51
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Liu Z, Tian C, Yu J, Li Y, Jiang W, Mao C. Self-assembly of responsive multilayered DNA nanocages. J Am Chem Soc 2015; 137:1730-3. [PMID: 25628147 DOI: 10.1021/ja5101307] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Here we report the assembly of multilayered DNA nanocages. The layers can be separated in response to a chemical cue, ATP. This is an effort to increase the structural complexity of DNA nanocages. The structures have been characterized by native polyacrylamide gel electrophoresis, atomic force microscopy, and cryogenic electron microscopy. We envision that the layer-by-layer assembly strategy used in this study can be easily applied to other DNA nanocages to form Russian-doll-like semisolid structures, while the chemically activated layer separation makes a contribution to the development of "smart" DNA nanocages.
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Affiliation(s)
- Zhiyu Liu
- Department of Chemistry and ‡Markey Center for Structural Biology and Department of Biological Sciences, Purdue University , West Lafayette, Indiana 47907, United States
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52
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Giamblanco N, Conoci S, Russo D, Marletta G. Single-step label-free hepatitis B virus detection by a piezoelectric biosensor. RSC Adv 2015. [DOI: 10.1039/c5ra03467a] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Probe densityvs.genome recognition selectivity.
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Affiliation(s)
- Nicoletta Giamblanco
- Laboratory for Molecular Surfaces and Nanotechnology (LAMSUN)
- Department of Chemical Sciences
- University of Catania and CSGI
- 95125 Catania
- Italy
| | | | | | - Giovanni Marletta
- Laboratory for Molecular Surfaces and Nanotechnology (LAMSUN)
- Department of Chemical Sciences
- University of Catania and CSGI
- 95125 Catania
- Italy
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53
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Nakata E, Dinh H, Ngo TA, Saimura M, Morii T. A modular zinc finger adaptor accelerates the covalent linkage of proteins at specific locations on DNA nanoscaffolds. Chem Commun (Camb) 2015; 51:1016-9. [DOI: 10.1039/c4cc08167f] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A modular adaptor assists efficient occupation of specific addresses on DNA nanostructures by proteins of interest through a covalent linkage.
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Affiliation(s)
- Eiji Nakata
- Institute of Advanced Energy
- Kyoto University
- Uji
- Japan
| | - Huyen Dinh
- Institute of Advanced Energy
- Kyoto University
- Uji
- Japan
| | - Tien Anh Ngo
- Institute of Advanced Energy
- Kyoto University
- Uji
- Japan
| | | | - Takashi Morii
- Institute of Advanced Energy
- Kyoto University
- Uji
- Japan
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54
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Afonin KA, Lindsay B, Shapiro BA. Engineered RNA Nanodesigns for Applications in RNA Nanotechnology. DNA AND RNA NANOTECHNOLOGY 2015; 1:1-15. [PMID: 34322585 PMCID: PMC8315564 DOI: 10.2478/rnan-2013-0001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Nucleic acids have emerged as an extremely promising platform for nanotechnological applications because of their unique biochemical properties and functions. RNA, in particular, is characterized by relatively high thermal stability, diverse structural flexibility, and its capacity to perform a variety of functions in nature. These properties make RNA a valuable platform for bio-nanotechnology, specifically RNA Nanotechnology, that can create de novo nanostructures with unique functionalities through the design, integration, and re-engineering of powerful mechanisms based on a variety of existing RNA structures and their fundamental biochemical properties. This review highlights the principles that underlie the rational design of RNA nanostructures, describes the main strategies used to construct self-assembling nanoparticles, and discusses the challenges and possibilities facing the application of RNA Nanotechnology in the future.
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Affiliation(s)
- Kirill A. Afonin
- Center for Cancer Research Nanobiology Program, National Cancer Institute, Frederick, MD 21702, USA
| | - Brian Lindsay
- Center for Cancer Research Nanobiology Program, National Cancer Institute, Frederick, MD 21702, USA
| | - Bruce A. Shapiro
- Center for Cancer Research Nanobiology Program, National Cancer Institute, Frederick, MD 21702, USA
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55
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Bose T, Kumar VA. Simple molecular engineering of glycol nucleic acid: Progression from self-pairing to cross-pairing with cDNA and RNA. Bioorg Med Chem 2014; 22:6227-32. [DOI: 10.1016/j.bmc.2014.08.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 08/15/2014] [Accepted: 08/20/2014] [Indexed: 10/24/2022]
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56
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Cheng XS, Zhang H, Jin X, Qiu WY. Ear decomposition of 3-regular polyhedral links with applications. J Theor Biol 2014; 359:146-54. [PMID: 24952099 DOI: 10.1016/j.jtbi.2014.06.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Revised: 06/03/2014] [Accepted: 06/04/2014] [Indexed: 11/17/2022]
Abstract
In this paper, we introduce a notion of ear decomposition of 3-regular polyhedral links based on the ear decomposition of the 3-regular polyhedral graphs. As a result, we obtain an upper bound for the braid index of 3-regular polyhedral links. Our results may be used to characterize and analyze the structure and complexity of protein polyhedra and entanglement in biopolymers.
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Affiliation(s)
- Xiao-Sheng Cheng
- Department of Mathematics, Huizhou University, Huizhou, Guangdong 516007, PR China; School of Mathematical Sciences, Xiamen University, Xiamen, Fujian 361005, PR China.
| | - Heping Zhang
- School of Mathematics and Statistics, Lanzhou University, Lanzhou, Gansu 730000, PR China
| | - Xian'an Jin
- School of Mathematical Sciences, Xiamen University, Xiamen, Fujian 361005, PR China
| | - Wen-Yuan Qiu
- Department of Chemistry, Lanzhou University, Lanzhou, Gansu 730000, PR China
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57
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Samanta A, Zhou Y, Zou S, Yan H, Liu Y. Fluorescence quenching of quantum dots by gold nanoparticles: a potential long range spectroscopic ruler. NANO LETTERS 2014; 14:5052-7. [PMID: 25084363 DOI: 10.1021/nl501709s] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The dependence of quantum dot (QD) fluorescence emission on the proximity of 30 nm gold nanoparticles (AuNPs) was studied with controlled interparticle distances ranging from 15 to 70 nm. This was achieved by coassembling DNA-conjugated QDs and AuNPs in a 1:1 ratio at precise positions on a triangular-shaped DNA origami platform. A profound, long-range quenching of the photoluminescence intensity of the QDs was observed. A combination of static and time-resolved fluorescence measurements suggests that the quenching is due to an increase in the nonradiative decay rate of QD emission. Unlike FRET, the energy transfer is inversely proportional to the 2.7th power of the distance between nanoparticles with half quenching at ∼28 nm. This long-range quenching phenomena may be useful for developing extended spectroscopic rulers in the future.
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Affiliation(s)
- Anirban Samanta
- Department of Chemistry and Biochemistry, and Center for Molecular Design and Biomimicry, Biodesign Institute at Arizona State University , 1001 South McAllister Avenue, Tempe, Arizona 85287-5601, United States
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58
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Liu X, Lu CH, Willner I. Switchable reconfiguration of nucleic acid nanostructures by stimuli-responsive DNA machines. Acc Chem Res 2014; 47:1673-80. [PMID: 24654959 DOI: 10.1021/ar400316h] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
CONSPECTUS: The base sequence in DNA dictates structural and reactivity features of the biopolymer. These properties are implemented to use DNA as a unique material for developing the area of DNA nanotechnology. The design of DNA machines represents a rapidly developing research field in the area of DNA nanotechnology. The present Account discusses the switchable reconfiguration of nucleic acid nanostructures by stimuli-responsive DNA machines, and it highlights potential applications and future perspectives of the area. Programmed switchable DNA machines driven by various fuels and antifuels, such as pH, Hg(2+) ions/cysteine, or nucleic acid strands/antistrands, are described. These include the assembly of DNA tweezers, walkers, a rotor, a pendulum, and more. Using a pH-oscillatory system, the oscillatory mechanical operation of a DNA pendulum is presented. Specifically, the synthesis and "mechanical" properties of interlocked DNA rings are described. This is exemplified with the preparation of interlocked DNA catenanes and a DNA rotaxane. The dynamic fuel-driven reconfiguration of the catenane/rotaxane structures is followed by fluorescence spectroscopy. The use of DNA machines as functional scaffolds to reconfigurate Au nanoparticle assemblies and to switch the fluorescence features within fluorophore/Au nanoparticle conjugates between quenching and surface-enhanced fluorescence states are addressed. Specifically, the fluorescence features of the different DNA machines are characterized as a function of the spatial separation between the fluorophore and Au nanoparticles. The experimental results are supported by theoretical calculations. The future development of reconfigurable stimuli-responsive DNA machines involves fundamental challenges, such as the synthesis of molecular devices exhibiting enhanced complexities, the introduction of new fuels and antifuels, and the integration of new payloads being reconfigured by the molecular devices, such as enzymes or catalytic nanoparticles. Exciting applications of these systems are ahead of us, and switchable catalytic nanoparticle systems, switchable enzyme cascades, and spatially programmed nanoparticles for innovative nanomedicine may be envisaged. Also, the intracellular reconfiguration of nucleic acids by stimuli-responsive DNA machines holds great promise as a means to silence genes or inhibit metabolic pathways.
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Affiliation(s)
- Xiaoqing Liu
- Institute of Chemistry, Center
for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Chun-Hua Lu
- Institute of Chemistry, Center
for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Itamar Willner
- Institute of Chemistry, Center
for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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59
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Kumar A, Kumar V. Biotemplated Inorganic Nanostructures: Supramolecular Directed Nanosystems of Semiconductor(s)/Metal(s) Mediated by Nucleic Acids and Their Properties. Chem Rev 2014; 114:7044-78. [DOI: 10.1021/cr4007285] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Anil Kumar
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee-247667, India
| | - Vinit Kumar
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee-247667, India
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60
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Qing Z, He X, Huang J, Wang K, Zou Z, Qing T, Mao Z, Shi H, He D. Target-Catalyzed Dynamic Assembly-Based Pyrene Excimer Switching for Enzyme-Free Nucleic Acid Amplified Detection. Anal Chem 2014; 86:4934-9. [DOI: 10.1021/ac500834g] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Zhihe Qing
- State Key
Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, College
of Biology, Key Laboratory for Bio-Nanotechnology and Molecular Engineering
of Hunan Province, Hunan University, Changsha 410082, People’s Republic of China
| | - Xiaoxiao He
- State Key
Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, College
of Biology, Key Laboratory for Bio-Nanotechnology and Molecular Engineering
of Hunan Province, Hunan University, Changsha 410082, People’s Republic of China
| | - Jin Huang
- State Key
Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, College
of Biology, Key Laboratory for Bio-Nanotechnology and Molecular Engineering
of Hunan Province, Hunan University, Changsha 410082, People’s Republic of China
| | - Kemin Wang
- State Key
Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, College
of Biology, Key Laboratory for Bio-Nanotechnology and Molecular Engineering
of Hunan Province, Hunan University, Changsha 410082, People’s Republic of China
| | - Zhen Zou
- State Key
Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, College
of Biology, Key Laboratory for Bio-Nanotechnology and Molecular Engineering
of Hunan Province, Hunan University, Changsha 410082, People’s Republic of China
| | - Taiping Qing
- State Key
Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, College
of Biology, Key Laboratory for Bio-Nanotechnology and Molecular Engineering
of Hunan Province, Hunan University, Changsha 410082, People’s Republic of China
| | - Zhengui Mao
- State Key
Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, College
of Biology, Key Laboratory for Bio-Nanotechnology and Molecular Engineering
of Hunan Province, Hunan University, Changsha 410082, People’s Republic of China
| | - Hui Shi
- State Key
Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, College
of Biology, Key Laboratory for Bio-Nanotechnology and Molecular Engineering
of Hunan Province, Hunan University, Changsha 410082, People’s Republic of China
| | - Dinggeng He
- State Key
Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, College
of Biology, Key Laboratory for Bio-Nanotechnology and Molecular Engineering
of Hunan Province, Hunan University, Changsha 410082, People’s Republic of China
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61
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A protein adaptor to locate a functional protein dimer on molecular switchboard. Methods 2014; 67:142-50. [DOI: 10.1016/j.ymeth.2013.10.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Revised: 10/09/2013] [Accepted: 10/16/2013] [Indexed: 01/25/2023] Open
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62
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Clauvelin N, Olson WK, Tobias I. Effect of the boundary conditions and influence of the rotational inertia on the vibrational modes of an elastic ring. JOURNAL OF ELASTICITY 2014; 115:193-224. [PMID: 24795495 PMCID: PMC4006106 DOI: 10.1007/s10659-013-9453-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We present the small-amplitude vibrations of a circular elastic ring with periodic and clamped boundary conditions. We model the rod as an inextensible, isotropic, naturally straight Kirchhoff elastic rod and obtain the vibrational modes of the ring analytically for periodic boundary conditions and numerically for clamped boundary conditions. Of particular interest are the dependence of the vibrational modes on the torsional stress in the ring and the influence of the rotational inertia of the rod on the mode frequencies and amplitudes. In rescaling the Kirchhoff equations, we introduce a parameter inversely proportional to the aspect ratio of the rod. This parameter makes it possible to capture the influence of the rotational inertia of the rod. We find that the rotational inertia has a minor influence on the vibrational modes with the exception of a specific category of modes corresponding to high-frequency twisting deformations in the ring. Moreover, some of the vibrational modes over or undertwist the elastic rod depending on the imposed torsional stress in the ring.
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Affiliation(s)
- Nicolas Clauvelin
- BioMaPS Institute for Quantitative Biology, Rutgers, the State University of New Jersey, Piscataway, USA,
| | - Wilma K Olson
- BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, USA
| | - Irwin Tobias
- Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, USA,
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63
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Lau KL, Hamblin GD, Sleiman HF. Gold nanoparticle 3D-DNA building blocks: high purity preparation and use for modular access to nanoparticle assemblies. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:660-666. [PMID: 24115591 DOI: 10.1002/smll.201301562] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 07/12/2013] [Indexed: 06/02/2023]
Abstract
Using highly functional 'building-blocks' of AuNPs mono-conjugated to three-dimensional DNA 'rung' structures, both discrete and extended linear assemblies are controllably prepared via addition of various templating backbone strands. This unique approach presents a facile alternative to other methods of AuNP organization through DNA, and has potential utility in the fields of nanophotonics and nanoelectronics.
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Affiliation(s)
- Kai Lin Lau
- Department of Chemistry, McGill University, Montreal, QC, H3A 2K6, Canada
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64
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Ma'ani Hessari N, Spindler L, Troha T, Lam WC, Drevenšek-Olenik I, Webba da Silva M. Programmed Self-Assembly of a Quadruplex DNA Nanowire. Chemistry 2014; 20:3626-30. [DOI: 10.1002/chem.201300692] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 12/02/2013] [Indexed: 12/30/2022]
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65
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Yildirim I, Eryazici I, Nguyen ST, Schatz GC. Hydrophobic organic linkers in the self-assembly of small molecule-DNA hybrid dimers: a computational-experimental study of the role of linkage direction in product distributions and stabilities. J Phys Chem B 2014; 118:2366-76. [PMID: 24494718 PMCID: PMC3954456 DOI: 10.1021/jp501041m] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Detailed computational and experimental studies reveal the crucial role that hydrophobic interactions play in the self-assembly of small molecule-DNA hybrids (SMDHs) into cyclic nanostructures. In aqueous environments, the distribution of the cyclic structures (dimers or higher-order structures) greatly depends on how well the hydrophobic surfaces of the organic cores in these nanostructures are minimized. Specifically, when the cores are attached to the 3'-ends of the DNA component strands, they can insert into the minor groove of the duplex that forms upon self-assembly, favoring the formation of cyclic dimers. However, when the cores are attached to the 5'-ends of the DNA component strands, such insertion is hindered, leading to the formation of higher-order cyclic structures. These computational insights are supported by experimental results that show clear differences in product distributions and stabilities for a broad range of organic core-linked DNA hybrids with different linkage directions and flexibilities.
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Affiliation(s)
- Ilyas Yildirim
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208
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66
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Li X, Hao C, Tian C, Wang P, Mao C. Vernier assembly: controlling DNA polymerization via length mismatching. Chem Commun (Camb) 2014; 50:6361-3. [DOI: 10.1039/c4cc01608d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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67
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Zheng HN, Ma YZ, Xiao SJ. Periodical assembly of repetitive RNA sequences synthesized by rolling circle transcription with short DNA staple strands to RNA–DNA hybrid nanowires. Chem Commun (Camb) 2014; 50:2100-3. [DOI: 10.1039/c3cc48808j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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68
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Khimji I, Kelly EY, Helwa Y, Hoang M, Liu J. Visual optical biosensors based on DNA-functionalized polyacrylamide hydrogels. Methods 2013; 64:292-8. [DOI: 10.1016/j.ymeth.2013.08.021] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Revised: 08/04/2013] [Accepted: 08/16/2013] [Indexed: 12/17/2022] Open
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69
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Juul S, Iacovelli F, Falconi M, Kragh SL, Christensen B, Frøhlich R, Franch O, Kristoffersen EL, Stougaard M, Leong KW, Ho YP, Sørensen ES, Birkedal V, Desideri A, Knudsen BR. Temperature-controlled encapsulation and release of an active enzyme in the cavity of a self-assembled DNA nanocage. ACS NANO 2013; 7:9724-9734. [PMID: 24168393 DOI: 10.1021/nn4030543] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
We demonstrate temperature-controlled encapsulation and release of the enzyme horseradish peroxidase using a preassembled and covalently closed three-dimensional DNA cage structure as a controllable encapsulation device. The utilized cage structure was covalently closed and composed of 12 double-stranded B-DNA helices that constituted the edges of the structure. The double stranded helices were interrupted by short single-stranded thymidine linkers constituting the cage corners except for one, which was composed by four 32 nucleotide long stretches of DNA with a sequence that allowed them to fold into hairpin structures. As demonstrated by gel-electrophoretic and fluorophore-quenching experiments this design imposed a temperature-controlled conformational transition capability to the structure, which allowed entrance or release of an enzyme cargo at 37 °C while ensuring retainment of the cargo in the central cavity of the cage at 4 °C. The entrapped enzyme was catalytically active inside the DNA cage and was able to convert substrate molecules penetrating the apertures in the DNA lattice that surrounded the central cavity of the cage.
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Affiliation(s)
- Sissel Juul
- Department of Biomedical Engineering, Duke University , Durham, North Carolina 27708, United States
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70
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Zhu J, Zhang L, Dong S, Wang E. Four-way junction-driven DNA strand displacement and its application in building majority logic circuit. ACS NANO 2013; 7:10211-10217. [PMID: 24134127 DOI: 10.1021/nn4044854] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
We introduced a four-way DNA junction-driven toehold-mediated strand displacement method. Separation of the different functional domains on different strands in the four-way junction structure and usage of glue strand to recombine them for different logic gates make the design more flexible. On the basis of this mechanism, a majority logic circuit fabricated by DNA strands was designed and constructed by assembling three AND gates and one OR gate together. The output strand drew the G-rich segments together to form a split G-quadruplex, which could specifically bind PPIX and enhance its fluorescence. Just like a poll with three voters, the high fluorescence signal would be given off only when two or three voters vote in favor. Upon slight modification, the majority circuit was utilized to select the composite number from 0 to 9 represented by excess-three code. It is a successful attempt to integrate the logic gates into a circuit and to achieve desired functions.
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Affiliation(s)
- Jinbo Zhu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun, Jilin 130022, P. R. China
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71
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A prospective overview of the essential requirements in molecular modeling for nanomedicine design. Future Med Chem 2013; 5:929-46. [PMID: 23682569 DOI: 10.4155/fmc.13.67] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Nanotechnology has presented many new challenges and opportunities in the area of nanomedicine design. The issues related to nanoconjugation, nanosystem-mediated targeted drug delivery, transitional stability of nanovehicles, the integrity of drug transport, drug-delivery mechanisms and chemical structural design require a pre-estimated and determined course of assumptive actions with property and characteristic estimations for optimal nanomedicine design. Molecular modeling in nanomedicine encompasses these pre-estimations and predictions of pertinent design data via interactive computographic software. Recently, an increasing amount of research has been reported where specialized software is being developed and employed in an attempt to bridge the gap between drug discovery, materials science and biology. This review provides an assimilative and concise incursion into the current and future strategies of molecular-modeling applications in nanomedicine design and aims to describe the utilization of molecular models and theoretical-chemistry computographic techniques for expansive nanomedicine design and development.
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72
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Jin Z, Sun W, Ke Y, Shih CJ, Paulus GLC, Hua Wang Q, Mu B, Yin P, Strano MS. Metallized DNA nanolithography for encoding and transferring spatial information for graphene patterning. Nat Commun 2013; 4:1663. [PMID: 23575667 DOI: 10.1038/ncomms2690] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 03/04/2013] [Indexed: 12/23/2022] Open
Abstract
The vision for graphene and other two-dimensional electronics is the direct production of nanoelectronic circuits and barrier materials from a single precursor sheet. DNA origami and single-stranded tiles are powerful methods to encode complex shapes within a DNA sequence, but their translation to patterning other nanomaterials has been limited. Here we develop a metallized DNA nanolithography that allows transfer of spatial information to pattern two-dimensional nanomaterials capable of plasma etching. Width, orientation and curvature can be programmed by specific sequence design and transferred, as we demonstrate for graphene. Spatial resolution is limited by distortion of the DNA template upon Au metallization and subsequent etching. The metallized DNA mask allows for plasmonic enhanced Raman spectroscopy of the underlying graphene, providing information on defects, doping and lattice symmetry. This DNA nanolithography enables wafer-scale patterning of two-dimensional electronic materials to create diverse circuit elements, including nanorings, three- and four-membered nanojunctions, and extended nanoribbons.
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Affiliation(s)
- Zhong Jin
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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73
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Qiu M, Khisamutdinov E, Zhao Z, Pan C, Choi JW, Leontis NB, Guo P. RNA nanotechnology for computer design and in vivo computation. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2013; 371:20120310. [PMID: 24000362 PMCID: PMC3758167 DOI: 10.1098/rsta.2012.0310] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Molecular-scale computing has been explored since 1989 owing to the foreseeable limitation of Moore's law for silicon-based computation devices. With the potential of massive parallelism, low energy consumption and capability of working in vivo, molecular-scale computing promises a new computational paradigm. Inspired by the concepts from the electronic computer, DNA computing has realized basic Boolean functions and has progressed into multi-layered circuits. Recently, RNA nanotechnology has emerged as an alternative approach. Owing to the newly discovered thermodynamic stability of a special RNA motif (Shu et al. 2011 Nat. Nanotechnol. 6, 658-667 (doi:10.1038/nnano.2011.105)), RNA nanoparticles are emerging as another promising medium for nanodevice and nanomedicine as well as molecular-scale computing. Like DNA, RNA sequences can be designed to form desired secondary structures in a straightforward manner, but RNA is structurally more versatile and more thermodynamically stable owing to its non-canonical base-pairing, tertiary interactions and base-stacking property. A 90-nucleotide RNA can exhibit 4⁹⁰ nanostructures, and its loops and tertiary architecture can serve as a mounting dovetail that eliminates the need for external linking dowels. Its enzymatic and fluorogenic activity creates diversity in computational design. Varieties of small RNA can work cooperatively, synergistically or antagonistically to carry out computational logic circuits. The riboswitch and enzymatic ribozyme activities and its special in vivo attributes offer a great potential for in vivo computation. Unique features in transcription, termination, self-assembly, self-processing and acid resistance enable in vivo production of RNA nanoparticles that harbour various regulators for intracellular manipulation. With all these advantages, RNA computation is promising, but it is still in its infancy. Many challenges still exist. Collaborations between RNA nanotechnologists and computer scientists are necessary to advance this nascent technology.
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Affiliation(s)
- Meikang Qiu
- Department of Computer Engineering, San Jose State University, San Jose, CA 95192, USA
| | - Emil Khisamutdinov
- Department of Pharmaceutical Science, University of Kentucky, Lexington, KY 40506, USA
| | - Zhengyi Zhao
- Department of Pharmaceutical Science, University of Kentucky, Lexington, KY 40506, USA
| | - Cheryl Pan
- Department of Electrical and Computer Engineering, University of Kentucky, Lexington, KY 40506, USA
| | - Jeong-Woo Choi
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul 121-742, Korea
| | - Neocles B. Leontis
- Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Peixuan Guo
- Department of Pharmaceutical Science, University of Kentucky, Lexington, KY 40506, USA
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74
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Edwardson TGW, Carneiro KMM, McLaughlin CK, Serpell CJ, Sleiman HF. Site-specific positioning of dendritic alkyl chains on DNA cages enables their geometry-dependent self-assembly. Nat Chem 2013; 5:868-75. [DOI: 10.1038/nchem.1745] [Citation(s) in RCA: 172] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 07/29/2013] [Indexed: 12/22/2022]
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75
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Zheng J, Zhu G, Li Y, Li C, You M, Chen T, Song E, Yang R, Tan W. A spherical nucleic acid platform based on self-assembled DNA biopolymer for high-performance cancer therapy. ACS NANO 2013; 7:6545-54. [PMID: 23841478 PMCID: PMC3793642 DOI: 10.1021/nn402344v] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Based on their enhanced cellular uptake, stability, biocompatibility, and versatile surface functionalization, spherical nucleic acids (SNAs) have become a potentially useful platform in biological applications. It still remains important to expand the SNAs' "toolbox", especially given the current interest in multimodal or theranostic nanomaterials, that is, composites capable of multiple simultaneous applications such as imaging, sensing, and drug delivery. In this paper, we have engineered a nanoparticle-conjugated initiator that triggers a cascade of hybridization reactions resulting in the formation of a long DNA polymer as the nanoparticle shell. By employing different DNA fragments, self-assembled multifunctional SNAs can be constructed. Therefore, using one capped ligand, these SNAs can combine imaging fluorescent tags, target recognition element, and targeted delivery molecules together. Since these SNAs possess high drug loading capacity and high specificity by the incorporation of an aptamer, our approach might find potential applications in new drug development, existing drug improvement, and drug delivery for cancer therapy.
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Affiliation(s)
- Jing Zheng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha, 410082, P. R. China
- Center For Research at Bio/nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - Guizhi Zhu
- Center For Research at Bio/nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - Yinhui Li
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha, 410082, P. R. China
| | - Chunmei Li
- Center For Research at Bio/nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, USA
- Ministry of Education Key Laboratory on Luminescence and Real-Time Analysis, College of Chemistry and Chemical Engineering, College of Pharmaceutical Science, Southwest University, Chongqing 400715, People's Republic of China
| | - Mingxu You
- Center For Research at Bio/nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - Tao Chen
- Center For Research at Bio/nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - Erqun Song
- Center For Research at Bio/nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, USA
- Ministry of Education Key Laboratory on Luminescence and Real-Time Analysis, College of Chemistry and Chemical Engineering, College of Pharmaceutical Science, Southwest University, Chongqing 400715, People's Republic of China
| | - Ronghua Yang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha, 410082, P. R. China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha, 410082, P. R. China
- Center For Research at Bio/nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, USA
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76
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Shu Y, Shu D, Haque F, Guo P. Fabrication of pRNA nanoparticles to deliver therapeutic RNAs and bioactive compounds into tumor cells. Nat Protoc 2013; 8:1635-59. [PMID: 23928498 DOI: 10.1038/nprot.2013.097] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
RNA nanotechnology is a term that refers to the design, fabrication and use of nanoparticles that are mainly composed of RNAs via bottom-up self-assembly. The packaging RNA (pRNA) of the bacteriophage phi29 DNA packaging motor has been developed into a nanodelivery platform. This protocol describes the synthesis, assembly and functionalization of pRNA nanoparticles on the basis of three 'toolkits' derived from pRNA structural features: interlocking loops for hand-in-hand interactions, palindrome sequences for foot-to-foot interactions and an RNA three-way junction for branch extension. siRNAs, ribozymes, aptamers, chemical ligands, fluorophores and other functionalities can also be fused to the pRNA before the assembly of the nanoparticles, so as to ensure the production of homogeneous nanoparticles and the retention of appropriate folding and function of the incorporated modules. The resulting self-assembled multivalent pRNA nanoparticles are thermodynamically and chemically stable, and they remain intact at ultralow concentrations. Gene-silencing effects are progressively enhanced with increasing numbers of siRNAs in each pRNA nanoparticle. Systemic injection of the pRNA nanoparticles into xenograft-bearing mice has revealed strong binding to tumors without accumulation in vital organs or tissues. The pRNA-based nanodelivery scaffold paves a new way for nanotechnological application of pRNA-based nanoparticles for disease detection and treatment. The time required for completing one round of this protocol is 3-4 weeks when including in vitro functional assays, or 2-3 months when including in vivo studies.
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Affiliation(s)
- Yi Shu
- Nanobiotechnology Center, Markey Cancer Center, Lexington, Kentucky, USA
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77
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Sikora JR, Rauzan B, Stegemann R, Deckert A. Modeling stopped-flow data for nucleic acid duplex formation reactions: the importance of off-path intermediates. J Phys Chem B 2013; 117:8966-76. [PMID: 23902467 DOI: 10.1021/jp404550a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Evidence for unexpected off-path intermediates to DNA duplex formation is presented. These off-path intermediates are shown to involve unimolecular and, in one case, bimolecular structure in one of the single strands of complementary DNA. Three models are developed to account for the observed single-stranded structures that are formed in parallel with duplex formation. These models are applied to the analysis of stopped-flow data for eight different nonself-complementary duplex formation reactions in order to extract the elementary rate constant for formation of the duplex from the complementary random coil single-stranded DNA. The free energy of activation (at 25 °C) for the denaturation of each duplex is calculated from these data and is shown to have a linear correlation to the overall standard free energy for duplex formation (also at 25 °C). Duplexes that contain mismatches obey a parallel linear free-energy (LFE) relationship with a y-intercept that is greater than that of duplexes without mismatches. Slopes near unity for the LFE relationships indicate that all duplexes go through an early, unstructured transition state.
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Affiliation(s)
- Jacqueline R Sikora
- Department of Chemistry, Allegheny College, 520 North Main Street, Meadville, Pennsylvania 16335, USA
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78
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79
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Sonay AY, Culha M. DNA-mediated self-assembly of single-walled carbon nanotubes into nanorings. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2013; 9:2059-2063. [PMID: 23390056 DOI: 10.1002/smll.201202804] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2012] [Indexed: 06/01/2023]
Affiliation(s)
- Ali Yasin Sonay
- Department of Genetics and Bioengineering, Yeditepe University, Ataşehir, Istanbul 34755, Turkey
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80
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Abstract
Synthetic nucleic acid analogues have profoundly advanced our knowledge of DNA and RNA, as well as the complex biological processes that involve nucleic acids. As a pivotal enzyme, eukaryotic RNA polymerase II (Pol II) is responsible for transcribing DNA into messenger RNA, which serves as a template to direct protein synthesis. Chemically modified nucleic acid analogues have greatly facilitated the structural elucidation of RNA Pol II elongation complex and understanding the key chemical interactions governing RNA Pol II transcriptional fidelity. This review addresses major progress in RNA polymerase II mechanistic studies using modified nucleic acid analogues in recent years.
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Affiliation(s)
- Su Zhang
- University of California, San Diego, Skaggs School of Pharmacy & Pharmaceutical Sciences
| | - Dong Wang
- University of California, San Diego, Skaggs School of Pharmacy & Pharmaceutical Sciences
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81
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Liu Z, Li Y, Tian C, Mao C. A Smart DNA Tetrahedron That Isothermally Assembles or Dissociates in Response to the Solution pH Value Changes. Biomacromolecules 2013; 14:1711-4. [PMID: 23647463 DOI: 10.1021/bm400426f] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Zhiyu Liu
- Department of Chemistry, Purdue University, West Lafayette, Indiana
47907, United
States
| | - Yingmei Li
- Department of Chemistry, Purdue University, West Lafayette, Indiana
47907, United
States
| | - Cheng Tian
- Department of Chemistry, Purdue University, West Lafayette, Indiana
47907, United
States
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, Indiana
47907, United
States
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82
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Hamblin GD, Hariri AA, Carneiro KMM, Lau KL, Cosa G, Sleiman HF. Simple design for DNA nanotubes from a minimal set of unmodified strands: rapid, room-temperature assembly and readily tunable structure. ACS NANO 2013; 7:3022-8. [PMID: 23452006 DOI: 10.1021/nn4006329] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
DNA nanotubes have great potential as nanoscale scaffolds for the organization of materials and the templation of nanowires and as drug delivery vehicles. Current methods for making DNA nanotubes either rely on a tile-based step-growth polymerization mechanism or use a large number of component strands and long annealing times. Step-growth polymerization gives little control over length, is sensitive to stoichiometry, and is slow to generate long products. Here, we present a design strategy for DNA nanotubes that uses an alternative, more controlled growth mechanism, while using just five unmodified component strands and a long enzymatically produced backbone. These tubes form rapidly at room temperature and have numerous, orthogonal sites available for the programmable incorporation of arrays of cargo along their length. As a proof-of-concept, cyanine dyes were organized into two distinct patterns by inclusion into these DNA nanotubes.
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Affiliation(s)
- Graham D Hamblin
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8 Canada
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83
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Separation of Short Single- and Double-Stranded DNA Based on Their Adsorption Kinetics Difference on Graphene Oxide. NANOMATERIALS 2013; 3:221-228. [PMID: 28348332 PMCID: PMC5327888 DOI: 10.3390/nano3020221] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 03/27/2013] [Accepted: 03/28/2013] [Indexed: 11/16/2022]
Abstract
Separation of short single- and double-stranded DNA typically requires gel electrophoresis followed by DNA extraction, which is a time consuming process. Graphene oxide adsorbs single-stranded DNA more quickly than double-stranded ones, allowing for selective removal of the former with a simple mixing and centrifugation operation. The effect of DNA length and salt on adsorption selectivity has been characterized and its application in DNA melting curve measurement has been demonstrated.
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84
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Choi J, Majima T. Reversible conformational switching of i-motif DNA studied by fluorescence spectroscopy. Photochem Photobiol 2013; 89:513-22. [PMID: 23311444 DOI: 10.1111/php.12042] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 01/04/2013] [Indexed: 12/19/2022]
Abstract
Non-B DNAs, which can form unique structures other than double helix of B-DNA, have attracted considerable attention from scientists in various fields including biology, chemistry and physics etc. Among them, i-motif DNA, which is formed from cytosine (C)-rich sequences found in telomeric DNA and the promoter region of oncogenes, has been extensively investigated as a signpost and controller for the oncogene expression at the transcription level and as a promising material in nanotechnology. Fluorescence techniques such as fluorescence resonance energy transfer (FRET) and the fluorescence quenching are important for studying DNA and in particular for the visualization of reversible conformational switching of i-motif DNA that is triggered by the protonation. Here, we review the latest studies on the conformational dynamics of i-motif DNA as well as the application of FRET and fluorescence quenching techniques to the visualization of reversible conformational switching of i-motif DNA in nano-biotechnology.
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Affiliation(s)
- Jungkweon Choi
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Osaka, Japan
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85
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86
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Kazane SA, Axup JY, Kim CH, Ciobanu M, Wold ED, Barluenga S, Hutchins BA, Schultz PG, Winssinger N, Smider VV. Self-assembled antibody multimers through peptide nucleic acid conjugation. J Am Chem Soc 2013; 135:340-6. [PMID: 23210862 PMCID: PMC3951380 DOI: 10.1021/ja309505c] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
With the recent clinical success of bispecific antibodies, a strategy to rapidly synthesize and evaluate bispecific or higher order multispecific molecules could facilitate the discovery of new therapeutic agents. Here, we show that unnatural amino acids (UAAs) with orthogonal chemical reactivity can be used to generate site-specific antibody-oligonucleotide conjugates. These constructs can then be self-assembled into multimeric complexes with defined composition, valency, and geometry. With this approach, we generated potent bispecific antibodies that recruit cytotoxic T lymphocytes to Her2 and CD20 positive cancer cells, as well as multimeric antibody fragments with enhanced activity. This strategy should accelerate the synthesis and in vitro characterization of antibody constructs with unique specificities and molecular architectures.
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Affiliation(s)
- Stephanie A. Kazane
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Jun Y Axup
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Chan Hyuk Kim
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Mihai Ciobanu
- Department of Chemistry, Institute for Science and Supramolecular Engineering, 8 allée Gaspard Monge, 67000 Strasbourg, France
| | - Erik D. Wold
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Sofia Barluenga
- Department of Chemistry, Institute for Science and Supramolecular Engineering, 8 allée Gaspard Monge, 67000 Strasbourg, France
| | - Benjamin A. Hutchins
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Peter G. Schultz
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Nicolas Winssinger
- Department of Chemistry, Institute for Science and Supramolecular Engineering, 8 allée Gaspard Monge, 67000 Strasbourg, France
- Department of Organic Chemistry, University of Geneva, Geneva CH-1211, Switzerland
| | - Vaughn V. Smider
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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87
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Tian C, Zhang C, Li X, Li Y, Wang G, Mao C. Artificial, Parallel, Left-Handed DNA Helices. J Am Chem Soc 2012; 134:20273-5. [PMID: 23215536 DOI: 10.1021/ja309908s] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Cheng Tian
- Department
of Chemistry, Purdue University, West Lafayette,
Indiana 47907, United
States
| | - Chuan Zhang
- Department
of Chemistry, Purdue University, West Lafayette,
Indiana 47907, United
States
| | - Xiang Li
- Department
of Chemistry, Purdue University, West Lafayette,
Indiana 47907, United
States
| | - Yingmei Li
- Department
of Chemistry, Purdue University, West Lafayette,
Indiana 47907, United
States
| | - Guansong Wang
- The Institute of
Respiratory
Diseases, Xinqiao Hospital, Chongqing 400037,
China
| | - Chengde Mao
- Department
of Chemistry, Purdue University, West Lafayette,
Indiana 47907, United
States
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88
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Submicrometre geometrically encoded fluorescent barcodes self-assembled from DNA. Nat Chem 2012; 4:832-9. [PMID: 23000997 DOI: 10.1038/nchem.1451] [Citation(s) in RCA: 211] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Accepted: 08/08/2012] [Indexed: 12/12/2022]
Abstract
The identification and differentiation of a large number of distinct molecular species with high temporal and spatial resolution is a major challenge in biomedical science. Fluorescence microscopy is a powerful tool, but its multiplexing ability is limited by the number of spectrally distinguishable fluorophores. Here, we used (deoxy)ribonucleic acid (DNA)-origami technology to construct submicrometre nanorods that act as fluorescent barcodes. We demonstrate that spatial control over the positioning of fluorophores on the surface of a stiff DNA nanorod can produce 216 distinct barcodes that can be decoded unambiguously using epifluorescence or total internal reflection fluorescence microscopy. Barcodes with higher spatial information density were demonstrated via the construction of super-resolution barcodes with features spaced by ∼40 nm. One species of the barcodes was used to tag yeast surface receptors, which suggests their potential applications as in situ imaging probes for diverse biomolecular and cellular entities in their native environments.
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89
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Abstract
The goal of this paper is to determine the braid index of two types of complicated DNA polyhedral links introduced by chemists and biologists in recent years. We shall study it in a more broad context and actually consider so-called Jaeger's links (more general Traldi's links) which contain, as special cases, both four types of simple polyhedral links whose braid indexes have been determined and the above two types of complicated DNA polyhedral links. Denote by and the braid index and crossing number of an oriented link , respectively. Roughly speaking, in this paper, we prove that for any link in a family including Jaeger's links and contained in Traldi's links, which is obtained by combining the MFW inequality and an Ohyama's result on upper bound of the braid index. Our result may be used to to characterize and analyze the structure and complexity of DNA polyhedra and entanglement in biopolymers.
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Affiliation(s)
- Xiao-Sheng Cheng
- Department of Mathematics, Huizhou University, Huizhou, Guangdong, P.R. China
- School of Mathematical Sciences, Xiamen University, Xiamen, Fujian, P.R. China
| | - Xian'an Jin
- School of Mathematical Sciences, Xiamen University, Xiamen, Fujian, P.R. China
- * E-mail:
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90
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Abstract
Bionanocomposites are a novel class of nanosized materials. They contain the constituent of biological origin and particles with at least one dimension in the range of 1–100 nm. There are similarities with nanocomposites but also fundamental differences in the methods of preparation, properties, functionalities, biodegradability, biocompatibility, and applications. The article includes two parts. Bionanocomposite definition and classification along with nanoparticles, biomaterials, and methods of their preparation are initially reviewed. Then, novel approaches developed by our team are presented. The first approach concerns the preparation of bionanocomposites from chitosan and nanoparticles. It is based on the regulated charging of polysaccharide by the gradual shift of solution pH. When charges appear, the biomacromolecules come into the electrostatic interactions with negatively charged nanoparticles that cause the jellification of solutions. It is also applied to form films. They have a nacre-like structure from stacked planar nanoparticles separated by aligned biomacromolecules. The second approach deals with the biomimicking mineralization of biopolymers by using a novel silica precursor. Its advantage over the current sol-gel processing is in the compatibility and regulation of processes and structure of generated silica. Another example of the mineralization is presented by titania. Syntheses are performed in anhydrous ethylene glycol. Processes and structure of bionanocomposites are regulated by water that is added in an amount to only hydrate functional groups in the carbohydrate macromolecule.
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Affiliation(s)
- Yury Shchipunov
- 1Institute of Chemistry, Far East Department, Russian Academy of Sciences, 690022 Vladivostok, Russia; The WCU Center for Synthetic Polymer Bioconjugate Hybrid Materials, Department of Polymer Science and Engineering, Pusan National University, San 30, Jangjun Dong, Geumjung Gu, Busan, 609-735 Korea
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91
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Yang W, Chen Y, Wong MS, Lo PK. Reinforced Self-Assembly of Donor–Acceptor π-Conjugated Molecules to DNA Templates by Dipole–Dipole Interactions Together with Complementary Hydrogen Bonding Interactions for Biomimetics. Biomacromolecules 2012; 13:3370-6. [DOI: 10.1021/bm301131k] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Wanggui Yang
- Department of Chemistry and Institute of Molecular Functional Materials, Hong Kong Baptist University, Kowloon Tong, Hong Kong,
SAR
| | - Yali Chen
- Department of Chemistry, Shanghai University, Shanghai, China
| | - Man Shing Wong
- Department of Chemistry and Institute of Molecular Functional Materials, Hong Kong Baptist University, Kowloon Tong, Hong Kong,
SAR
| | - Pik Kwan Lo
- Department of Biology
and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, SAR
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92
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Fu J, Liu M, Liu Y, Yan H. Spatially-interactive biomolecular networks organized by nucleic acid nanostructures. Acc Chem Res 2012; 45:1215-26. [PMID: 22642503 DOI: 10.1021/ar200295q] [Citation(s) in RCA: 129] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
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.
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Affiliation(s)
- Jinglin Fu
- Center for Single Molecule Biophysics, ‡Center for Innovations in Medicine at the Biodesign Institute, and §Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Minghui Liu
- Center for Single Molecule Biophysics, ‡Center for Innovations in Medicine at the Biodesign Institute, and §Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Yan Liu
- Center for Single Molecule Biophysics, ‡Center for Innovations in Medicine at the Biodesign Institute, and §Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Hao Yan
- Center for Single Molecule Biophysics, ‡Center for Innovations in Medicine at the Biodesign Institute, and §Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
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93
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Ohya Y, Miyoshi N, Hashizume M, Tamaki T, Uehara T, Shingubara S, Kuzuya A. Formation of 1D and 2D gold nanoparticle arrays by divalent DNA-gold nanoparticle conjugates. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2012; 8:2335-2340. [PMID: 22549919 DOI: 10.1002/smll.201200092] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Revised: 02/03/2012] [Indexed: 05/31/2023]
Abstract
Divalent DNA-AuNP (gold nanoparticle) conjugates comprising two DNA strands at diametrically opposed positions are prepared. Highly linear 1D and tetragonal lattice-like 2D AuNP arrays are constructed using the conjugates and DNA assemblies based on T- and double-crossover motifs and the Holliday junction.
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Affiliation(s)
- Yuichi Ohya
- Department of Chemistry and Materials Engineering, Kansai University, 3-3-35 Yamate, Suita, Osaka 564-8680, Japan.
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94
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Zhang C, Tian C, Li X, Qian H, Hao C, Jiang W, Mao C. Reversibly Switching the Surface Porosity of a DNA Tetrahedron. J Am Chem Soc 2012; 134:11998-2001. [DOI: 10.1021/ja305969c] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | - Hang Qian
- College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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95
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Zhang C, Wu W, Li X, Tian C, Qian H, Wang G, Jiang W, Mao C. Controlling the Chirality of DNA Nanocages. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201203875] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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96
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Zhang C, Wu W, Li X, Tian C, Qian H, Wang G, Jiang W, Mao C. Controlling the Chirality of DNA Nanocages. Angew Chem Int Ed Engl 2012; 51:7999-8002. [DOI: 10.1002/anie.201203875] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2012] [Indexed: 11/10/2022]
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97
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98
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Mashimo Y, Maeda H, Mie M, Kobatake E. Construction of semisynthetic DNA-protein conjugates with Phi X174 Gene-A* protein. Bioconjug Chem 2012; 23:1349-55. [PMID: 22616938 DOI: 10.1021/bc300118m] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
DNA-protein conjugates have frequently been used as versatile molecular tools for a variety of applications in biotechnology to harness synergistic effects of DNA and protein functions. With applications for DNA-protein conjugates growing, easy-to-use and economical methods for the synthesis of DNA-protein conjugates are required. In this study, we developed a method for site-specific labeling of single-stranded DNA (ssDNA) to a recombinant protein of interest (POI) through the Gene-A* protein (Gene-A*) from bacteriophage phi X174, without any chemical modifications of ssDNA. Gene-A* protein is an enzyme that site-selectively cleaves an oligodeoxyribonucleotide (ODN) containing a Gene-A* recognition sequence, at which point a tyrosine residue of Gene-A* is bonded to the 5'-phosphoryl group of the cleavage site via a stable phosphotyrosine linkage. Here, we constructed three kinds of recombinant proteins fused to Gene-A*: N-terminally Gene-A*-fused enhanced green fluorescent protein (EGFP), C-terminally Gene-A*-fused EGFP, and N-terminally Gene-A*-fused firefly luciferase (FLuc). The reaction yields of DNA-protein conjugation catalyzed by the Gene-A* moiety reached 80-90% in the three proteins, and kinetic study revealed that the reaction achieved a steady state after 10 min. Moreover, dot blot analyses were performed to evaluate the hybridization and aptamer-forming ability of ssDNA conjugated to the Gene-A* moiety of a recombinant Gene-A*-FLuc protein. This study demonstrated that a strategy using recombinant proteins fused to Gene-A* could offer a versatile, rapid, easy-to-use, and economical platform for producing DNA-protein conjugates.
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Affiliation(s)
- Yasumasa Mashimo
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology , 4259, Nagatsuta, Midori-ku, Yokohama-shi, 226-8501, Japan
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99
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Eryazici I, Yildirim I, Schatz GC, Nguyen ST. Enhancing the Melting Properties of Small Molecule-DNA Hybrids through Designed Hydrophobic Interactions: An Experimental-Computational Study. J Am Chem Soc 2012; 134:7450-8. [DOI: 10.1021/ja300322a] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Ibrahim Eryazici
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208,
United States
| | - Ilyas Yildirim
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208,
United States
| | - George C. Schatz
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208,
United States
| | - SonBinh T. Nguyen
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208,
United States
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100
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Zhang X, Yadavalli VK. Functional self-assembled DNA nanostructures for molecular recognition. NANOSCALE 2012; 4:2439-2446. [PMID: 22399156 DOI: 10.1039/c2nr11711h] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Nucleic acids present a wonderful toolkit of structural motifs for nanoconstruction. Functional DNA nanostructures can enable protein recognition by the use of aptamers attached to a basic core shape formed by DNA self-assembly. Here, we present a facile, programmable strategy for the assembly of discrete aptamer-tagged DNA shapes and nanostructures that can function for molecular recognition and binding in an aqueous environment. These nanostructures, presented here to bind two different protein targets, are easily synthesized in large numbers, and are portable and stable over long periods of time. This construction modality can facilitate on-demand production of libraries of diverse shapes to recognize and bind proteins or catalyze reactions via functional nucleic acid tags.
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Affiliation(s)
- Xiaojuan Zhang
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond, VA 23284, USA
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