1
|
Kaymaz SV, Nobar HM, Sarıgül H, Soylukan C, Akyüz L, Yüce M. Nanomaterial surface modification toolkit: Principles, components, recipes, and applications. Adv Colloid Interface Sci 2023; 322:103035. [PMID: 37931382 DOI: 10.1016/j.cis.2023.103035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 09/11/2023] [Accepted: 10/26/2023] [Indexed: 11/08/2023]
Abstract
Surface-functionalized nanostructures are at the forefront of biotechnology, providing new opportunities for biosensors, drug delivery, therapy, and bioimaging applications. The modification of nanostructures significantly impacts the performance and success of various applications by enabling selective and precise targeting. This review elucidates widely practiced surface modification strategies, including click chemistry, cross-coupling, silanization, aldehyde linkers, active ester chemistry, maleimide chemistry, epoxy linkers, and other protein and DNA-based methodologies. We also delve into the application-focused landscape of the nano-bio interface, emphasizing four key domains: therapeutics, biosensing, environmental monitoring, and point-of-care technologies, by highlighting prominent studies. The insights presented herein pave the way for further innovations at the intersection of nanotechnology and biotechnology, providing a useful handbook for beginners and professionals. The review draws on various sources, including the latest research articles (2018-2023), to provide a comprehensive overview of the field.
Collapse
Affiliation(s)
- Sümeyra Vural Kaymaz
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey; SUNUM Nanotechnology Research and Application Centre, Sabanci University, Istanbul 34956, Turkey
| | | | - Hasan Sarıgül
- SUNUM Nanotechnology Research and Application Centre, Sabanci University, Istanbul 34956, Turkey
| | - Caner Soylukan
- SUNUM Nanotechnology Research and Application Centre, Sabanci University, Istanbul 34956, Turkey
| | - Lalehan Akyüz
- Department of Molecular Biology and Genetics, Aksaray University, 68100 Aksaray, Turkey
| | - Meral Yüce
- SUNUM Nanotechnology Research and Application Centre, Sabanci University, Istanbul 34956, Turkey.
| |
Collapse
|
2
|
Hartung J, McCann N, Doe E, Hayth H, Benkato K, Johnson MB, Viard M, Afonin KA, Khisamutdinov EF. Toehold-Mediated Shape Transition of Nucleic Acid Nanoparticles. ACS APPLIED MATERIALS & INTERFACES 2023; 15:25300-25312. [PMID: 37204867 PMCID: PMC10331730 DOI: 10.1021/acsami.3c01604] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
We introduce a toehold-mediated strand displacement strategy for regulated shape-switching of nucleic acid nanoparticles (NANPs) enabling their sequential transformation from triangular to hexagonal architectures at isothermal conditions. The successful shape transitions were confirmed by electrophoretic mobility shift assays, atomic force microscopy, and dynamic light scattering. Furthermore, implementation of split fluorogenic aptamers allowed for monitoring the individual transitions in real time. Three distinct RNA aptamers─malachite green (MG), broccoli, and mango─were embedded within NANPs as reporter domains to confirm shape transitions. While MG "lights up" within the square, pentagonal, and hexagonal constructs, the broccoli is activated only upon formation of pentagon and hexagon NANPs, and mango reports only the presence of hexagons. Moreover, the designed RNA fluorogenic platform can be employed to construct a logic gate that performs an AND operation with three single-stranded RNA inputs by implementing a non-sequential polygon transformation approach. Importantly, the polygonal scaffolds displayed promising potential as drug delivery agents and biosensors. All polygons exhibited effective cellular internalization followed by specific gene silencing when decorated with fluorophores and RNAi inducers. This work offers a new perspective for the design of toehold-mediated shape-switching nanodevices to activate different light-up aptamers for the development of biosensors, logic gates, and therapeutic devices in the nucleic acid nanotechnology.
Collapse
Affiliation(s)
- Jordan Hartung
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Nathan McCann
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Erwin Doe
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Hannah Hayth
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Kheiria Benkato
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - M Brittany Johnson
- Department of Biology, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Mathias Viard
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, United States
- Basic Science Program, Leidos Biomedical Research Inc. National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Kirill A Afonin
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Emil F Khisamutdinov
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| |
Collapse
|
3
|
Kansara K, Mansuri A, Rajwar A, Vaswani P, Singh R, Kumar A, Bhatia D. Spatiotemporal dynamics of DNA nanocage uptake in zebrafish embryos for targeted tissue bioimaging applications. NANOSCALE ADVANCES 2023; 5:2558-2564. [PMID: 37143798 PMCID: PMC10153486 DOI: 10.1039/d2na00905f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 04/02/2023] [Indexed: 05/06/2023]
Abstract
Three-dimensional DNA nanocages have attracted significant attention for various biomedical applications including targeted bioimaging in vivo. Despite the numerous advantages, the use and in vivo exploration of DNA nanocages are limited as the cellular targeting and intracellular fate of these DNA nanocages within various model systems have not been explored well. Herein, using a zebrafish model system, we provide a detailed understanding of time-, tissue- and geometry-dependent DNA nanocage uptake in developing embryos and larvae. Of all the geometries tested, tetrahedrons showed significant internalization in 72 hours post-fertilized larvae upon exposure, without disturbing the expression of genes involved in embryo development. Our study provides a detailed understanding of the time and tissue-specific uptake of DNA nanocages in the zebrafish embryos and larvae. These findings will provide valuable insights into the internalization and biocompatible potential of DNA nanocages and will help to predict their candidature for biomedical applications.
Collapse
Affiliation(s)
- Krupa Kansara
- Biological and Engineering Discipline, Indian Institute of Technology - Gandhinagar (IITGN) India
| | - Abdulkhalik Mansuri
- Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University Central Campus Navrangpura India
| | - Anjali Rajwar
- Biological and Engineering Discipline, Indian Institute of Technology - Gandhinagar (IITGN) India
| | - Payal Vaswani
- Biological and Engineering Discipline, Indian Institute of Technology - Gandhinagar (IITGN) India
| | - Ramesh Singh
- Biological and Engineering Discipline, Indian Institute of Technology - Gandhinagar (IITGN) India
| | - Ashutosh Kumar
- Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University Central Campus Navrangpura India
| | - Dhiraj Bhatia
- Biological and Engineering Discipline, Indian Institute of Technology - Gandhinagar (IITGN) India
| |
Collapse
|
4
|
van Dyck JF, Burns JR, Le Huray KIP, Konijnenberg A, Howorka S, Sobott F. Sizing up DNA nanostructure assembly with native mass spectrometry and ion mobility. Nat Commun 2022; 13:3610. [PMID: 35750666 PMCID: PMC9232653 DOI: 10.1038/s41467-022-31029-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 05/30/2022] [Indexed: 11/09/2022] Open
Abstract
Recent interest in biological and synthetic DNA nanostructures has highlighted the need for methods to comprehensively characterize intermediates and end products of multimeric DNA assembly. Here we use native mass spectrometry in combination with ion mobility to determine the mass, charge state and collision cross section of noncovalent DNA assemblies, and thereby elucidate their structural composition, oligomeric state, overall size and shape. We showcase the approach with a prototypical six-subunit DNA nanostructure to reveal how its assembly is governed by the ionic strength of the buffer, as well as how the mass and mobility of heterogeneous species can be well resolved by careful tuning of instrumental parameters. We find that the assembly of the hexameric, barrel-shaped complex is guided by positive cooperativity, while previously undetected higher-order 12- and 18-mer assemblies are assigned to defined larger-diameter geometric structures. Guided by our insight, ion mobility-mass spectrometry is poised to make significant contributions to understanding the formation and structural diversity of natural and synthetic oligonucleotide assemblies relevant in science and technology.
Collapse
Affiliation(s)
- Jeroen F van Dyck
- Biomolecular & Analytical Mass Spectrometry, Chemistry Department, University of Antwerp, Antwerpen, Belgium
| | - Jonathan R Burns
- Department of Chemistry & Institute of Structural and Molecular Biology, University College London, London, UK
| | - Kyle I P Le Huray
- School of Molecular and Cellular Biology & Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Albert Konijnenberg
- Biomolecular & Analytical Mass Spectrometry, Chemistry Department, University of Antwerp, Antwerpen, Belgium.,Thermo Fisher Scientific, Eindhoven, The Netherlands
| | - Stefan Howorka
- Department of Chemistry & Institute of Structural and Molecular Biology, University College London, London, UK.
| | - Frank Sobott
- Biomolecular & Analytical Mass Spectrometry, Chemistry Department, University of Antwerp, Antwerpen, Belgium. .,School of Molecular and Cellular Biology & Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK.
| |
Collapse
|
5
|
Chen S, Hermann T. RNA-DNA Hybrid Nanoshape Synthesis by Facile Module Exchange. J Am Chem Soc 2021; 143:20356-20362. [PMID: 34818893 DOI: 10.1021/jacs.1c09739] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The preparation of nucleic acid nanostructures has relied predominantly on procedures of additive fabrication in which complex architectures are assembled by concerted self-assembly and sequential addition of building blocks. We had previously established RNA-DNA hybrid nanoshapes with modular architectures that enable multistep synthetic approaches inspired by organic molecular synthesis where additive and transformative steps are used to prepare complex molecular architectures. We report the establishment of module replacement and strand exchange as synthetic transformations in nucleic acid hybrid nanoshapes, which are enabled by minimally destabilizing sequence elements such as a single unpaired overhang nucleotide or a mismatch base pair. Module exchange facilitated by thermodynamic lability triggers adds a powerful transformative approach to the repertoire of additive and transformative synthetic methods for the preparation of complex composite materials.
Collapse
|
6
|
Xue C, Zhang S, Yu X, Hu S, Lu Y, Wu Z. Periodically Ordered, Nuclease‐Resistant DNA Nanowires Decorated with Cell‐Specific Aptamers as Selective Theranostic Agents. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004805] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Chang Xue
- Cancer Metastasis Alert and Prevention Center Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy National and Local Joint Biomedical Engineering Research Center on Photodynamic Technologies Pharmaceutical Photocatalysis of State Key Laboratory of, Photocatalysis on Energy and Environment College of Chemistry Fuzhou University Fuzhou 350002 China
| | - Songbai Zhang
- Cancer Metastasis Alert and Prevention Center Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy National and Local Joint Biomedical Engineering Research Center on Photodynamic Technologies Pharmaceutical Photocatalysis of State Key Laboratory of, Photocatalysis on Energy and Environment College of Chemistry Fuzhou University Fuzhou 350002 China
- College of Chemistry and Materials Engineering Hunan University of Arts and Science Changde 415000 China
| | - Xin Yu
- Cancer Metastasis Alert and Prevention Center Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy National and Local Joint Biomedical Engineering Research Center on Photodynamic Technologies Pharmaceutical Photocatalysis of State Key Laboratory of, Photocatalysis on Energy and Environment College of Chemistry Fuzhou University Fuzhou 350002 China
| | - Shuyao Hu
- Cancer Metastasis Alert and Prevention Center Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy National and Local Joint Biomedical Engineering Research Center on Photodynamic Technologies Pharmaceutical Photocatalysis of State Key Laboratory of, Photocatalysis on Energy and Environment College of Chemistry Fuzhou University Fuzhou 350002 China
| | - Yi Lu
- Department of Chemistry Cancer Center at Illinois University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Zai‐Sheng Wu
- Cancer Metastasis Alert and Prevention Center Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy National and Local Joint Biomedical Engineering Research Center on Photodynamic Technologies Pharmaceutical Photocatalysis of State Key Laboratory of, Photocatalysis on Energy and Environment College of Chemistry Fuzhou University Fuzhou 350002 China
| |
Collapse
|
7
|
Xue C, Zhang S, Yu X, Hu S, Lu Y, Wu ZS. Periodically Ordered, Nuclease-Resistant DNA Nanowires Decorated with Cell-Specific Aptamers as Selective Theranostic Agents. Angew Chem Int Ed Engl 2020; 59:17540-17547. [PMID: 32613705 DOI: 10.1002/anie.202004805] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Indexed: 12/21/2022]
Abstract
DNA nanostructures have shown potential in cancer therapy. However, their clinical application is hampered by the difficulty to deliver them into cancer cells and susceptibility to nuclease degradation. To overcome these limitations, we report herein a periodically ordered nick-hidden DNA nanowire (NW) with high serum stability and active targeting functionality. The inner core is made of multiple connected DNA double helices, and the outer shell is composed of regularly arranged standing-up hairpin aptamers. All termini of the components are hidden from nuclease attack, whereas the target-binding sites are exposed to allow delivery to the cancer target. The DNA NW remained intact during incubation for 24 h in serum solution. Animal imaging and cell apoptosis showed that NWs loaded with an anticancer drug displayed long blood-circulation time and high specificity in inducing cancer-cell apoptosis, thus validating this approach for the targeted imaging and therapy of cancers.
Collapse
Affiliation(s)
- Chang Xue
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, National and Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, Pharmaceutical Photocatalysis of State Key Laboratory of, Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China
| | - Songbai Zhang
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, National and Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, Pharmaceutical Photocatalysis of State Key Laboratory of, Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China.,College of Chemistry and Materials Engineering, Hunan University of Arts and Science, Changde, 415000, China
| | - Xin Yu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, National and Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, Pharmaceutical Photocatalysis of State Key Laboratory of, Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China
| | - Shuyao Hu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, National and Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, Pharmaceutical Photocatalysis of State Key Laboratory of, Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China
| | - Yi Lu
- Department of Chemistry, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Zai-Sheng Wu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, National and Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, Pharmaceutical Photocatalysis of State Key Laboratory of, Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China
| |
Collapse
|
8
|
Chen Z, Su Y, Liu Y, Huang J, Cao W. Key technologies of intelligent transportation based on image recognition. INT J ADV ROBOT SYST 2020. [DOI: 10.1177/1729881420917277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
With the development of economy, the research of urban intelligent transportation system is becoming more and more important. The research and development of plate number recognition system is an important factor to realize the intelligence and modernization of transportation system. It uses each car to have a unique plate number and recognizes the vehicle number through the vehicle image captured by the camera. On the basis of image recognition, this article takes plate number image as the research object and discusses the key technologies of plate number recognition system. First, this article uses image preprocessing technology to process images to improve image quality. Second, the plate number location algorithm based on the connected region search is analyzed. According to the characteristics of the plate number itself, the regional features of the plate number are extracted to locate the plate number accurately. Then, an improved vertical projection-based plate number character segmentation method is proposed to segment plate number characters. Finally, combined with character characteristics, the template matching method is used to recognize plate number characters. The simulation results show that, on the basis of image recognition, this article studies the key technologies of plate number recognition system, which effectively improves the performance of the system and makes the recognition of plate number more effective and accurate.
Collapse
Affiliation(s)
- Zeyou Chen
- School of Civil Engineering, Architecture, and Environment, Xihua University, Chengdu, China
| | - Yangyang Su
- School of Civil Engineering, Architecture, and Environment, Xihua University, Chengdu, China
| | - Yong Liu
- China State Construction International Investments (Shannxi) Limited, Shannxi, China
| | - Jiazhen Huang
- School of Civil Engineering, Architecture, and Environment, Xihua University, Chengdu, China
| | - Wuwen Cao
- School of Civil Engineering, Architecture, and Environment, Xihua University, Chengdu, China
| |
Collapse
|
9
|
Ghosh D, Datta LP, Govindaraju T. Molecular architectonics of DNA for functional nanoarchitectures. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2020; 11:124-140. [PMID: 31976202 PMCID: PMC6964666 DOI: 10.3762/bjnano.11.11] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 12/09/2019] [Indexed: 05/08/2023]
Abstract
DNA is the key biomolecule central to almost all processes in living organisms. The eccentric idea of utilizing DNA as a material building block in molecular and structural engineering led to the creation of numerous molecular-assembly systems and materials at the nanoscale. The molecular structure of DNA is believed to have evolved over billions of years, with structure and stability optimizations that allow life forms to sustain through the storage and transmission of genetic information with fidelity. The nanoscale structural characteristics of DNA (2 nm thickness and ca. 40-50 nm persistence length) have inspired the creation of numerous functional patterns and architectures through noncovalent conventional and unconventional base pairings as well as through mutual templating-interactions with small organic molecules and metal ions. The recent advancements in structural DNA nanotechnology allowed researchers to design new DNA-based functional materials with chemical and biological properties distinct from their parent components. The modulation of structural and functional properties of hybrid DNA ensembles of small functional molecules (SFMs) and short oligonucleotides by adapting the principles of molecular architectonics enabled the creation of novel DNA nanoarchitectures with potential applications, which has been termed as templated DNA nanotechnology or functional DNA nanoarchitectonics. This review highlights the molecular architectonics-guided design principles and applications of the derived DNA nanoarchitectures. The advantages and ability of functional DNA nanoarchitectonics to overcome the trivial drawbacks of classical DNA nanotechnology to fulfill realistic and practical applications are highlighted, and an outlook on future developments is presented.
Collapse
Affiliation(s)
- Debasis Ghosh
- Bioorganic Chemistry Laboratory, New Chemistry Unit and The School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P. O., Bengaluru 560064, Karnataka, India
| | - Lakshmi P Datta
- Bioorganic Chemistry Laboratory, New Chemistry Unit and The School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P. O., Bengaluru 560064, Karnataka, India
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit and The School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P. O., Bengaluru 560064, Karnataka, India
| |
Collapse
|
10
|
Burns JR, Howorka S. Structural and Functional Stability of DNA Nanopores in Biological Media. NANOMATERIALS 2019; 9:nano9040490. [PMID: 30934927 PMCID: PMC6523550 DOI: 10.3390/nano9040490] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 03/22/2019] [Accepted: 03/23/2019] [Indexed: 01/20/2023]
Abstract
DNA nanopores offer a unique nano-scale foothold at the membrane interface that can help advance the life sciences as biophysical research tools or gate-keepers for drug delivery. Biological applications require sufficient physiological stability and membrane activity for viable biological action. In this report, we determine essential parameters for efficient nanopore folding and membrane binding in biocompatible cell media. The parameters are identified for an archetypal DNA nanopore composed of six interwoven strands carrying cholesterol lipid anchors. Using gel electrophoresis and fluorescence spectroscopy, the nanostructures are found to assemble efficiently in cell media, such as LB and DMEM, and remain structurally stable at physiological temperatures. Furthermore, the pores’ oligomerization state is monitored using fluorescence spectroscopy and confocal microscopy. The pores remain predominately water-soluble over 24 h in all buffer systems, and were able to bind to lipid vesicles after 24 h to confirm membrane activity. However, the addition of fetal bovine serum to DMEM causes a significant reduction in nanopore activity. Serum proteins complex rapidly to the pore, most likely via ionic interactions, to reduce the effective nanopore concentration in solution. Our findings outline crucial conditions for maintaining lipidated DNA nanodevices, structurally and functionally intact in cell media, and pave the way for biological studies in the future.
Collapse
Affiliation(s)
- Jonathan R Burns
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, UK.
| | - Stefan Howorka
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, UK.
- Institute of Biophysics, Johannes Kepler University, A-4020 Linz, Austria.
| |
Collapse
|
11
|
Tomaszewska-Antczak A, Jastrzębska K, Maciaszek A, Mikołajczyk B, Guga P. P-Stereodefined phosphorothioate analogs of glycol nucleic acids-synthesis and structural properties. RSC Adv 2018; 8:24942-24952. [PMID: 35542141 PMCID: PMC9082371 DOI: 10.1039/c8ra05568h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 07/02/2018] [Indexed: 11/21/2022] Open
Abstract
Enantiomerically pure, protected acyclic nucleosides of the GNA type (glycol nucleic acids) (GN′), obtained from (R)-(+)- and (S)-(−)-glycidols and the four canonical DNA nucleobases (Ade, Cyt, Gua and Thy), were transformed into 3′-O-DMT-protected 2-thio-4,4-pentamethylene-1,3,2-oxathiaphospholane derivatives (OTP-GN′) containing a second stereogenic center at the phosphorus atom. These monomers were chromatographically separated into P-diastereoisomers, which were further used for the synthesis of P-stereodefined “dinucleoside” phosphorothioates GNPST (GN = GA, GC, GG, GT). The absolute configuration at the phosphorus atom for all eight GNPST was established enzymatically and verified chemically, and correlated with chromatographic mobility of the OTP-GN′ monomers on silica gel. The GNPS units (derived from (R)-(+)-glycidol) were introduced into self-complementary PS-(DNA/GNA) octamers of preselected, uniform absolute configuration at P-atoms. Thermal dissociation experiments showed that the thermodynamic stability of the duplexes depends on the stereochemistry of the phosphorus centers and relative arrangement of the GN units in the oligonucleotide strands. These results correlate with the changes of conformation assessed from circular dichroism spectra. The stability of P-stereodefined PS-(DNA/GNA) duplexes depends on the stereochemistry of the phosphorus centers and arrangement of –GNPS– units in the strands.![]()
Collapse
Affiliation(s)
- Agnieszka Tomaszewska-Antczak
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry Sienkiewicza 112 90-363 Łódź Poland
| | - Katarzyna Jastrzębska
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry Sienkiewicza 112 90-363 Łódź Poland
| | - Anna Maciaszek
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry Sienkiewicza 112 90-363 Łódź Poland
| | - Barbara Mikołajczyk
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry Sienkiewicza 112 90-363 Łódź Poland
| | - Piotr Guga
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry Sienkiewicza 112 90-363 Łódź Poland
| |
Collapse
|
12
|
Liu Y, Kumar S, Taylor RE. Mix-and-match nanobiosensor design: Logical and spatial programming of biosensors using self-assembled DNA nanostructures. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2018; 10:e1518. [PMID: 29633568 DOI: 10.1002/wnan.1518] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 01/23/2018] [Accepted: 02/14/2018] [Indexed: 01/04/2023]
Abstract
The evergrowing need to understand and engineer biological and biochemical mechanisms has led to the emergence of the field of nanobiosensing. Structural DNA nanotechnology, encompassing methods such as DNA origami and single-stranded tiles, involves the base pairing-driven knitting of DNA into discrete one-, two-, and three-dimensional shapes at nanoscale. Such nanostructures enable a versatile design and fabrication of nanobiosensors. These systems benefit from DNA's programmability, inherent biocompatibility, and the ability to incorporate and organize functional materials such as proteins and metallic nanoparticles. In this review, we present a mix-and-match taxonomy and approach to designing nanobiosensors in which the choices of bioanalyte and transduction mechanism are fully independent of each other. We also highlight opportunities for greater complexity and programmability of these systems that are built using structural DNA nanotechnology. This article is categorized under: Implantable Materials and Surgical Technologies > Nanomaterials and Implants Diagnostic Tools > Biosensing Biology-Inspired Nanomaterials > Nucleic Acid-Based Structures Nanotechnology Approaches to Biology > Nanoscale Systems in Biology.
Collapse
Affiliation(s)
- Ying Liu
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Sriram Kumar
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Rebecca E Taylor
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania.,Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania
| |
Collapse
|
13
|
Baig MMFA, Khan S, Naeem MA, Khan GJ, Ansari MT. Vildagliptin loaded triangular DNA nanospheres coated with eudragit for oral delivery and better glycemic control in type 2 diabetes mellitus. Biomed Pharmacother 2017; 97:1250-1258. [PMID: 29145151 DOI: 10.1016/j.biopha.2017.11.059] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 10/31/2017] [Accepted: 11/10/2017] [Indexed: 11/18/2022] Open
Abstract
Diabetes mellitus type 2 is a multidimensional disease associated with poor glycemic control through compromised sensitivity of pancreatic islet α and β cells against glucose and dwindled secretion of insulin which is linked with the quantity of incretin hormones that are abridged by dipeptidyl peptidase-4 (DPP-4) in diseased condition. Vildagliptin (VG) inhibits DPP-4 therefore regulates the incretins that conversely maintains glycemic control. The safe reach and absorption of VG from intestine was dubious. Therefore we used Electrostatic Attraction Method to develop drug loaded DNA nanotechnology triangles coated by Eudragit (Eud) to make stable nanospheres of Vildagliptin (VG). We further analyzed the formulated nanospheres by AFM, XRD, DSC, SEM, TGA, ATR-FTIR and native PAGE. Additionally the efficacy of formulated nanospheres for drug release and glycemic control was assessed in Db/Db mouse. Our results showed that formulated nanospheres are smooth, spherical, stable and uniform in size ranging from 500 to 2000 nm with drug entrapment efficiency up to 95 ± 2% and extended drug release up to 15 ± 2 h. FTIR and DSC results confirmed the absence of VG-DNA-Eud interaction and XRD studies revealed a change in the crystalline status of the VG in nanospheres. Ex-vivo studies indicate that Eud-DNA-VG nanospheres effectively bypasses the acidic pH of the stomach and enhances glycemic control in Db/Db mouse without any risk of pancreatitis or pancreatic cancer. To the best of our knowledge, this is the first study conclusively reporting that VG loaded DNA Nano-architects coated with Eudragit are stable, safe and may improve therapeutic outcomes after oral delivery.
Collapse
Affiliation(s)
- Mirza Muhammad Faran Ashraf Baig
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Bahauddin Zakariya University, Multan, Pakistan; School of Chemistry and Chemical Engineering, Nanjing University, PR China
| | - Sara Khan
- Department of Pharmaceutical Chemistry, University College of Pharmacy, University of the Punjab, Lahore Pakistan
| | - Muhammad Ahsan Naeem
- Department of Mechatronics and Control Engineering, University of Engineering and Technology, Lahore, Pakistan
| | - Ghulam Jilany Khan
- Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University, Nanjing 210009, PR China; Department of Pharmacology, Faculty of Pharmacy (FOP), University of Central Punjab, Lahore, Pakistan; Jiangsu Center for Pharmacodynamics Research and Evaluation, China Pharmaceutical University, Nanjing 210009, China.
| | - Muhammad Tayyab Ansari
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Bahauddin Zakariya University, Multan, Pakistan
| |
Collapse
|
14
|
Chung WJ, Cui Y, Chen CS, Wei WH, Chang RS, Shu WY, Hsu IC. Freezing shortens the lifetime of DNA molecules under tension. J Biol Phys 2017; 43:511-524. [PMID: 28887655 PMCID: PMC5696304 DOI: 10.1007/s10867-017-9466-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 08/16/2017] [Indexed: 12/24/2022] Open
Abstract
DNA samples are commonly frozen for storage. However, freezing can compromise the integrity of DNA molecules. Considering the wide applications of DNA molecules in nanotechnology, changes to DNA integrity at the molecular level may cause undesirable outcomes. However, the effects of freezing on DNA integrity have not been fully explored. To investigate the impact of freezing on DNA integrity, samples of frozen and non-frozen bacteriophage lambda DNA were studied using optical tweezers. Tension (5–35 pN) was applied to DNA molecules to mimic mechanical interactions between DNA and other biomolecules. The integrity of the DNA molecules was evaluated by measuring the time taken for single DNA molecules to break under tension. Mean lifetimes were determined by maximum likelihood estimates and variances were obtained through bootstrapping simulations. Under 5 pN of force, the mean lifetime of frozen samples is 44.3 min with 95% confidence interval (CI) between 36.7 min and 53.6 min while the mean lifetime of non-frozen samples is 133.2 min (95% CI: 97.8–190.1 min). Under 15 pN of force, the mean lifetimes are 10.8 min (95% CI: 7.6–12.6 min) and 78.5 min (95% CI: 58.1–108.9 min). The lifetimes of frozen DNA molecules are significantly reduced, implying that freezing compromises DNA integrity. Moreover, we found that the reduced DNA structural integrity cannot be restored using regular ligation process. These results indicate that freezing can alter the structural integrity of the DNA molecules.
Collapse
Affiliation(s)
- Wei-Ju Chung
- Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu, 30013, Taiwan
| | - Yujia Cui
- Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu, 30013, Taiwan.
| | - Chi-Shuo Chen
- Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu, 30013, Taiwan
| | - Wesley H Wei
- Department of Computer Science, Tufts University, 419 Boston Avenue, Medford, MA, 02155, USA
| | - Rong-Shing Chang
- Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu, 30013, Taiwan
| | - Wun-Yi Shu
- Institute of Statistics, National Tsing Hua University, 101, Section 2, Kuang-Fu road, Hsinchu, 30013, Taiwan
| | - Ian C Hsu
- Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu, 30013, Taiwan.
| |
Collapse
|
15
|
Roberts CC, Chang CEA. Modeling of enhanced catalysis in multienzyme nanostructures: effect of molecular scaffolds, spatial organization, and concentration. J Chem Theory Comput 2016; 11:286-92. [PMID: 26574226 DOI: 10.1021/ct5007482] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Colocalized multistep enzymatic reaction pathways within biological catabolic and metabolic processes occur with high yield and specificity. Spatial organization on membranes or surfaces may be associated with increased efficiency of intermediate substrate transfer. Using a new Brownian dynamics package, GeomBD, we explored the geometric features of a surface-anchored enzyme system by parallel coarse-grained Brownian dynamics simulations of substrate diffusion over microsecond (μs) to millisecond (ms) time scales. We focused on a recently developed glucose oxidase (GOx), horseradish peroxidase (HRP), and DNA origami-scaffold enzyme system, where the H2O2 substrate of HRP is produced by GOx. The results revealed and explained a significant advantage in catalytic enhancement by optimizing interenzyme distance and orientation in the presence of the scaffold model. The planar scaffold colocalized the enzymes and provided a diffusive barrier that enhanced substrate transfer probability, becoming more relevant with increasing interenzyme distance. The results highlight the importance of protein geometry in the proper assessment of distance and orientation dependence on the probability of substrate transfer. They shed light on strategies for engineering multienzyme complexes and further investigation of enhanced catalytic efficiency for substrate diffusion between membrane-anchoring proteins.
Collapse
Affiliation(s)
- Christopher C Roberts
- Department of Chemistry, University of California , Riverside, California 92521, United States
| | - Chia-en A Chang
- Department of Chemistry, University of California , Riverside, California 92521, United States
| |
Collapse
|
16
|
Roberts CC, Chang CEA. Analysis of Ligand-Receptor Association and Intermediate Transfer Rates in Multienzyme Nanostructures with All-Atom Brownian Dynamics Simulations. J Phys Chem B 2016; 120:8518-31. [PMID: 27248669 DOI: 10.1021/acs.jpcb.6b02236] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present the second-generation GeomBD Brownian dynamics software for determining interenzyme intermediate transfer rates and substrate association rates in biomolecular complexes. Substrate and intermediate association rates for a series of enzymes or biomolecules can be compared between the freely diffusing disorganized configuration and various colocalized or complexed arrangements for kinetic investigation of enhanced intermediate transfer. In addition, enzyme engineering techniques, such as synthetic protein conjugation, can be computationally modeled and analyzed to better understand changes in substrate association relative to native enzymes. Tools are provided to determine nonspecific ligand-receptor association residence times, and to visualize common sites of nonspecific association of substrates on receptor surfaces. To demonstrate features of the software, interenzyme intermediate substrate transfer rate constants are calculated and compared for all-atom models of DNA origami scaffold-bound bienzyme systems of glucose oxidase and horseradish peroxidase. Also, a DNA conjugated horseradish peroxidase enzyme was analyzed for its propensity to increase substrate association rates and substrate local residence times relative to the unmodified enzyme. We also demonstrate the rapid determination and visualization of common sites of nonspecific ligand-receptor association by using HIV-1 protease and an inhibitor, XK263. GeomBD2 accelerates simulations by precomputing van der Waals potential energy grids and electrostatic potential grid maps, and has a flexible and extensible support for all-atom and coarse-grained force fields. Simulation software is written in C++ and utilizes modern parallelization techniques for potential grid preparation and Brownian dynamics simulation processes. Analysis scripts, written in the Python scripting language, are provided for quantitative simulation analysis. GeomBD2 is applicable to the fields of biophysics, bioengineering, and enzymology in both predictive and explanatory roles.
Collapse
Affiliation(s)
- Christopher C Roberts
- Department of Chemistry, University of California , Riverside, California 92521, United States
| | - Chia-En A Chang
- Department of Chemistry, University of California , Riverside, California 92521, United States
| |
Collapse
|
17
|
Abstract
Nanomanufacturing, the commercially scalable and economically sustainable mass production of nanoscale materials and devices, represents the tangible outcome of the nanotechnology revolution. In contrast to those used in nanofabrication for research purposes, nanomanufacturing processes must satisfy the additional constraints of cost, throughput, and time to market. Taking silicon integrated circuit manufacturing as a baseline, we consider the factors involved in matching processes with products, examining the characteristics and potential of top-down and bottom-up processes, and their combination. We also discuss how a careful assessment of the way in which function can be made to follow form can enable high-volume manufacturing of nanoscale structures with the desired useful, and exciting, properties.
Collapse
Affiliation(s)
- J. Alexander Liddle
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899
| | | |
Collapse
|
18
|
Dhakal S, Adendorff MR, Liu M, Yan H, Bathe M, Walter NG. Rational design of DNA-actuated enzyme nanoreactors guided by single molecule analysis. NANOSCALE 2016; 8:3125-3137. [PMID: 26788713 DOI: 10.1039/c5nr07263h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The control of enzymatic reactions using nanoscale DNA devices offers a powerful application of DNA nanotechnology uniquely derived from actuation. However, previous characterization of enzymatic reaction rates using bulk biochemical assays reported suboptimal function of DNA devices such as tweezers. To gain mechanistic insight into this deficiency and to identify design rules to improve their function, here we exploit the synergy of single molecule imaging and computational modeling to characterize the three-dimensional structures and catalytic functions of DNA tweezer-actuated nanoreactors. Our analysis revealed two important deficiencies--incomplete closure upon actuation and conformational heterogeneity. Upon rational redesign of the Holliday junctions located at their hinge and arms, we found that the DNA tweezers could be more completely and uniformly closed. A novel single molecule enzyme assay was developed to demonstrate that our design improvements yield significant, independent enhancements in the fraction of active enzyme nanoreactors and their individual substrate turnover frequencies. The sequence-level design strategies explored here may aid more broadly in improving the performance of DNA-based nanodevices including biological and chemical sensors.
Collapse
Affiliation(s)
- Soma Dhakal
- Department of Chemistry, Single Molecule Analysis Group, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Matthew R Adendorff
- Department of Biological Engineering, Laboratory for Computational Biology & Biophysics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Minghui Liu
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA.
| | - Hao Yan
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA.
| | - Mark Bathe
- Department of Biological Engineering, Laboratory for Computational Biology & Biophysics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Nils G Walter
- Department of Chemistry, Single Molecule Analysis Group, University of Michigan, Ann Arbor, MI 48109, USA.
| |
Collapse
|
19
|
Mallik L, Dhakal S, Nichols J, Mahoney J, Dosey AM, Jiang S, Sunahara RK, Skiniotis G, Walter NG. Electron Microscopic Visualization of Protein Assemblies on Flattened DNA Origami. ACS NANO 2015; 9:7133-41. [PMID: 26149412 PMCID: PMC5835357 DOI: 10.1021/acsnano.5b01841] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
DNA provides an ideal substrate for the engineering of versatile nanostructures due to its reliable Watson-Crick base pairing and well-characterized conformation. One of the most promising applications of DNA nanostructures arises from the site-directed spatial arrangement with nanometer precision of guest components such as proteins, metal nanoparticles, and small molecules. Two-dimensional DNA origami architectures, in particular, offer a simple design, high yield of assembly, and large surface area for use as a nanoplatform. However, such single-layer DNA origami were recently found to be structurally polymorphous due to their high flexibility, leading to the development of conformationally restrained multilayered origami that lack some of the advantages of the single-layer designs. Here we monitored single-layer DNA origami by transmission electron microscopy (EM) and discovered that their conformational heterogeneity is dramatically reduced in the presence of a low concentration of dimethyl sulfoxide, allowing for an efficient flattening onto the carbon support of an EM grid. We further demonstrated that streptavidin and a biotinylated target protein (cocaine esterase, CocE) can be captured at predesignated sites on these flattened origami while maintaining their functional integrity. Our demonstration that protein assemblies can be constructed with high spatial precision (within ∼2 nm of their predicted position on the platforms) by using strategically flattened single-layer origami paves the way for exploiting well-defined guest molecule assemblies for biochemistry and nanotechnology applications.
Collapse
Affiliation(s)
- Leena Mallik
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Soma Dhakal
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Joseph Nichols
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jacob Mahoney
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Anne M. Dosey
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Shuoxing Jiang
- The Biodesign Institute and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Roger K. Sunahara
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Georgios Skiniotis
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Nils G. Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| |
Collapse
|
20
|
|
21
|
Widom JR, Dhakal S, Heinicke LA, Walter NG. Single-molecule tools for enzymology, structural biology, systems biology and nanotechnology: an update. Arch Toxicol 2014; 88:1965-85. [PMID: 25212907 PMCID: PMC4615698 DOI: 10.1007/s00204-014-1357-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 08/28/2014] [Indexed: 12/22/2022]
Abstract
Toxicology is the highly interdisciplinary field studying the adverse effects of chemicals on living organisms. It requires sensitive tools to detect such effects. After their initial implementation during the 1990s, single-molecule fluorescence detection tools were quickly recognized for their potential to contribute greatly to many different areas of scientific inquiry. In the intervening time, technical advances in the field have generated ever-improving spatial and temporal resolution and have enabled the application of single-molecule fluorescence to increasingly complex systems, such as live cells. In this review, we give an overview of the optical components necessary to implement the most common versions of single-molecule fluorescence detection. We then discuss current applications to enzymology and structural studies, systems biology, and nanotechnology, presenting the technical considerations that are unique to each area of study, along with noteworthy recent results. We also highlight future directions that have the potential to revolutionize these areas of study by further exploiting the capabilities of single-molecule fluorescence microscopy.
Collapse
Affiliation(s)
- Julia R Widom
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI, 48109-1055, USA
| | | | | | | |
Collapse
|
22
|
Analogues of nucleosides: synthesis of chiral pyrrolidin-2-ones or pyrrolidines-bearing nucleobases. MONATSHEFTE FUR CHEMIE 2014. [DOI: 10.1007/s00706-014-1251-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
23
|
Poritz MA, Ririe KM. Getting things backwards to prevent primer dimers. J Mol Diagn 2014; 16:159-62. [PMID: 24457120 DOI: 10.1016/j.jmoldx.2014.01.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 12/30/2013] [Accepted: 01/09/2014] [Indexed: 02/04/2023] Open
Abstract
This Commentary highlights the article by Satterfield that describes a new class of primer technology-cooperative primers, which prevent primer-dimer amplification.
Collapse
|
24
|
Rekhi R, Qutub AA. Systems approaches for synthetic biology: a pathway toward mammalian design. Front Physiol 2013; 4:285. [PMID: 24130532 PMCID: PMC3793170 DOI: 10.3389/fphys.2013.00285] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 09/19/2013] [Indexed: 01/08/2023] Open
Abstract
We review methods of understanding cellular interactions through computation in order to guide the synthetic design of mammalian cells for translational applications, such as regenerative medicine and cancer therapies. In doing so, we argue that the challenges of engineering mammalian cells provide a prime opportunity to leverage advances in computational systems biology. We support this claim systematically, by addressing each of the principal challenges to existing synthetic bioengineering approaches—stochasticity, complexity, and scale—with specific methods and paradigms in systems biology. Moreover, we characterize a key set of diverse computational techniques, including agent-based modeling, Bayesian network analysis, graph theory, and Gillespie simulations, with specific utility toward synthetic biology. Lastly, we examine the mammalian applications of synthetic biology for medicine and health, and how computational systems biology can aid in the continued development of these applications.
Collapse
Affiliation(s)
- Rahul Rekhi
- Department of Bioengineering, Rice University Houston, TX, USA
| | | |
Collapse
|
25
|
Spillmann CM, Ancona MG, Buckhout-White S, Algar WR, Stewart MH, Susumu K, Huston AL, Goldman ER, Medintz IL. Achieving effective terminal exciton delivery in quantum dot antenna-sensitized multistep DNA photonic wires. ACS NANO 2013; 7:7101-7118. [PMID: 23844838 DOI: 10.1021/nn402468t] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Assembling DNA-based photonic wires around semiconductor quantum dots (QDs) creates optically active hybrid architectures that exploit the unique properties of both components. DNA hybridization allows positioning of multiple, carefully arranged fluorophores that can engage in sequential energy transfer steps while the QDs provide a superior energy harvesting antenna capacity that drives a Förster resonance energy transfer (FRET) cascade through the structures. Although the first generation of these composites demonstrated four-sequential energy transfer steps across a distance >150 Å, the exciton transfer efficiency reaching the final, terminal dye was estimated to be only ~0.7% with no concomitant sensitized emission observed. Had the terminal Cy7 dye utilized in that construct provided a sensitized emission, we estimate that this would have equated to an overall end-to-end ET efficiency of ≤ 0.1%. In this report, we demonstrate that overall energy flow through a second generation hybrid architecture can be significantly improved by reengineering four key aspects of the composite structure: (1) making the initial DNA modification chemistry smaller and more facile to implement, (2) optimizing donor-acceptor dye pairings, (3) varying donor-acceptor dye spacing as a function of the Förster distance R0, and (4) increasing the number of DNA wires displayed around each central QD donor. These cumulative changes lead to a 2 orders of magnitude improvement in the exciton transfer efficiency to the final terminal dye in comparison to the first-generation construct. The overall end-to-end efficiency through the optimized, five-fluorophore/four-step cascaded energy transfer system now approaches 10%. The results are analyzed using Förster theory with various sources of randomness accounted for by averaging over ensembles of modeled constructs. Fits to the spectra suggest near-ideal behavior when the photonic wires have two sequential acceptor dyes (Cy3 and Cy3.5) and exciton transfer efficiencies approaching 100% are seen when the dye spacings are 0.5 × R0. However, as additional dyes are included in each wire, strong nonidealities appear that are suspected to arise predominantly from the poor photophysical performance of the last two acceptor dyes (Cy5 and Cy5.5). The results are discussed in the context of improving exciton transfer efficiency along photonic wires and the contributions these architectures can make to understanding multistep FRET processes.
Collapse
Affiliation(s)
- Christopher M Spillmann
- Center for Bio/Molecular Science and Engineering, Code 6900, US Naval Research Laboratory, Washington, DC 20375, United States
| | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Johnson-Buck A, Nangreave J, Kim DN, Bathe M, Yan H, Walter NG. Super-resolution fingerprinting detects chemical reactions and idiosyncrasies of single DNA pegboards. NANO LETTERS 2013; 13:728-33. [PMID: 23356935 PMCID: PMC8273705 DOI: 10.1021/nl304415b] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We employ the single-particle fluorescence nanoscopy technique points accumulation for imaging in nanoscale topography (PAINT) using site-specific DNA probes to acquire two-dimensional density maps of specific features patterned on nanoscale DNA origami pegboards. We show that PAINT has a localization accuracy of ~10 nm that is sufficient to reliably distinguish dense (>10(4) features μm(-2)) sub-100 nm patterns of oligonucleotide features. We employ two-color PAINT to follow enzyme-catalyzed modification of features on individual origami and to show that single nanopegboards exhibit stable, spatially heterogeneous probe-binding patterns, or "fingerprints." Finally, we present experimental and modeling evidence suggesting that these fingerprints may arise from feature spacing variations that locally modulate the probe binding kinetics. Our study highlights the power of fluorescence nanoscopy to perform quality control on individual soft nanodevices that interact with and position reagents in solution.
Collapse
Affiliation(s)
- Alexander Johnson-Buck
- Department of Chemistry, 930 N. University Ave., University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Jeanette Nangreave
- The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA
| | - Do-Nyun Kim
- Department of Biological Engineering, MIT, Cambridge, MA 02139
| | - Mark Bathe
- Department of Biological Engineering, MIT, Cambridge, MA 02139
| | - Hao Yan
- The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA
| | - Nils G. Walter
- Department of Chemistry, 930 N. University Ave., University of Michigan, Ann Arbor, MI 48109-1055, USA
| |
Collapse
|
27
|
Saaem I, LaBean TH. Overview of DNA origami for molecular self-assembly. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2013; 5:150-62. [DOI: 10.1002/wnan.1204] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
|
28
|
Goodman BS, Derr ND, Reck-Peterson SL. Engineered, harnessed, and hijacked: synthetic uses for cytoskeletal systems. Trends Cell Biol 2012; 22:644-52. [PMID: 23059001 DOI: 10.1016/j.tcb.2012.09.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Revised: 09/11/2012] [Accepted: 09/12/2012] [Indexed: 12/19/2022]
Abstract
Synthetic biology re-imagines existing biological systems by designing and constructing new biological parts, devices, and systems. In the arena of cytoskeleton-based transport, synthetic approaches are currently used in two broad ways. First, molecular motors are harnessed for non-physiological functions in cells. Second, transport systems are engineered in vitro to determine the biophysical rules that govern motility. These rules are then applied to synthetic nanotechnological systems. We review recent advances in both of these areas and conclude by discussing future directions in engineering the cytoskeleton and its motors for transport.
Collapse
Affiliation(s)
- Brian S Goodman
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | | |
Collapse
|
29
|
Chen Y, Cheng W. DNA-based plasmonic nanoarchitectures: from structural design to emerging applications. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2012; 4:587-604. [DOI: 10.1002/wnan.1184] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|