB26942B
Constructing intricate geometric arrangements of components is one of the central challenges of nanotechnology. Here we report a convenient, versatile method to organize discrete length single-walled carbon nanotubes (SWNT) into complex geometries using 2D DNA origami structures. First, a size exclusion HPLC purification protocol was used to isolate uniform length, SWNTs labelled with single stranded DNA (ssDNA). The nanotube-bound ssDNAs are composed of two domains: a SWNT binding domain and a linker binding domain. Although initially bound to the SWNTs, the linker domain is displaced from the surface by the addition of an external ssDNA linker strand. One portion of the linker strand is designed to form a double helix with the linker binding domain, compelling the DNA to project away from the SWNT surface. The remainder of the linker strand contains an ssDNA origami recognition sequence available for hybridization to a DNA origami nanostructure. Two different 2D DNA origami structures, a triangle and a rectangle, were used to organize the nanotubes. Several arrangements of nanotubes were constructed, with defined tube lengths and inter-tube angles. The uniform tube lengths and positional precision that this method affords may have applications in electronic device fabrication.
Co-reporter:Xiaowei Liu;Yan Liu
Israel Journal of Chemistry 2013 Volume 53( Issue 8) pp:555-566
Publication Date(Web):
DOI:10.1002/ijch.201300002
Abstract
DNA nanotechnology utilizes synthetic DNA strands as the building material to construct nanoscale devices, and the field has developed rapidly over the past decade. Recently, the use of DNA nanostructures for various applications, particularly biomedical ones, has drawn great interest. This review focuses on the most recent research directed at utilizing functionalized DNA devices for nanomedical applications and presents representative research progress in disease diagnosis, treatment and prevention. In addition, the safety and future clinical applications of DNA nanostructures are discussed.
Co-reporter:Qian Mei;Roger H. Johnson;Xixi Wei;Fengyu Su;Yan Liu
Nano Research 2013 Volume 6( Issue 10) pp:712-719
Publication Date(Web):2013/10/01
DOI:10.1007/s12274-013-0347-1
Co-reporter:Anirban Samanta;Zhengtao Deng;Yan Liu
Nano Research 2013 Volume 6( Issue 12) pp:853-870
Publication Date(Web):2013 December
DOI:10.1007/s12274-013-0367-x
Co-reporter:Dr. Dongran Han;Shuoxing Jiang;Anirban Samanta; Yan Liu; Hao Yan
Angewandte Chemie 2013 Volume 125( Issue 34) pp:9201-9204
Publication Date(Web):
DOI:10.1002/ange.201302177
Co-reporter:Dr. Dongran Han;Shuoxing Jiang;Anirban Samanta; Yan Liu; Hao Yan
Angewandte Chemie International Edition 2013 Volume 52( Issue 34) pp:9031-9034
Publication Date(Web):
DOI:10.1002/anie.201302177
Co-reporter:Jinglin Fu, Minghui Liu, Yan Liu, and Hao Yan
Accounts of Chemical Research 2012 Volume 45(Issue 8) pp:1215
Publication Date(Web):May 29, 2012
DOI:10.1021/ar200295q
Living systems have evolved a variety of nanostructures to control the molecular interactions that mediate many functions including the recognition of targets by receptors, the binding of enzymes to substrates, and the regulation of enzymatic activity. Mimicking these structures outside of the cell requires methods that offer nanoscale control over the organization of individual network components. Advances in DNA nanotechnology have enabled the design and fabrication of sophisticated one-, two- and three-dimensional (1D, 2D, and 3D) nanostructures that utilize spontaneous and sequence-specific DNA hybridization. Compared with other self-assembling biopolymers, DNA nanostructures offer predictable and programmable interactions and surface features to which other nanoparticles and biomolecules can be precisely positioned.The ability to control the spatial arrangement of the components while constructing highly organized networks will lead to various applications of these systems. For example, DNA nanoarrays with surface displays of molecular probes can sense noncovalent hybridization interactions with DNA, RNA, and proteins and covalent chemical reactions. DNA nanostructures can also align external molecules into well-defined arrays, which may improve the resolution of many structural determination methods, such as X-ray diffraction, cryo-EM, NMR, and super-resolution fluorescence. Moreover, by constraint of target entities to specific conformations, self-assembled DNA nanostructures can serve as molecular rulers to evaluate conformation-dependent activities.This Account describes the most recent advances in the DNA nanostructure directed assembly of biomolecular networks and explores the possibility of applying this technology to other fields of study. Recently, several reports have demonstrated the DNA nanostructure directed assembly of spatially interactive biomolecular networks. For example, researchers have constructed synthetic multienzyme cascades by organizing the position of the components using DNA nanoscaffolds in vitro or by utilizing RNA matrices in vivo. These structures display enhanced efficiency compared with the corresponding unstructured enzyme mixtures. Such systems are designed to mimic cellular function, where substrate diffusion between enzymes is facilitated and reactions are catalyzed with high efficiency and specificity. In addition, researchers have assembled multiple choromophores into arrays using a DNA nanoscaffold that optimizes the relative distance between the dyes and their spatial organization. The resulting artificial light-harvesting system exhibits efficient cascading energy transfers. Finally, DNA nanostructures have been used as assembly templates to construct nanodevices that execute rationally designed behaviors, including cargo loading, transportation, and route control.
Co-reporter:Fei Zhang, Jeanette Nangreave, Yan Liu, and Hao Yan
Nano Letters 2012 Volume 12(Issue 6) pp:3290-3295
Publication Date(Web):May 7, 2012
DOI:10.1021/nl301399z
The specificity of Watson–Crick base pairing, unique mechanical properties of DNA, and intrinsic stability of DNA double helices makes DNA an ideal material for the construction of dynamic nanodevices. Rationally designed strand displacement reactions can be used to produce dynamic reconfiguration of DNA nanostructures postassembly. Here we describe a ‘fold–release–fold’ strategy of multiple strand displacement and hybridization reactions to reconfigure a simple DNA origami structure into a complex, quasifractal pattern, demonstrating a complex transformation of DNA nanoarchitectures.
Co-reporter:Xiaowei Liu, Yang Xu, Tao Yu, Craig Clifford, Yan Liu, Hao Yan, and Yung Chang
Nano Letters 2012 Volume 12(Issue 8) pp:4254-4259
Publication Date(Web):July 3, 2012
DOI:10.1021/nl301877k
Safe and effective vaccines offer the best intervention for disease control. One strategy to maximize vaccine immunogenicity without compromising safety is to rationally design molecular complexes that mimic the natural structure of immunogenic microbes but without the disease-causing components. Here we use highly programmable DNA nanostructures as platforms to assemble a model antigen and CpG adjuvants together into nanoscale complexes with precise control of the valency and spatial arrangement of each element. Our results from immunized mice show that compared to a mixture of antigen and CpG molecules, the assembled antigen-adjuvant-DNA complexes induce strong and long-lasting antibody responses against the antigen without stimulating a reaction to the DNA nanostructure itself. This result demonstrates the potential of DNA nanostructures to serve as general platforms for the rational design and construction of a variety of vaccines.
Co-reporter:Jinglin Fu ; Minghui Liu ; Yan Liu ; Neal W. Woodbury
Journal of the American Chemical Society 2012 Volume 134(Issue 12) pp:5516-5519
Publication Date(Web):March 13, 2012
DOI:10.1021/ja300897h
Spatially addressable DNA nanostructures facilitate the self-assembly of heterogeneous elements with precisely controlled patterns. Here we organized discrete glucose oxidase (GOx)/horseradish peroxidase (HRP) enzyme pairs on specific DNA origami tiles with controlled interenzyme spacing and position. The distance between enzymes was systematically varied from 10 to 65 nm, and the corresponding activities were evaluated. The study revealed two different distance-dependent kinetic processes associated with the assembled enzyme pairs. Strongly enhanced activity was observed for those assemblies in which the enzymes were closely spaced, while the activity dropped dramatically for enzymes as little as 20 nm apart. Increasing the spacing further resulted in a much weaker distance dependence. Combined with diffusion modeling, the results suggest that Brownian diffusion of intermediates in solution governed the variations in activity for more distant enzyme pairs, while dimensionally limited diffusion of intermediates across connected protein surfaces contributed to the enhancement in activity for closely spaced GOx/HRP assemblies. To further test the role of limited dimensional diffusion along protein surfaces, a noncatalytic protein bridge was inserted between GOx and HRP to connect their hydration shells. This resulted in substantially enhanced activity of the enzyme pair.
Co-reporter:Na Lu ; Hao Pei ; Zhilei Ge ; Chad R. Simmons ; Hao Yan ;Chunhai Fan
Journal of the American Chemical Society 2012 Volume 134(Issue 32) pp:13148-13151
Publication Date(Web):July 18, 2012
DOI:10.1021/ja302447r
Three-dimensional (3D) DNA nanostructures have shown great promise for various applications including molecular sensing and therapeutics. Here we report kinetic studies of DNA-mediated charge transport (CT) within a 3D DNA nanostructure framework. A tetrahedral DNA nanostructure was used to investigate the through-duplex and through-space CT of small redox molecules (methylene blue (MB) and ferrocene (Fc)) that were bound to specific positions above the surface of the gold electrode. CT rate measurements provide unambiguous evidence that the intercalative MB probe undergoes efficient mediated CT over longer distances along the duplex, whereas the nonintercalative Fc probe tunnels electrons through the space. This study sheds new light on DNA-based molecular electronics and on designing high-performance biosensor devices.
Co-reporter:Zhengtao Deng ; Anirban Samanta ; Jeanette Nangreave ; Hao Yan ;Yan Liu
Journal of the American Chemical Society 2012 Volume 134(Issue 42) pp:17424-17427
Publication Date(Web):October 5, 2012
DOI:10.1021/ja3081023
The assembly and isolation of DNA oligonucleotide-functionalized gold nanoparticles (AuNPs) has become a well-developed technology that is based on the strong bonding interactions between gold and thiolated DNA. However, achieving DNA-functionalized semiconductor quantum dots (QDs) that are robust enough to withstand precipitation at high temperature and ionic strength through simple attachment of modified DNA to the QD surface remains a challenge. We report the synthesis of stable core/shell (1–20 monolayers) QD–DNA conjugates in which the end of the phosphorothiolated oligonucleotide (5–10 nucleotides) is “embedded” within the shell of the QD. These reliable QD–DNA conjugates exhibit excellent chemical and photonic stability, colloidal stability over a wide pH range (4–12) and at high salt concentrations (>100 mM Na+ or Mg2+), bright fluorescence emission with quantum yields of up to 70%, and broad spectral tunability with emission ranging from the UV to the NIR (360–800 nm).
Co-reporter:Qiao Jiang ; Chen Song ; Jeanette Nangreave ; Xiaowei Liu ; Lin Lin ; Dengli Qiu ; Zhen-Gang Wang ; Guozhang Zou ; Xingjie Liang ; Hao Yan ;Baoquan Ding
Journal of the American Chemical Society 2012 Volume 134(Issue 32) pp:13396-13403
Publication Date(Web):July 17, 2012
DOI:10.1021/ja304263n
Although a multitude of promising anti-cancer drugs have been developed over the past 50 years, effective delivery of the drugs to diseased cells remains a challenge. Recently, nanoparticles have been used as drug delivery vehicles due to their high delivery efficiencies and the possibility to circumvent cellular drug resistance. However, the lack of biocompatibility and inability to engineer spatially addressable surfaces for multi-functional activity remains an obstacle to their widespread use. Here we present a novel drug carrier system based on self-assembled, spatially addressable DNA origami nanostructures that confronts these limitations. Doxorubicin, a well-known anti-cancer drug, was non-covalently attached to DNA origami nanostructures through intercalation. A high level of drug loading efficiency was achieved, and the complex exhibited prominent cytotoxicity not only to regular human breast adenocarcinoma cancer cells (MCF 7), but more importantly to doxorubicin-resistant cancer cells, inducing a remarkable reversal of phenotype resistance. With the DNA origami drug delivery vehicles, the cellular internalization of doxorubicin was increased, which contributed to the significant enhancement of cell-killing activity to doxorubicin-resistant MCF 7 cells. Presumably, the activity of doxorubicin-loaded DNA origami inhibits lysosomal acidification, resulting in cellular redistribution of the drug to action sites. Our results suggest that DNA origami has immense potential as an efficient, biocompatible drug carrier and delivery vehicle in the treatment of cancer.
Co-reporter:Yang Yang, Dongran Han, Jeanette Nangreave, Yan Liu, and Hao Yan
ACS Nano 2012 Volume 6(Issue 9) pp:8209
Publication Date(Web):July 25, 2012
DOI:10.1021/nn302896c
Scaffolded DNA origami is a widely used technology for self-assembling precisely structured nanoscale objects that contain a large number of addressable features. Typical scaffolds are long, single strands of DNA (ssDNA) that are folded into distinct shapes through the action of many, short ssDNA staples that are complementary to several different domains of the scaffold. However, sources of long single-stranded DNA are scarce, limiting the size and complexity of structures that can be assembled. Here we demonstrated that dsDNA (double-stranded DNA) scaffolds can be directly used to fabricate integrated DNA origami structures that incorporate both of the constituent ssDNA molecules. Two basic principles were employed in the design of scaffold folding paths: folding path asymmetry and periodic convergence of the two ssDNA scaffold strands. Asymmetry in the folding path minimizes unwanted complementarity between staples, and incorporating an offset between the folding paths of each ssDNA scaffold strand reduces the number of times that complementary portions of the strands are brought into close proximity with one another, both of which decrease the likelihood of dsDNA scaffold recovery. Meanwhile, the folding paths of the two ssDNA scaffold strands were designed to periodically converge to promote the assembly of a single, unified structure rather than two individual ones. Our results reveal that this basic strategy can be used to reliably assemble integrated DNA nanostructures from dsDNA scaffolds.Keywords: DNA nanotechnology; DNA origami; double-stranded DNA scaffold; scaleup; self-assembly
Co-reporter:Qian Mei, Xixi Wei, Fengyu Su, Yan Liu, Cody Youngbull, Roger Johnson, Stuart Lindsay, Hao Yan, and Deirdre Meldrum
Nano Letters 2011 Volume 11(Issue 4) pp:1477-1482
Publication Date(Web):March 2, 2011
DOI:10.1021/nl1040836
Scaffolded DNA origami, a method to create self-assembled nanostructures with spatially addressable features, has recently been used to develop water-soluble molecular chips for label-free RNA detection, platforms for deterministic protein positioning, and single molecule reaction observatories. These applications highlight the possibility of exploiting the unique properties and biocompatibility of DNA nanostructures in live, cellular systems. Herein, we assembled several DNA origami nanostructures of differing shape, size and probes, and investigated their interaction with lysate obtained from various normal and cancerous cell lines. We separated and analyzed the origami−lysate mixtures using agarose gel electrophoresis and recovered the DNA structures for functional assay and subsequent microscopic examination. Our results demonstrate that DNA origami nanostructures are stable in cell lysate and can be easily separated from lysate mixtures, in contrast to natural, single- and double-stranded DNA. Atomic force microscope (AFM) and transmission electron microscope (TEM) images show that the DNA origami structures are fully intact after separation from cell lysates and hybridize to their targets, verifying the superior structural integrity and functionality of self-assembled DNA origami nanostructures relative to conventional oligonucleotides. The stability and functionality of DNA origami structures in cell lysate validate their use for biological applications, for example, as programmable molecular rafts or disease detection platforms.
Co-reporter:Zhao Zhao, Yan Liu, and Hao Yan
Nano Letters 2011 Volume 11(Issue 7) pp:2997-3002
Publication Date(Web):June 20, 2011
DOI:10.1021/nl201603a
Structural DNA nanotechnology utilizes DNA molecules as programmable information-coding polymers to create higher order structures at the nanometer scale. An important milestone in structural DNA nanotechnology was the development of scaffolded DNA origami in which a long single-stranded viral genome (scaffold strand) is folded into arbitrary shapes by hundreds of short synthetic oligonucleotides (staple strands). The achievable dimensions of the DNA origami tile units are currently limited by the length of the scaffold strand. Here we demonstrate a strategy referred to as “superorigami” or “origami of origami” to scale up DNA origami technology. First, this method uses a collection of bridge strands to prefold a single-stranded DNA scaffold into a loose framework. Subsequently, preformed individual DNA origami tiles are directed onto the loose framework so that each origami tile serves as a large staple. Using this strategy, we demonstrate the ability to organize DNA origami nanostructures into larger spatially addressable architectures.
Co-reporter:Suchetan Pal ; Zhengtao Deng ; Haining Wang ; Shengli Zou ; Yan Liu
Journal of the American Chemical Society 2011 Volume 133(Issue 44) pp:17606-17609
Publication Date(Web):October 8, 2011
DOI:10.1021/ja207898r
Programmable positioning of one-dimensional (1D) gold nanorods (AuNRs) was achieved by DNA directed self-assembly. AuNR dimer structures with various predetermined inter-rod angles and relative distances were constructed with high efficiency. These discrete anisotropic metallic nanostructures exhibit unique plasmonic properties, as measured experimentally and simulated by the discrete dipole approximation method.
Co-reporter:Suchetan Pal;Dr. Reji Varghese;Dr. Zhengtao Deng;Zhao Zhao;Ashok Kumar; Hao Yan; Yan Liu
Angewandte Chemie International Edition 2011 Volume 50( Issue 18) pp:4176-4179
Publication Date(Web):
DOI:10.1002/anie.201007529
Co-reporter:Zhao Zhao;Erica L. Jacovetty; Yan Liu; Hao Yan
Angewandte Chemie International Edition 2011 Volume 50( Issue 9) pp:2041-2044
Publication Date(Web):
DOI:10.1002/anie.201006818
Co-reporter:Chad R. Simmons, Dominik Schmitt, Xixi Wei, Dongran Han, Alex M. Volosin, Danielle M. Ladd, Dong-Kyun Seo, Yan Liu, and Hao Yan
ACS Nano 2011 Volume 5(Issue 7) pp:6060
Publication Date(Web):June 22, 2011
DOI:10.1021/nn2019286
A conductive nanoporous antimony-doped tin oxide (ATO) powder has been prepared using the sol–gel method that contains three-dimensionally interconnected pores within the metal oxide and highly tunable pore sizes on the nanoscale. It is demonstrated that these porous materials possess the capability of hosting a tetrahedral-shaped DNA nanostructure of defined dimensions with high affinity. The tunability of pore size enables the porous substrate to selectively absorb the DNA nanostructures into the metal oxide cavities or exclude them from entering the surface layer. Both confocal fluorescence microscopy and solution FRET experiments revealed that the DNA nanostructures maintained their integrity upon the size-selective incorporation into the cavities of the porous materials. As DNA nanostructures can serve as a stable three-dimensional nanoscaffold for the coordination of electron transfer mediators, this work opens up new possibilities of incorporating functionalized DNA architectures as guest molecules to nanoporous conductive metal oxides for applications such as photovoltaics, sensors, and solar fuel cells.Keywords: antimony-doped tin oxide (ATO); conductive metal oxides; DNA nanocages; DNA nanotechnology; nanoporous materials
Co-reporter:Zhao Zhao;Erica L. Jacovetty; Yan Liu; Hao Yan
Angewandte Chemie 2011 Volume 123( Issue 9) pp:2089-2092
Publication Date(Web):
DOI:10.1002/ange.201006818
Co-reporter:Hao Pei;Na Lu;Yanli Wen;Shiping Song;Yan Liu;Chunhai Fan
Advanced Materials 2010 Volume 22( Issue 42) pp:4754-4758
Publication Date(Web):
DOI:10.1002/adma.201002767
Co-reporter:Hao Pei;Na Lu;Yanli Wen;Shiping Song;Yan Liu;Chunhai Fan
Advanced Materials 2010 Volume 22( Issue 42) pp:
Publication Date(Web):
DOI:10.1002/adma.201090136
Co-reporter:Nicholas Stephanopoulos, Minghui Liu, Gary J. Tong, Zhe Li, Yan Liu, Hao Yan and Matthew B. Francis
Nano Letters 2010 Volume 10(Issue 7) pp:2714-2720
Publication Date(Web):June 24, 2010
DOI:10.1021/nl1018468
DNA origami was used as a scaffold to arrange spherical virus capsids into one-dimensional arrays with precise nanoscale positioning. To do this, we first modified the interior surface of bacteriophage MS2 capsids with fluorescent dyes as a model cargo. An unnatural amino acid on the external surface was then coupled to DNA strands that were complementary to those extending from origami tiles. Two different geometries of DNA tiles (rectangular and triangular) were used. The capsids associated with tiles of both geometries with virtually 100% efficiency under mild annealing conditions, and the location of capsid immobilization on the tile could be controlled by the position of the probe strands. The rectangular tiles and capsids could then be arranged into one-dimensional arrays by adding DNA strands linking the corners of the tiles. The resulting structures consisted of multiple capsids with even spacing (∼100 nm). We also used a second set of tiles that had probe strands at both ends, resulting in a one-dimensional array of alternating capsids and tiles. This hierarchical self-assembly allows us to position the virus particles with unprecedented control and allows the future construction of integrated multicomponent systems from biological scaffolds using the power of rationally engineered DNA nanostructures.
Co-reporter:Baoquan Ding, Hao Wu, Wei Xu, Zhao Zhao, Yan Liu, Hongbin Yu, and Hao Yan
Nano Letters 2010 Volume 10(Issue 12) pp:5065-5069
Publication Date(Web):November 11, 2010
DOI:10.1021/nl1033073
Scaffolded DNA origami has recently emerged as a versatile, programmable method to fold DNA into arbitrarily shaped nanostructures that are spatially addressable, with sub-10-nm resolution. Toward functional DNA nanotechnology, one of the key challenges is to integrate the bottom-up self-assembly of DNA origami with the top-down lithographic methods used to generate surface patterning. In this report we demonstrate that fixed length DNA origami nanotubes, modified with multiple thiol groups near both ends, can be used to connect surface patterned gold islands (tens of nanometers in diameter) fabricated by electron beam lithography (EBL). Atomic force microscopic imaging verified that the DNA origami nanotubes can be efficiently aligned between gold islands with various interisland distances and relative locations. This development represents progress toward the goal of bridging bottom-up and top-down assembly approaches.
Co-reporter:Zhao Zhao, Dr. ;Yan Liu Dr.
Angewandte Chemie International Edition 2010 Volume 49( Issue 8) pp:1414-1417
Publication Date(Web):
DOI:10.1002/anie.200906225
Co-reporter:Suchetan Pal;Zhengtao Deng Dr.;Baoquan Ding, Dr. ;Yan Liu Dr.
Angewandte Chemie International Edition 2010 Volume 49( Issue 15) pp:2700-2704
Publication Date(Web):
DOI:10.1002/anie.201000330
Co-reporter:Suchetan Pal;Zhengtao Deng Dr.;Baoquan Ding, Dr. ;Yan Liu Dr.
Angewandte Chemie 2010 Volume 122( Issue 15) pp:2760-2764
Publication Date(Web):
DOI:10.1002/ange.201000330
Co-reporter:Chenxiang Lin, Yonggang Ke, Zhe Li, James H. Wang, Yan Liu and Hao Yan
Nano Letters 2009 Volume 9(Issue 1) pp:433-436
Publication Date(Web):December 8, 2008
DOI:10.1021/nl803328v
L-DNA, the mirror image of natural D-DNA, can be readily self-assembled into designer discrete or periodic nanostructures. The assembly products are characterized by polyacrylamide gel electrophoresis, circular dichroism spectrum, atomic force microscope, and fluorescence microscope. We found that the use of enantiomer DNA as building material leads to the formation of DNA supramolecules with opposite chirality. Therefore, the L-DNA self-assembly is a substantial complement to the structural DNA nanotechnology. Moreover, the L-DNA architectures feature superior nuclease resistance thus are appealing for in vivo medical applications.
Co-reporter:Yonggang Ke, Jaswinder Sharma, Minghui Liu, Kasper Jahn, Yan Liu and Hao Yan
Nano Letters 2009 Volume 9(Issue 6) pp:2445-2447
Publication Date(Web):May 6, 2009
DOI:10.1021/nl901165f
We describe a strategy of scaffolded DNA origami to design and construct 3D molecular cages of tetrahedron geometry with inside volume closed by triangular faces. Each edge of the triangular face is ∼54 nm in dimension. The estimated total external volume and the internal cavity of the triangular pyramid are about 1.8 × 10−23 and 1.5 × 10−23 m3, respectively. Correct formation of the tetrahedron DNA cage was verified by gel electrophoresis, atomic force microscopy, transmission electron microscopy, and dynamic light scattering techniques.
Co-reporter:Casper S. Andersen, Martin M. Knudsen, Rahul Chhabra, Yan Liu, Hao Yan and Kurt V. Gothelf
Bioconjugate Chemistry 2009 Volume 20(Issue 8) pp:1538
Publication Date(Web):July 2, 2009
DOI:10.1021/bc900078c
The synthesis of a conjugated linear organic module containing terminal salicylaldehyde groups and a central activated ester, designed for conjugation to amino-modified oligonucleotides, is presented. The organic module has a phenylene−ethynylene backbone and is highly fluorescent. It is conjugated to oligonucleotide sequences and incorporated into specific locations in a well-defined DNA 4-helix bundle (4-HB). The DNA-nanostructure offers precise location control of the organic modules which allows for selective interhelical coupling reactions. In this study, metal-salen formation as well as dihydrazone formation are used to covalently interlink the organic modules. Both coupling reactions are highly dependent on the distances between the organic modules in the 4-HB. Neighboring modules dimerize easier, whereas more distanced modules are less prone to react, even when the linkers are extended. The dimeric products are characterized by denaturing polyacrylamide gel electrophoresis (PAGE), high performance liquid chromatography (HPLC), and matrix assisted laser desorption/absorption ionization time-of-flight (MALDI TOF) mass spectrometry.
Co-reporter:Chenxiang Lin, Yan Liu and Hao Yan
Biochemistry 2009 Volume 48(Issue 8) pp:
Publication Date(Web):January 27, 2009
DOI:10.1021/bi802324w
Naturally existing biological systems, from the simplest unicellular diatom to the most sophisticated organ such as the human brain, are functional self-assembled architectures. Scientists have long been dreaming about building artificial nanostructures that can mimic such elegance in nature. Structural DNA nanotechnology, which uses DNA as a blueprint and building material to organize matter with nanometer precision, represents an appealing solution to this challenge. On the basis of the knowledge of helical DNA structure and Watson−Crick base pairing rules, scientists have constructed a number of DNA nanoarchitectures with a large variety of geometries, topologies, and periodicities with considerably high yields. Modified by functional groups, those DNA nanostructures can serve as scaffolds to control the positioning of other molecular species, which opens opportunities to study intermolecular synergies, such as protein−protein interactions, as well as to build artificial multicomponent nanomachines. In this review, we summarize the principle of DNA self-assembly, describe the exciting progress of structural DNA nanotechnology in recent years, and discuss the current frontier.
Co-reporter:Rahul Chhabra;Yan Liu;Anchi Cheng;Jonathan Brownell;Jaswinder Sharma
Science 2009 Volume 323(Issue 5910) pp:
Publication Date(Web):
DOI:10.1126/science.1165831
Abstract
The assembly of nanoparticles into three-dimensional (3D) architectures could allow for greater control of the interactions between these particles or with molecules. DNA tubes are known to form through either self-association of multi-helix DNA bundle structures or closing up of 2D DNA tile lattices. By the attachment of single-stranded DNA to gold nanoparticles, nanotubes of various 3D architectures can form, ranging in shape from stacked rings to single spirals, double spirals, and nested spirals. The nanoparticles are active elements that control the preference for specific tube conformations through size-dependent steric repulsion effects. For example, we can control the tube assembly to favor stacked-ring structures using 10-nanometer gold nanoparticles. Electron tomography revealed a left-handed chirality in the spiral tubes, double-wall tube features, and conformational transitions between tubes.
Co-reporter:LindaA. Stearns;Rahul Chhabra;Jaswinder Sharma;Yan Liu ;WilliamT. Petuskey ;JohnC. Chaput
Angewandte Chemie International Edition 2009 Volume 48( Issue 45) pp:8494-8496
Publication Date(Web):
DOI:10.1002/anie.200903319
Co-reporter:LindaA. Stearns;Rahul Chhabra;Jaswinder Sharma;Yan Liu ;WilliamT. Petuskey ;JohnC. Chaput
Angewandte Chemie 2009 Volume 121( Issue 45) pp:8646-8648
Publication Date(Web):
DOI:10.1002/ange.200903319
Co-reporter:Yang Xu;Qiangbin Wang;Ping He;Qiaomei Dong;Fang Liu;Yan Liu;Lin Lin;Xiaohang Zhao
Advanced Materials 2008 Volume 20( Issue 18) pp:3468-3473
Publication Date(Web):
DOI:10.1002/adma.200703238
Co-reporter:Jaswinder Sharma;Yonggang Ke;Chenxiang Lin;Rahul Chhabra;Qiangbin Wang Dr.;Jeanette Nangreave;Yan Liu Dr. Dr.
Angewandte Chemie International Edition 2008 Volume 47( Issue 28) pp:5157-5159
Publication Date(Web):
DOI:10.1002/anie.200801485
Co-reporter:Yonggang Ke;Yan Liu;Yung Chang;Stuart Lindsay
Science 2008 Volume 319(Issue 5860) pp:
Publication Date(Web):
DOI:10.1126/science.1150082
Abstract
The DNA origami method, in which long, single-stranded DNA segments are folded into shapes by short staple segments, was used to create nucleic acid probe tiles that are molecular analogs of macroscopic DNA chips. One hundred trillion probe tiles were fabricated in one step and bear pairs of 20-nucleotide-long single-stranded DNA segments that act as probe sequences. These tiles can hybridize to their targets in solution and, after adsorption onto mica surfaces, can be examined by atomic force microscopy in order to quantify binding events, because the probe segments greatly increase in stiffness upon hybridization. The nucleic acid probe tiles have been used to study position-dependent hybridization on the nanoscale and have also been used for label-free detection of RNA.
Co-reporter:Chenxiang Lin;Sherri Rinker;Xing Wang;Nadrian C. Seeman;Yan Liu
PNAS 2008 Volume 105 (Issue 46 ) pp:17626-17631
Publication Date(Web):2008-11-18
DOI:10.1073/pnas.0805416105
Mimicking nature is both a key goal and a difficult challenge for the scientific enterprise. DNA, well known as the genetic-information
carrier in nature, can be replicated efficiently in living cells. Today, despite the dramatic evolution of DNA nanotechnology,
a versatile method that replicates artificial DNA nanostructures with complex secondary structures remains an appealing target.
Previous success in replicating DNA nanostructures enzymatically in vitro suggests that a possible solution could be cloning
these nanostructures by using viruses. Here, we report a system where a single-stranded DNA nanostructure (Holliday junction
or paranemic cross-over DNA) is inserted into a phagemid, transformed into XL1-Blue cells and amplified in vivo in the presence
of helper phages. High copy numbers of cloned nanostructures can be obtained readily by using standard molecular biology techniques.
Correct replication is verified by a number of assays including nondenaturing PAGE, Ferguson analysis, endonuclease VII digestion,
and hydroxyl radical autofootprinting. The simplicity, efficiency, and fidelity of nature are fully reflected in this system.
UV-induced psoralen cross-linking is used to probe the secondary structure of the inserted junction in infected cells. Our
data suggest the possible formation of the immobile four-arm junction in vivo.
Co-reporter:Qiangbin Wang, Yan Liu and Hao Yan
Chemical Communications 2007 (Issue 23) pp:2339-2341
Publication Date(Web):17 May 2007
DOI:10.1039/B701572K
This study clarifies the mechanism of the hollow structure formation in the simple self-templating preparation of monodispersed hollow silica structures; the role of the polarity of washing solvent in creating the hollow structure is emphasized.
Co-reporter:Chenxiang Lin;Yonggang Ke;Yan Liu Dr.;Michael Mertig ;Jian Gu Dr. Dr.
Angewandte Chemie 2007 Volume 119(Issue 32) pp:
Publication Date(Web):12 JUL 2007
DOI:10.1002/ange.200701767
In der Mitte getroffen: Regelmäßige Anordnungen selbstorganisierter funktioneller DNA-Nanoröhren sind mithilfe einer Kombination aus „Bottom-up“- und „Top-down“-Methoden zugänglich. Diese wiederum ermöglichen den Aufbau von Anordnungen aus Quantenpunkten, Proteinen und DNA-Zielmolekülen (siehe Bild; grün: DNA-Nanoröhre, rot: Streptavidin-Quantenpunkt-Konjugat; Maßstab: 20 μm).
Co-reporter:Berea A. R. Williams;Kyle Lund;Yan Liu Dr. Dr.;John C. Chaput Dr.
Angewandte Chemie 2007 Volume 119(Issue 17) pp:
Publication Date(Web):16 MAR 2007
DOI:10.1002/ange.200603919
Hochdichte Peptidanordnungen, die eine Vielzahl unterschiedlicher Aminosäuresequenzen an genau definierten und addressierbaren Stellen derselben DNA-Nanostruktur präsentieren können, wurden erzeugt. Dabei wurde die genetische Information genutzt, die im Nucleinsäureteil eines DNA-markierten Peptids verschlüsselt ist, um die Aminosäuresequenz an der vorbestimmten Stelle zu positionieren.
Co-reporter:Chenxiang Lin;Yonggang Ke;Yan Liu Dr.;Michael Mertig ;Jian Gu Dr. Dr.
Angewandte Chemie International Edition 2007 Volume 46(Issue 32) pp:
Publication Date(Web):12 JUL 2007
DOI:10.1002/anie.200701767
Meeting in the middle: Well-organized arrays of self-assembled functional DNA nanotubes can be constructed by combining bottom-up and top-down methods. Such DNA-nanotube arrays allow the construction of arrays of quantum dots, proteins, and DNA targets (see picture; green: DNA nanotube, red: streptavidin–quantum dot conjugate; scale bar: 20 μm).
Co-reporter:Berea A. R. Williams;Kyle Lund;Yan Liu Dr. Dr.;John C. Chaput Dr.
Angewandte Chemie International Edition 2007 Volume 46(Issue 17) pp:
Publication Date(Web):16 MAR 2007
DOI:10.1002/anie.200603919
On show: High-density peptide arrays capable of displaying many different amino acid sequences at well-defined and addressable locations on the same DNA nanostructure have been produced. The strategy used relies on the genetic information encoded in the nucleic acid portion of a DNA-tagged peptide to position the amino acid sequence at a predetermined location on the array.
Co-reporter:Qiangbin Wang Dr.;Yan Liu ;Yonggang Ke Dr.
Angewandte Chemie International Edition 2007 Volume 47( Issue 2) pp:316-319
Publication Date(Web):
DOI:10.1002/anie.200703648
Co-reporter:Sherri Rinker, Yan Liu and Hao Yan
Chemical Communications 2006 (Issue 25) pp:2675-2677
Publication Date(Web):23 May 2006
DOI:10.1039/B603872G
We measured the helical repeats of a non-natural nucleic acid, locked nucleic acid (LNA), by incorporating LNA strands into the outer arms of a DNA double crossover (DX) molecule; atomic force microscopy (AFM) imaging of the two-dimensional (2D) arrays self-assembled from these DX molecules allows us to derive the helical repeat of the LNA/DNA hetero-duplex to be 13.2 ± 0.9 base pairs per turn.
Co-reporter:Kyle Lund, Yan Liu and Hao Yan
Organic & Biomolecular Chemistry 2006 vol. 4(Issue 18) pp:3402-3403
Publication Date(Web):17 May 2006
DOI:10.1039/B605208H
Here we report a modular design of self-assembly of DNA nanostructures in a combinatorial approach; a square with ∼25 nm cavity dimension, a chair with ∼80 nm in height and a line with ∼100 nm in length are formed through combinations of four cross-shaped DNA tiles which are kept constant and six variable linker tiles.
Co-reporter:Chenxiang Lin;Mingyi Xie;Julian J. L. Chen Dr.;Yan Liu Dr. Dr.
Angewandte Chemie 2006 Volume 118(Issue 45) pp:
Publication Date(Web):18 OCT 2006
DOI:10.1002/ange.200602113
DNA bekommt Gesellschaft: Durch das „Rolling-circle“-Amplifikationsverfahren wurde ein vierarmiges DNA-Kreuzungsmotiv vervielfältigt. Unter geeigneten Bedingungen gelingt diese Vervielfältigung effizient und fehlerfrei, sodass die enzymatische Synthese von DNA-Nanostrukturen im großen Maßstab möglich wird.
Co-reporter:Jaswinder Sharma;Rahul Chhabra;Yan Liu Dr.;Yonggang Ke
Angewandte Chemie 2006 Volume 118(Issue 5) pp:
Publication Date(Web):19 DEC 2005
DOI:10.1002/ange.200503208
Die Eingliederung eines einzigen Goldnanopartikels in eine eigens entworfene DNA-Nanostruktur wird beschrieben. Durch Templat-Selbstorganisation bilden die nanopartikelhaltigen DNA-Nanostrukturen periodische Anordnungen. Mithilfe dieses Ansatzes können die Abstände zwischen den Partikeln festgelegt und hierarchische Nanopartikelarchitekturen erzeugt werden.
Co-reporter:Chenxiang Lin;Evaldas Katilius Dr.;Yan Liu Dr.;Junping Zhang Dr. Dr.
Angewandte Chemie International Edition 2006 Volume 45(Issue 32) pp:
Publication Date(Web):17 JUL 2006
DOI:10.1002/anie.200600438
Sticking the tiles: A DNA-tile-directed self-assembly of signaling aptamers into high-density nanoarrays allows subnanomolar detection of protein molecules by using confocal fluorescence microscopy imaging. This water-soluble aptamer microarray provides a novel strategy for developing programmable sensor arrays.
Co-reporter:Yan Liu Dr.;Sherri Rinker;Chenxiang Lin Dr.
ChemPhysChem 2006 Volume 7(Issue 8) pp:1641-1647
Publication Date(Web):10 JUL 2006
DOI:10.1002/cphc.200600260
DNA tile based self-assembly provides an attractive route to create nanoarchitectures of programmable patterns. It also offers excellent scaffolds for directed self-assembly of nanometer-scale materials, ranging from nanoparticles to proteins, with potential applications in constructing nanoelectronic/nanophotonic devices and protein/ligand nanoarrays. This Review first summarizes the currently available DNA tile toolboxes and further emphasizes recent developments toward self-assembling DNA nanostructures with increasing complexity. Exciting progress using DNA tiles for directed self-assembly of other nanometer scale components is also discussed.
Co-reporter:Chenxiang Lin;Evaldas Katilius Dr.;Yan Liu Dr.;Junping Zhang Dr. Dr.
Angewandte Chemie 2006 Volume 118(Issue 32) pp:
Publication Date(Web):17 JUL 2006
DOI:10.1002/ange.200600438
Fliesenlegen: Eine durch DNA-„Fliesen“ gesteuerte Selbstorganisation signalgebender Aptamere in hochdichte Nanogitter ermöglicht den subnanomolaren Nachweis von Proteinmolekülen mithilfe von konfokaler Fluoreszenzmikroskopie. Die wasserlösliche Aptameranordnung bietet eine neuartige Strategie zur Entwicklung programmierbarer Sensoren.
Co-reporter:Jaswinder Sharma, Rahul Chhabra, Yan Liu, Yonggang Ke,Hao Yan
Angewandte Chemie International Edition 2006 45(5) pp:730-735
Publication Date(Web):
DOI:10.1002/anie.200503208
Co-reporter:Chenxiang Lin;Mingyi Xie;Julian J. L. Chen Dr.;Yan Liu Dr. Dr.
Angewandte Chemie International Edition 2006 Volume 45(Issue 45) pp:
Publication Date(Web):18 OCT 2006
DOI:10.1002/anie.200602113
Armed forces: The rolling-circle amplification method has been used to replicate a four-arm DNA nanojunction. Under appropriate conditions, the DNA nano-objects can be replicated efficiently and correctly, therefore opening a new avenue for large-scale enzymatic synthesis of DNA nanostructures.
Co-reporter:Yan Liu Dr.;Chenxiang Lin;Hanying Li Dr.
Angewandte Chemie International Edition 2005 Volume 44(Issue 28) pp:
Publication Date(Web):9 JUN 2005
DOI:10.1002/anie.200501089
Lined up nicely: The self-assembly of proteins on rationally designed nanostructures into periodic linear arrays has been demonstrated. Triple-crossover DNA tiles 1 containing an aptamer sequence (AS) to which thrombin specifically binds can form linear arrays 2. These direct the ultimate positioning of thrombin proteins (green spheres) in 3. This system should facilitate the construction of other such programmable nanoscale protein arrays.
Co-reporter:Yan Liu Dr.;Chenxiang Lin;Hanying Li Dr.
Angewandte Chemie 2005 Volume 117(Issue 28) pp:
Publication Date(Web):9 JUN 2005
DOI:10.1002/ange.200501089
Sauber ausgerichtet: Die Selbstorganisation von Proteinen an rational entworfenen Nanostrukturen zu periodischen linearen Systemen wurde gezeigt. Tripel-Crossover-DNA-Fliesen 1, die eine spezifisch Thrombin bindende Aptamersequenz (AS) enthalten, bildeten lineare Systeme 2; diese steuern die Platzierung der Thrombinproteine (grüne Kugeln) in 3. Der Ansatz könnte auf die Konstruktion anderer programmierbarer nanoskaliger Proteinanordnungen übertragbar sein.
Co-reporter:Rahul Chhabra, Jaswinder Sharma, Yan Liu, Sherri Rinker, Hao Yan
Advanced Drug Delivery Reviews (30 April 2010) Volume 62(Issue 6) pp:617-625
Publication Date(Web):30 April 2010
DOI:10.1016/j.addr.2010.03.005
Self-assembling DNA nanostructures based on rationally designed DNA branch junction molecules has recently led to the construction of patterned supramolecular structures with increased complexities. An intrinsic value of DNA tiles and patterns lies in their utility as molecular pegboard for deterministic positioning of molecules or particles with accurate distance and architectural control. This review will discuss the state-of-art developments in self-assembled DNA nanostructural system. Biomedical aspects of information guided DNA nanostructures will also be summarized. We illustrate both the use of simple DNA artworks for sensing, computation, drug delivery and the application of more complex DNA architectures as scaffolds for the construction of protein and nanoparticle arrays.
Co-reporter:Jeanette Nangreave, Hao Yan, Yan Liu
Biophysical Journal (22 July 2009) Volume 97(Issue 2) pp:
Publication Date(Web):22 July 2009
DOI:10.1016/j.bpj.2009.05.013
A fundamental understanding of molecular self-assembly processes is important for improving the design and construction of higher-order supramolecular structures. DNA tile based self-assembly has recently been used to generate periodic and aperiodic nanostructures of different geometries, but there have been very few studies that focus on the thermodynamic properties of the inter-tile interactions. Here we demonstrate that fluorescently-labeled multihelical DNA tiles can be used as a model platform to systematically investigate multivalent DNA hybridization. Real-time monitoring of DNA tile assembly using fluorescence resonance energy transfer revealed that both the number and the relative position of DNA sticky-ends play a significant role in the stability of the final assembly. As multivalent interactions are important factors in nature's delicate macromolecular systems, our quantitative analysis of the stability and cooperativity of a network of DNA sticky-end associations could lead to greater control over hierarchical nanostructure formation and algorithmic self-assembly.
Co-reporter:Zhao Zhao, Yan Liu and Hao Yan
Organic & Biomolecular Chemistry 2013 - vol. 11(Issue 4) pp:NaN598-598
Publication Date(Web):2012/12/03
DOI:10.1039/C2OB26942B
Constructing intricate geometric arrangements of components is one of the central challenges of nanotechnology. Here we report a convenient, versatile method to organize discrete length single-walled carbon nanotubes (SWNT) into complex geometries using 2D DNA origami structures. First, a size exclusion HPLC purification protocol was used to isolate uniform length, SWNTs labelled with single stranded DNA (ssDNA). The nanotube-bound ssDNAs are composed of two domains: a SWNT binding domain and a linker binding domain. Although initially bound to the SWNTs, the linker domain is displaced from the surface by the addition of an external ssDNA linker strand. One portion of the linker strand is designed to form a double helix with the linker binding domain, compelling the DNA to project away from the SWNT surface. The remainder of the linker strand contains an ssDNA origami recognition sequence available for hybridization to a DNA origami nanostructure. Two different 2D DNA origami structures, a triangle and a rectangle, were used to organize the nanotubes. Several arrangements of nanotubes were constructed, with defined tube lengths and inter-tube angles. The uniform tube lengths and positional precision that this method affords may have applications in electronic device fabrication.
Co-reporter:Qiangbin Wang, Yan Liu and Hao Yan
Chemical Communications 2007(Issue 23) pp:NaN2341-2341
Publication Date(Web):2007/05/17
DOI:10.1039/B701572K
This study clarifies the mechanism of the hollow structure formation in the simple self-templating preparation of monodispersed hollow silica structures; the role of the polarity of washing solvent in creating the hollow structure is emphasized.
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