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Li Q, Chao J, Zhang H, Fan C. Single-Molecule Nanomechanical Genotyping with DNA Origami-Based Shape IDs. Methods Mol Biol 2023; 2639:147-156. [PMID: 37166716 DOI: 10.1007/978-1-0716-3028-0_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Atomic force microscopy (AFM)-based nanomechanical imaging provides a sub-10-nm-resolution approach for imaging biomolecules under ambient conditions. Here we describe how to generate a set of DNA origami-based shape IDs (triangular and cross shape, with and without streptavidin) to site-specifically label target genomic DNA sequences containing two single-nucleotide polymorphisms (SNPs). Adjacent labeling sites separated by only 30 nucleobases (~10 nm) can be differentiated under AFM imaging. We can directly genotype single molecules of human genomic DNA.
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Affiliation(s)
- Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Chao
- Key Laboratory for Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials, National Synergetic Innovation Center for Advanced Materials, Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Honglu Zhang
- School of Biomedical Sciences and Engineering, National Engineering Research Center for Tissue Restoration and Reconstruction, Key Laboratory of Biomedical Materials and Engineering of the Ministry of Education, South China University of Technology, Guangzhou, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China.
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2
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Use of Nanoparticles to Prevent Resistance to Antibiotics-Synthesis and Characterization of Gold Nanosystems Based on Tetracycline. Pharmaceutics 2022; 14:pharmaceutics14091941. [PMID: 36145689 PMCID: PMC9500715 DOI: 10.3390/pharmaceutics14091941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/03/2022] [Accepted: 09/07/2022] [Indexed: 11/30/2022] Open
Abstract
Antimicrobial resistance (AMR) is a serious public health problem worldwide which, according to the World Health Organization (WHO), requires research into new and more effective drugs. In this work, both gold nanoparticles covered with 16-3-16 cationic gemini surfactant (Au@16-3-16) and DNA/tetracycline (DNA/TC) intercalated complexes were prepared to effectively transport tetracycline (TC). Synthesis of the Au@16-3-16 precursor was carried out by using trihydrated gold, adding sodium borohydride as a reducing agent and the gemini surfactant 16-3-16 as stabilizing agent. Circular dichroism and atomic force microscopy techniques were then used to ascertain the optimal R range of the relationship between the concentrations of Au@16-3-16 and the DNA/TC complex (R = CAu@16-3-16/CDNA) that allow the obtainment of stable and compact nanosystems, these characteristics being fundamental for their use as antibiotic transporters. Stability studies over time were carried out for distinct selected Au@16-3-16 and Au@16-3-16/DNA-TC nanoformulations using the ultraviolet−visible spectrophotometry technique, checking their stability for at least one month. In addition, in order to know the charge and size distribution of the nanocomplexes, DLS and zeta potential measurements were performed in the solution. The results showed that the characterized nanosystems were highly charged, stable and of a reduced size (<100 nm) that allows them to cross bacterial membranes effectively (>1 μm). Once the different physicochemical characteristics of the gold nanosystems were measured, Au@16-3-16 and Au@16-3-16/DNA-TC were tested on Escherichia coli and Staphylococcus aureus to study their antibacterial properties and internalization capacity in microbes. Differences in the interaction of the precursors and the compacted nanosystems generated were observed in Gram-positive and Gram-negative bacteria, possibly due to membrane damage or electrostatic interaction with internalization by endocytosis. In the internalization experiments, depending on the treatment application time, the greatest bacterial destruction was observed for all nanoformulations explored at 18 h of incubation. Importantly, the results obtained demonstrate that both new nanosystems based on TC and Au@16-3-16 precursors have optimal antimicrobial properties and would be beneficial for use in patients, avoiding possible side effects.
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Hansma HG. Potassium at the Origins of Life: Did Biology Emerge from Biotite in Micaceous Clay? Life (Basel) 2022; 12:life12020301. [PMID: 35207588 PMCID: PMC8880093 DOI: 10.3390/life12020301] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/31/2022] [Accepted: 01/31/2022] [Indexed: 12/15/2022] Open
Abstract
Intracellular potassium concentrations, [K+], are high in all types of living cells, but the origins of this K+ are unknown. The simplest hypothesis is that life emerged in an environment that was high in K+. One such environment is the spaces between the sheets of the clay mineral mica. The best mica for life’s origins is the black mica, biotite, because it has a high content of Mg++ and because it has iron in various oxidation states. Life also has many of the characteristics of the environment between mica sheets, giving further support for the possibility that mica was the substrate on and within which life emerged. Here, a scenario for life’s origins is presented, in which the necessary processes and components for life arise in niches between mica sheets; vesicle membranes encapsulate these processes and components; the resulting vesicles fuse, forming protocells; and eventually, all of the necessary components and processes are encapsulated within individual cells, some of which survive to seed the early Earth with life. This paper presents three new foci for the hypothesis of life’s origins between mica sheets: (1) that potassium is essential for life’s origins on Earth; (2) that biotite mica has advantages over muscovite mica; and (3) that micaceous clay is a better environment than isolated mica for life’s origins.
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4
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Chen SWW, Banneville AS, Teulon JM, Timmins J, Pellequer JL. Nanoscale surface structures of DNA bound to Deinococcus radiodurans HU unveiled by atomic force microscopy. NANOSCALE 2020; 12:22628-22638. [PMID: 33150905 DOI: 10.1039/d0nr05320a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The Deinococcus radiodurans protein HU (DrHU) was shown to be critical for nucleoid activities, yet its functional and structural properties remain largely unexplored. We have applied atomic force microscopy (AFM) imaging to study DrHU binding to pUC19-DNA in vitro and analyzed the topographic structures formed at the nanoscale. At the single-molecule level, AFM imaging allows visualization of super-helical turns on naked DNA surfaces and characterization of free DrHU molecules observed as homodimers. When enhancing the molecular surface structures of AFM images by the Laplacian weight filter, the distribution of bound DrHUs was visibly varied as a function of the DrHU/DNA molar ratio. At a low molar ratio, DrHU binding was found to reduce the volume of condensed DNA configuration by about 50%. We also show that DrHU is capable of bridging distinct DNA segments. Moreover, at a low molar ratio, the binding orientation of individual DrHU dimers could be perceived on partially "open" DNA configuration. At a high molar ratio, DrHU stiffened the DNA molecule and enlarged the spread of the open DNA configuration. Furthermore, a lattice-like pattern could be seen on the surface of DrHU-DNA complex, indicating that DrHU multimerization had occurred leading to the formation of a higher order architecture. Together, our results show that the functional plasticity of DrHU in mediating DNA organization is subject to both the conformational dynamics of DNA molecules and protein abundance.
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Affiliation(s)
- Shu-Wen W Chen
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), F-38000 Grenoble, France.
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5
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Giráldez-Pérez RM, Grueso E, Lhamyani S, Perez-Tejeda P, Gentile AM, Kuliszewska E, Roman-Perez J, El Bekay R. miR-21/Gemini surfactant-capped gold nanoparticles as potential therapeutic complexes: Synthesis, characterization and in vivo nanotoxicity probes. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113577] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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6
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Grueso E, Giráldez-Pérez RM, Perez-Tejeda P, Roldán E, Prado-Gotor R. What controls the unusual melting profiles of small AuNPs/DNA complexes. Phys Chem Chem Phys 2019; 21:11019-11032. [PMID: 31089595 DOI: 10.1039/c9cp01162e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The effect of the addition of low concentrations of an inner electrolyte on ds-DNA CT-DNA (calf thymus DNA) and ss-DNA conformational changes induced by small N-(2-mercaptopropionyl)glycine gold nanoparticles (AuNPs) is here studied in detail by using different spectroscopic and structural techniques. The high affinity of ss-DNA to AuNPs compared with ds-DNA is easily demonstrated by the results of competitive binding with SYBR Green I (SG). Additionally, it is proven that at 25.0 °C, AuNPs/ds-DNA and AuNPs/ss-DNA complexes undergo a transition from extended-coil to more compact structures when the AuNPs concentration (CAuNPs) is increased, which for the ds-DNA system is accompanied by partial denaturation. Particularly, for the AuNPs/ss-DNA system all of these techniques confirm that at a high CAuNPs, the compaction process is followed by a discrete transition to aggregation and an increase in structure size. A thorough analysis of the conformational changes described indicates that these processes are larger in low salt concentration and at high temperature. However, the most striking feature of this work is the abnormal melting temperature profiles (Tm) registered at high R = CAuNPs/CDNA ratios, which are remarkable and of interest for chemical sensing. At a suitable R ratio, which varies depending on CNaCl, a complex melting profile for the AuNPs/ds-DNA system was registered with two characteristic transitions: Tm,1 = 65.0 °C and Tm,2 = 95.0 °C. The highly sensitive atomic force microscopy technique performed at 25.0 °C and 65.0 °C also showed a different behaviour in both ss- and AuNPs/ds-DNA systems, which explains the characteristic melting curves. Specifically for the AuNPs/ss-DNA system, AFM at 25.0 °C revealed the formation of large-sized aggregates formed by AuNPs/ss-DNA compact structures linked by AuNPs. However, when both AuNPs/ds-DNA and AuNPs/ss-DNA complexes were incubated at 65.0 °C, the formation of highly stable ordered structures was always visualized at high R. Therefore, this shows that some key parameters for effective control of the formation of DNA/RNA-linked particles are: the selection of an optimal temperature below the ds-DNA melting point, an appropriate CAuNPs, and the addition of low CNaCl. The optimization of these parameters for each AuNPs/DNA system could improve biological sensing and DNA/RNA delivery.
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Affiliation(s)
- Elia Grueso
- Department of Physical Chemistry, University of Sevilla, C/Profesor García González s/n, 41012 Sevilla, Spain.
| | - Rosa M Giráldez-Pérez
- Department of Physical Chemistry, University of Sevilla, C/Profesor García González s/n, 41012 Sevilla, Spain.
| | - Pilar Perez-Tejeda
- Department of Physical Chemistry, University of Sevilla, C/Profesor García González s/n, 41012 Sevilla, Spain.
| | - Emilio Roldán
- Department of Physical Chemistry, University of Sevilla, C/Profesor García González s/n, 41012 Sevilla, Spain.
| | - R Prado-Gotor
- Department of Physical Chemistry, University of Sevilla, C/Profesor García González s/n, 41012 Sevilla, Spain.
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7
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Recombinases and Related Proteins in the Context of Homologous Recombination Analyzed by Molecular Microscopy. Methods Mol Biol 2019; 1805:251-270. [PMID: 29971722 DOI: 10.1007/978-1-4939-8556-2_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Transmission electron microscopy (TEM) and atomic force microscopy (AFM) are powerful tools to study the behavior of various actors in homologous recombination including molecular motors such as recombinases and helicases/translocases. Here we present specific approaches developed in terms of sample preparation and imaging methods to contribute to the understanding of homologous recombination process and its regulation focusing on the interplay between recombinases and other related proteins such as mediators or antirecombinase actors.Homologous recombination (HR) is a high-fidelity DNA repair pathway since it uses a homologous DNA as template. Recombinases such as RecA in bacteria, RadA in archaea, and Rad51 in eukaryotes are key proteins in the HR pathway: HR is initiated with formation of an ssDNA overhang on which recombinases polymerize and form a dynamic active nucleoprotein filament able to search for homology and to exchange DNA strand in an ATP-dependent manner. We provide practical methods to analyze presynaptic filament formation on ssDNA, its composition and regulation in presence of mediator partners, antirecombinase activity of translocase, and chromatin remodeling events.
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8
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Grueso E, Roldan E, Perez-Tejeda P, Kuliszewska E, Molero B, Brecker L, Giráldez-Pérez RM. Reversible DNA compaction induced by partial intercalation of 16-Ph-16 gemini surfactants: evidence of triple helix formation. Phys Chem Chem Phys 2018; 20:24902-24914. [PMID: 30234871 DOI: 10.1039/c8cp02791a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The interaction between calf thymus DNA and the gemini surfactants N,N'-[α,ω-phenylenebis(methylene)bis [N,N'-dimethyl-N-(1-hexadecyl)]-ammonium dibromide], p-16-Ph-16 (α = 1, ω = 3) and m-16-Ph-16 (α = 1, ω = 2), has been investigated via circular dichroism, fluorescence and UV-vis spectroscopy, zeta potential, dynamic light scattering, and AFM microscopy. Measurements were carried out in aqueous media at different molar ratios, R = (C16-Ph-16)/CDNA and C16-Ph-16 always below the critical micellar concentration (CMC) of the surfactant. Under these conditions, DNA undergoes two reversible conformational changes, compaction and decompaction, due to interaction with the surfactant molecules at low and high molar ratios, respectively. The extent of such conformational changes is correlated with both the degree of surfactant partial intercalation, and the size and charge of the surfactant aggregates formed, in each case. Comparison of the results shows that the para-form of the surfactant intercalates into the DNA to a major extent; therefore, the compaction/decompaction processes are more effective. Among these, the structure of the resulting 16-Ph-16/DNA decompacted complex is worthy of note. For the first time it can be demonstrated that the partial intercalation of the 16-Ph-16 gemini surfactants induces the formation of triplex DNA-like structures at a high R ratio.
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Affiliation(s)
- Elia Grueso
- Department of Physical Chemistry, Faculty of Chemistry, University of Seville, C/ Profesor García González, s/n, 41012, Sevilla, Spain.
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9
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Chao J, Zhang H, Xing Y, Li Q, Liu H, Wang L, Wang L, Fan C. Programming DNA origami assembly for shape-resolved nanomechanical imaging labels. Nat Protoc 2018; 13:1569-1585. [DOI: 10.1038/s41596-018-0004-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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10
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Cavalcanti DP, de Souza W. The Kinetoplast of Trypanosomatids: From Early Studies of Electron Microscopy to Recent Advances in Atomic Force Microscopy. SCANNING 2018; 2018:9603051. [PMID: 30018700 PMCID: PMC6029474 DOI: 10.1155/2018/9603051] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 05/07/2018] [Accepted: 05/15/2018] [Indexed: 06/08/2023]
Abstract
The kinetoplast is a specialized region of the mitochondria of trypanosomatids that harbors the most complex and unusual mitochondrial DNA found in nature. Kinetoplast DNA (kDNA) is composed of thousands of circular molecules topologically interlocked to form a single network. Two types of DNA circles are present in the kinetoplast: minicircles (0.5-10 kb) and maxicircles (20-40 kb). Knowledge of kinetoplast architecture is crucial to understanding the replication and segregation of kDNA circles because the molecules involved in these processes are precisely positioned in functional domains throughout the kinetoplast. The fine structure of the kinetoplast was revealed in early electron microscopy (EM) studies. However, an understanding of the topological organization of kDNA was only demonstrated after the development of protocols to separate kDNA from nuclear DNA, followed by EM observations. Electron microscopy analysis of thin sections of trypanosomatids, spreading of isolated kDNA networks onto EM grids, deep-etching studies, and cytochemical and immunocytochemical approaches are examples of techniques that were useful for elucidating the structure and replication of the kinetoplast. Recently, atomic force microscopy has joined this set of techniques and improved our knowledge about the kDNA network and revealed new details about kDNA topology in trypanosomatids.
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Affiliation(s)
- Danielle Pereira Cavalcanti
- Laboratório de Microbiologia, Diretoria de Metrologia Aplicada às Ciências da Vida, Instituto Nacional de Metrologia, Qualidade e Tecnologia-Inmetro, Rio de Janeiro, RJ, Brazil
- Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem and Centro Nacional de Biologia Estrutural e Bioimagem (CENABIO), Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Wanderley de Souza
- Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem and Centro Nacional de Biologia Estrutural e Bioimagem (CENABIO), Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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11
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Sharma S, LeClaire M, Gimzewski JK. Ascent of atomic force microscopy as a nanoanalytical tool for exosomes and other extracellular vesicles. NANOTECHNOLOGY 2018; 29:132001. [PMID: 29376505 DOI: 10.1088/1361-6528/aaab06] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Over the last 30 years, atomic force microscopy (AFM) has made several significant contributions to the field of biology and medicine. In this review, we draw our attention to the recent applications and promise of AFM as a high-resolution imaging and force sensing technology for probing subcellular vesicles: exosomes and other extracellular vesicles. Exosomes are naturally occurring nanoparticles found in several body fluids such as blood, saliva, cerebrospinal fluid, amniotic fluid and urine. Exosomes mediate cell-cell communication, transport proteins and genetic content between distant cells, and are now known to play important roles in progression of diseases such as cancers, neurodegenerative disorders and infectious diseases. Because exosomes are smaller than 100 nm (about 30-120 nm), the structural and molecular characterization of these vesicles at the individual level has been challenging. AFM has revealed a new degree of complexity in these nanosized vesicles and generated growing interest as a nanoscale tool for characterizing the abundance, morphology, biomechanics, and biomolecular make-up of exosomes. With the recent interest in exosomes for diagnostic and therapeutic applications, AFM-based characterization promises to contribute towards improved understanding of these particles at the single vesicle and sub-vesicular levels. When coupled with complementary methods like optical super resolution STED and Raman, AFM could further unlock the potential of exosomes as disease biomarkers and as therapeutic agents.
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Affiliation(s)
- S Sharma
- California NanoSystems Institute, University of California, Los Angeles, CA 90095, United States of America
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12
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Li Z, Kumarasinghe R, Collinson MM, Higgins DA. Probing the Local Dielectric Constant of Plasmid DNA in Solution and Adsorbed on Chemically Graded Aminosilane Surfaces. J Phys Chem B 2018; 122:2307-2313. [DOI: 10.1021/acs.jpcb.8b00077] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Zi Li
- Department
of Chemistry, Kansas State University, Manhattan, Kansas 66506-0401, United States
| | - Ruwandi Kumarasinghe
- Department
of Chemistry, Kansas State University, Manhattan, Kansas 66506-0401, United States
| | - Maryanne M. Collinson
- Department
of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006, United States
| | - Daniel A. Higgins
- Department
of Chemistry, Kansas State University, Manhattan, Kansas 66506-0401, United States
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13
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Carnerero JM, Jimenez-Ruiz A, Grueso EM, Prado-Gotor R. Understanding and improving aggregated gold nanoparticle/dsDNA interactions by molecular spectroscopy and deconvolution methods. Phys Chem Chem Phys 2018; 19:16113-16123. [PMID: 28604877 DOI: 10.1039/c7cp02219k] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
It is well known that single-stranded DNA (ssDNA) is easily able to adsorb on citrate-capped, non-functionalized gold nanoparticles (AuNPs). However, the affinity of double-stranded DNA (dsDNA) for them is much more limited. The present work demonstrates that long dsDNA suffers from a bending conformational change when anionic nanoparticles are present in solution. A striking decrease in the persistence length of the double helix in the absence of salt is observed through dynamic light scattering (DLS), viscometric, and atomic force microscopy (AFM) methods. Long dsDNA is therefore shown to be able to interact with anionic gold nanoparticles. To date, only ssDNA detection has been described by making use of interparticle cross-linking aggregation mechanisms; however, the data shown in this work allow for the development of new methods for detecting dsDNA in solution by using aggregated AuNPs as a starting point. The aggregation state is induced by the controlled addition of an inert electrolyte. A deconvolution procedure of the experimental plasmon shows how individual bands corresponding to aggregated nanoclusters diminish as the DNA concentration increases in the presence of 0.075 M NaCl.
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Affiliation(s)
- Jose M Carnerero
- Department of Physical Chemistry, Faculty of Chemistry, University of Seville. c/ Profesor García González, 1. 41012, Seville, Spain.
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14
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Liu K, Pan D, Wen Y, Zhang H, Chao J, Wang L, Song S, Fan C, Shi Y. Identifying the Genotypes of Hepatitis B Virus (HBV) with DNA Origami Label. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:1701718. [PMID: 29283218 DOI: 10.1002/smll.201701718] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 11/10/2017] [Indexed: 06/07/2023]
Abstract
The hepatitis B virus (HBV) genotyping may profoundly affect the accurate diagnosis and antiviral treatment of viral hepatitis. Existing genotyping methods such as serological, immunological, or molecular testing are still suffered from substandard specificity and low sensitivity in laboratory or clinical application. In a previous study, a set of high-efficiency hybridizable DNA origami-based shape ID probes to target the templates through which genetic variation could be determined in an ultrahigh resolution of atomic force microscopy (AFM) nanomechanical imaging are established. Here, as a further confirmatory research to explore the sensitivity and applicability of this assay, differentially predesigned DNA origami shape ID probes are also developed for precisely HBV genotyping. Through the specific identification of visualized DNA origami nanostructure with clinical HBV DNA samples, the genetic variation information of genotypes can be directly identified under AFM. As a proof-of-concept, five genotype B and six genotype C are detected in 11 HBV-infected patients' blood DNA samples of Han Chinese population in the single-blinded test. The AFM image-based DNA origami shape ID genotyping approach shows high specificity and sensitivity, which could be promising for virus infection diagnosis and precision medicine in the future.
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Affiliation(s)
- Ke Liu
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Dun Pan
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Yanqin Wen
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Honglu Zhang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Jie Chao
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Institute of Advanced Materials (IAM), and School of Materials Science and Engineering, Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing, 210046, China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Shiping Song
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Yongyong Shi
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, 200030, China
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15
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Wan N, Hong Z, Wang H, Fu X, Zhang Z, Li C, Xia H, Fang Y, Li M, Zhan Y, Yang X. A DNA Origami Mechanical Device for the Regulation of Microcosmic Structural Rigidity. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1700866. [PMID: 28902974 DOI: 10.1002/smll.201700866] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 07/28/2017] [Indexed: 06/07/2023]
Abstract
DNA origami makes it feasible to fabricate a tremendous number of DNA nanostructures with various geometries, dimensions, and functionalities. Moreover, an increasing amount of research on DNA nanostructures is focused on biological and biomedical applications. Here, the reversible regulation of microcosmic structural rigidity is accomplished using a DNA origami device in vitro. The designed DNA origami monomer is composed of an internal central axis and an external sliding tube. Due to the external tube sliding, the device transforms between flexible and rigid states. By transporting the device into the liposome, the conformational change of the origami device induces a structural change in the liposome. The results obtained demonstrate that the programmed DNA origami device can be applied to regulate the microcosmic structural rigidity of liposomes. Because microcosmic structural rigidity is important to cell proliferation and function, the results obtained potentially provide a foundation for the regulation of cell microcosmic structural rigidity using DNA nanostructures.
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Affiliation(s)
- Neng Wan
- National Education Base of Biological Science, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Zhouping Hong
- National Education Base of Biological Science, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- Bei Shizhang Advanced Class of Life Science Research, co-founded by Huazhong University of Science and Technology & Institute of Biophysics, Chinese Academy of Sciences & University of Chinese Academy of Sciences, Wuhan, 430074, P. R. China
| | - Huading Wang
- Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Xin Fu
- Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Ziyue Zhang
- Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Chao Li
- Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- Department of Bioinformatics, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Han Xia
- Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Yan Fang
- Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- Department of Nanomedicine and Biopharmaceutics, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Yi Zhan
- Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- Bei Shizhang Advanced Class of Life Science Research, co-founded by Huazhong University of Science and Technology & Institute of Biophysics, Chinese Academy of Sciences & University of Chinese Academy of Sciences, Wuhan, 430074, P. R. China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- Student Affairs Office, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Xiangliang Yang
- Department of Nanomedicine and Biopharmaceutics, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
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16
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In Situ Atomic Force Microscopy Studies on Nucleation and Self-Assembly of Biogenic and Bio-Inspired Materials. MINERALS 2017. [DOI: 10.3390/min7090158] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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17
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Zhang H, Chao J, Pan D, Liu H, Qiang Y, Liu K, Cui C, Chen J, Huang Q, Hu J, Wang L, Huang W, Shi Y, Fan C. DNA origami-based shape IDs for single-molecule nanomechanical genotyping. Nat Commun 2017; 8:14738. [PMID: 28382928 PMCID: PMC5384221 DOI: 10.1038/ncomms14738] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 01/27/2017] [Indexed: 01/28/2023] Open
Abstract
Variations on DNA sequences profoundly affect how we develop diseases and respond to pathogens and drugs. Atomic force microscopy (AFM) provides a nanomechanical imaging approach for genetic analysis with nanometre resolution. However, unlike fluorescence imaging that has wavelength-specific fluorophores, the lack of shape-specific labels largely hampers widespread applications of AFM imaging. Here we report the development of a set of differentially shaped, highly hybridizable self-assembled DNA origami nanostructures serving as shape IDs for magnified nanomechanical imaging of single-nucleotide polymorphisms. Using these origami shape IDs, we directly genotype single molecules of human genomic DNA with an ultrahigh resolution of ∼10 nm and the multiplexing ability. Further, we determine three types of disease-associated, long-range haplotypes in samples from the Han Chinese population. Single-molecule analysis allows robust haplotyping even for samples with low labelling efficiency. We expect this generic shape ID-based nanomechanical approach to hold great potential in genetic analysis at the single-molecule level.
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Affiliation(s)
- Honglu Zhang
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, PO Box 800-204, Shanghai 201800, China
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Jie Chao
- Key Laboratory for Organic Electronics and Information Displays (KLOEID), Institute of Advanced Materials (IAM), School of Materials Science and Engineering, Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210046, China
| | - Dun Pan
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, PO Box 800-204, Shanghai 201800, China
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Huajie Liu
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, PO Box 800-204, Shanghai 201800, China
| | - Yu Qiang
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Ke Liu
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Chengjun Cui
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, PO Box 800-204, Shanghai 201800, China
| | - Jianhua Chen
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Qing Huang
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, PO Box 800-204, Shanghai 201800, China
| | - Jun Hu
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, PO Box 800-204, Shanghai 201800, China
| | - Lianhui Wang
- Key Laboratory for Organic Electronics and Information Displays (KLOEID), Institute of Advanced Materials (IAM), School of Materials Science and Engineering, Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210046, China
| | - Wei Huang
- Key Laboratory for Organic Electronics and Information Displays (KLOEID), Institute of Advanced Materials (IAM), School of Materials Science and Engineering, Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210046, China
| | - Yongyong Shi
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Chunhai Fan
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, PO Box 800-204, Shanghai 201800, China
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18
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Aslan H, Krissanaprasit A, Besenbacher F, Gothelf KV, Dong M. Protein patterning by a DNA origami framework. NANOSCALE 2016; 8:15233-15240. [PMID: 27487933 DOI: 10.1039/c6nr03199d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A spatial arrangement of proteins provides structural and functional advantages in vast technological applications as well as fundamental research. Most protein patterning procedures employ complicated, time consuming and very costly nanofabrication techniques. As an alternative route, we developed a fully biomolecular self-assembly method using DNA Origami Frames (DOF) as a template for both small and large scale protein patterning. We employed a triangular DOF (tDOF) to arrange the Bovine Serum Albumin (BSA) protein. Our in situ protein patterning strategy provides a novel, fully organic platform using a fast and low-cost surface approach with possible utilization in fundamental science and technological applications.
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Affiliation(s)
- Hüsnü Aslan
- Center for DNA Nanotechnology (CDNA) and Interdisciplinary Nanoscience (iNANO) Center, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark.
| | - Abhichart Krissanaprasit
- Center for DNA Nanotechnology (CDNA) and Interdisciplinary Nanoscience (iNANO) Center, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark.
| | - Flemming Besenbacher
- Center for DNA Nanotechnology (CDNA) and Interdisciplinary Nanoscience (iNANO) Center, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark.
| | - Kurt V Gothelf
- Center for DNA Nanotechnology (CDNA) and Interdisciplinary Nanoscience (iNANO) Center, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark.
| | - Mingdong Dong
- Center for DNA Nanotechnology (CDNA) and Interdisciplinary Nanoscience (iNANO) Center, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark.
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19
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A Quick-responsive DNA Nanotechnology Device for Bio-molecular Homeostasis Regulation. Sci Rep 2016; 6:31379. [PMID: 27506964 PMCID: PMC4979213 DOI: 10.1038/srep31379] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 07/12/2016] [Indexed: 01/01/2023] Open
Abstract
Physiological processes such as metabolism, cell apoptosis and immune responses, must be strictly regulated to maintain their homeostasis and achieve their normal physiological functions. The speed with which bio-molecular homeostatic regulation occurs directly determines the ability of an organism to adapt to conditional changes. To produce a quick-responsive regulatory system that can be easily utilized for various types of homeostasis, a device called nano-fingers that facilitates the regulation of physiological processes was constructed using DNA origami nanotechnology. This nano-fingers device functioned in linked open and closed phases using two types of DNA tweezers, which were covalently coupled with aptamers that captured specific molecules when the tweezer arms were sufficiently close. Via this specific interaction mechanism, certain physiological processes could be simultaneously regulated from two directions by capturing one biofactor and releasing the other to enhance the regulatory capacity of the device. To validate the universal application of this device, regulation of the homeostasis of the blood coagulant thrombin was attempted using the nano-fingers device. It was successfully demonstrated that this nano-fingers device achieved coagulation buffering upon the input of fuel DNA. This nano-device could also be utilized to regulate the homeostasis of other types of bio-molecules.
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20
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Ghosh S, Dixit H, Chakrabarti R. Ion assisted structural collapse of a single stranded DNA: A molecular dynamics approach. Chem Phys 2015. [DOI: 10.1016/j.chemphys.2015.07.038] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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21
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Russell C, Roy S, Ganguly S, Qian X, Caruthers MH, Nilsson M. Formation of Silver Nanostructures by Rolling Circle Amplification Using Boranephosphonate-Modified Nucleotides. Anal Chem 2015; 87:6660-6. [PMID: 26059318 DOI: 10.1021/acs.analchem.5b00783] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We investigate the efficiency of incorporation of boranephosphonate-modified nucleotides by phi29 DNA polymerase and present a simple method for forming large defined silver nanostructures by rolling circle amplification (RCA) using boranephosphonate internucleotide linkages. RCA is a linear DNA amplification technique that can use specifically circularized DNA probes for detection of target nucleic acids and proteins. The resulting product is a collapsed single-stranded DNA molecule with tandem repeats of the DNA probe. By substituting each of the natural nucleotides with the corresponding 5'-(α-P-borano)deoxynucleosidetriphosphate, only a small reduction in amplification rate is observed. Also, by substituting all four natural nucleotides, it is possible to enzymatically synthesize a micrometer-sized, single-stranded DNA molecule with only boranephosphonate internucleotide linkages. Well-defined silver particles are then readily formed along the rolling circle product.
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Affiliation(s)
- Camilla Russell
- †Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, SE-751 85, Sweden
| | - Subhadeep Roy
- ‡Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, United States
| | - Saheli Ganguly
- ‡Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, United States
| | - Xiaoyan Qian
- §Science for Life laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, SE-171 21, Sweden
| | - Marvin H Caruthers
- ‡Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, United States
| | - Mats Nilsson
- †Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, SE-751 85, Sweden.,§Science for Life laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, SE-171 21, Sweden
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22
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Grueso E, Kuliszewska E, Roldan E, Perez-Tejeda P, Prado-Gotor R, Brecker L. DNA conformational changes induced by cationic gemini surfactants: the key to switching DNA compact structures into elongated forms. RSC Adv 2015. [DOI: 10.1039/c5ra03944d] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The extent of DNA decompaction induced by m-s-m gemini surfactants depend on the surfactant's tail length and on spacer's length.
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Affiliation(s)
- Elia Grueso
- Department of Physical Chemistry
- Faculty of Chemistry
- University of Seville
- Sevilla
- Spain
| | - Edyta Kuliszewska
- Institute of Heavy Organic Synthesis-Ul
- Kedzierzyn-Kozle 47-225
- Poland
| | - Emilio Roldan
- Department of Physical Chemistry
- Faculty of Chemistry
- University of Seville
- Sevilla
- Spain
| | - Pilar Perez-Tejeda
- Department of Physical Chemistry
- Faculty of Chemistry
- University of Seville
- Sevilla
- Spain
| | - Rafael Prado-Gotor
- Department of Physical Chemistry
- Faculty of Chemistry
- University of Seville
- Sevilla
- Spain
| | - Lothar Brecker
- Institute of Organic Chemistry
- University of Vienna
- A-1090 Wien
- Austria
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23
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de Pablo PJ, Carrión-Vázquez M. Imaging biological samples with atomic force microscopy. Cold Spring Harb Protoc 2014; 2014:167-77. [PMID: 24492779 DOI: 10.1101/pdb.top080473] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Atomic force microscopy (AFM) is an invaluable tool both for obtaining high-resolution topographical images and for determining the values of mechanical and structural properties of specimens adsorbed onto a surface. AFM is useful in an array of fields and applications, from materials science to biology. It is an extremely versatile technique that can be applied to almost any surface-mounted sample and can be operated in ambient air, ultrahigh vacuum, and, most importantly for biology, liquids. AFM can be used to explore samples ranging in size from atoms to molecules, molecular aggregates, and cells. Individual biomolecules can be viewed and manipulated at the nanoscale, providing fundamental biological information. In particular, the study of the mechanical properties of biomolecular aggregates at the nanoscale constitutes an important source of data to elaborate mechanochemical structure/function models of single-particle biomachines, expanding and complementing the information obtained from bulk experiments.
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24
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Danilevich VN, Artemov VV, Smith SS, Gainutdinov RV, Mulyukin AL. The structural peculiarities of condensed DNA micro- and nanoparticles formed in PCR. J Biomol Struct Dyn 2013; 32:1979-92. [DOI: 10.1080/07391102.2013.848411] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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25
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Modern biophysical approaches probe transcription-factor-induced DNA bending and looping. Biochem Soc Trans 2013; 41:368-73. [PMID: 23356313 DOI: 10.1042/bst20120301] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The genetic information of every living organism is stored in its genomic DNA that is perceived as a chemically stable and robust macromolecule. But at the same time, to fulfil its functions properly, it also needs to be highly dynamic and flexible. This includes partial melting of the double helix or compaction and bending of the DNA often brought about by protein factors that are able to interact with DNA stretches in a specific and non-specific manner. The conformational changes in the DNA need to be understood in order to describe biological systems in detail. As these events play out on the nanometre scale, new biophysical approaches have been employed to monitor conformational changes in this regime at the single-molecule level. Focusing on transcription factor action on promoter DNA, we discuss how current biophysical techniques are able to quantitatively describe this molecular process.
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26
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Dai X, Wei C, Li Z, Sun Z, Shen R, Zhang Y. Self-assembly of DNA networks at the air–water interface over time. RSC Adv 2013. [DOI: 10.1039/c3ra42099j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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27
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Abstract
Atomic force microscopy (AFM) is a helpful tool to acquire nanometric-resolution images, and also to perform a certain physical characterization of specimens, including their stiffness and mechanical resilience. Besides of the wide range of applications, from materials science to biology, this technique works in a variety of conditions as long as the sample is supported on a solid surface, in air, ultra high vacuum or, most importantly for virus research, in liquids. The adaptability of this technique is also fostered by the variety of sizes of the specimens that it can dealt with, such as atoms, molecules, molecular complexes including viruses and cells, and the possibility to observe dynamic processes in real time. Indeed, AFM facilitates single molecule experiments enabling not only to see but also to touch the material under study (i.e., to undertake mechanical manipulations), and constitutes a fundamental source of information for material characterization. In particular, the study of the mechanical properties at the nanoscale of viruses and other biomolecular aggregates, is providing an important set of data which help to elaborate mechano-chemical structure/function models of molecular biomachines, expanding and complementing the information obtained by other structural techniques.
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Affiliation(s)
- Pedro J de Pablo
- Department of Physics of the Condensed Matter, C03, Facultad de Ciencias, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049, Madrid, Spain,
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28
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Grueso E, Cerrillos C, Hidalgo J, Lopez-Cornejo P. Compaction and decompaction of DNA induced by the cationic surfactant CTAB. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:10968-10979. [PMID: 22755509 DOI: 10.1021/la302373m] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
A multifaceted study on the interaction of the cationic surfactant CTAB with calf thymus DNA was carried out by using different techniques. The measurements were done at different molar ratios X = [CTAB]/[DNA]. Results show the conformational change that DNA suffers due to the interaction with surfactant molecules at low molar ratios: the condensation of the polynucleotide, from an extended coil state to a globular state. The effect observed at the higher molar ratios is worth noting: the decondensation of DNA, that is, the transition from a compact state to a more extended conformation. Experimental data obtained confirm that this latter state is not exactly the same as that found in the absence of the surfactant. Attractive interactions between different parts of the molecule by ion correlation effects are the driving force to produce both the compaction and decompaction events. Results also show the importance of choosing both a proper system for the study and the most seeming measuring technique to use. The study demonstrates that, in some cases, the use of several techniques is desirable in obtaining reliable and accurate results.
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Affiliation(s)
- E Grueso
- Department of Physical Chemistry, Faculty of Chemistry, University of Seville, Sevilla, Spain
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29
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Abstract
Atomic force microscopy (AFM) is an invaluable tool not only to obtain high-resolution topographical images, but also to determine certain physical properties of specimens, such as their mechanical properties and composition. In addition to the wide range of applications, from materials science to biology, this technique can be operated in a number of environments as long as the specimen is attached to a surface, including ambient air, ultra high vacuum (UHV), and most importantly for biology, in liquids. The versatility of this technique is also reflected by the wide range of sizes of the sample that can dealt with, such as atoms, molecules, molecular aggregates, and cells. Indeed, this technique enables biological problems to be tackled from the single-molecule point of view and it allows not only to see but also to touch the material under study (i.e., mechanical manipulation at the nanoscale), a fundamental source of information for its characterization. In particular, the study of the mechanical properties at the nanoscale of biomolecular aggregates constitute an important source of data to elaborate mechano-chemical structure/function models of single-particle biomachines, expanding and complementing the information obtained from bulk experiments.
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Affiliation(s)
- Pedro J de Pablo
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, Spain.
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30
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Liu CP, Wey MT, Chang CC, Kan LS. Direct observation of single molecule conformational change of tight-turn paperclip DNA triplex in solution. Appl Biochem Biotechnol 2008; 159:261-9. [PMID: 18931945 DOI: 10.1007/s12010-008-8390-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2008] [Accepted: 09/30/2008] [Indexed: 10/21/2022]
Abstract
DNA triplex modulates gene expression by forming stable conformation in physiological condition. However, it is not feasible to observe this unique molecular structure of large molecule with 54 oligodeoxynucleotides directly by conventional nuclear magnetic approach. In this study, we observed directly single molecular images of paperclip DNA triplexes formation in a buffer solution of pH 6.0 by atomic force microscopy (AFM). Meanwhile, a diffuse "tail" of unwound DNA was observed in pH 8.0 solution. This designable approach in visualizing the overall structures and shapes of oligo-DNAs at the single molecular level, by AFM, is applicable to other biopolymers as well.
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31
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Adamcik J, Valle F, Witz G, Rechendorff K, Dietler G. The promotion of secondary structures in single-stranded DNA by drugs that bind to duplex DNA: an atomic force microscopy study. NANOTECHNOLOGY 2008; 19:384016. [PMID: 21832575 DOI: 10.1088/0957-4484/19/38/384016] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We study the behavior of single-stranded DNA (ssDNA) in the presence of well-known drugs with either an intercalating binding mode, such as daunorubicin, actinomycin D, and chloroquine, or a minor groove binding mode, such as netropsin and berenil, by atomic force microscopy (AFM). At very low salt conditions, ssDNA molecules adopt an unstructured conformation without secondary structures. We observe that under these conditions additions of drugs that bind to double-stranded DNA (dsDNA) promote the formation of secondary structures in ssDNA. Furthermore, with an increase of concentration of the drugs, the extension as well as the thermal stabilization of these hairpins was observed.
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Affiliation(s)
- Jozef Adamcik
- Laboratoire de Physique de la Matière Vivante, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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32
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Douarche C, Cortès R, Henry de Villeneuve C, Roser SJ, Braslau A. DNA adsorption at functionalized Si/buffer interfaces studied by x-ray reflectivity. J Chem Phys 2008; 128:225108. [DOI: 10.1063/1.2927256] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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33
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An historical perspective on cell mechanics. Pflugers Arch 2007; 456:3-12. [DOI: 10.1007/s00424-007-0405-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2007] [Revised: 11/12/2007] [Accepted: 11/15/2007] [Indexed: 11/26/2022]
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34
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Dolci D, Aloisi G, Lanzi L, Carlà M. A study of the ionic conduction of mica surface by admittance spectroscopy. J Chem Phys 2007; 127:074701. [PMID: 17718621 DOI: 10.1063/1.2754679] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The ionic conduction on the surface of humid mica has been analyzed by admittance spectroscopy as a function of relative humidity for different surface treatments. Measurements at low frequency indicate that water adsorption proceeds first in the form of a strongly adsorbed uniform thin layer, then with the formation of highly inhomogeneous thick aggregates.
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Affiliation(s)
- D Dolci
- Department of Physics, University of Florence, Via G. Sansone 1, Sesto Fiorentino, I 50019 Firenze, Italy
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35
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Galindo MA, Olea D, Romero MA, Gómez J, del Castillo P, Hannon MJ, Rodger A, Zamora F, Navarro JAR. Design and Non-Covalent DNA Binding of Platinum(II) Metallacalix[4]arenes. Chemistry 2007; 13:5075-81. [PMID: 17465426 DOI: 10.1002/chem.200601581] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A set of cyclic tetranuclear complexes of the metallacalix[4]arene type with formula [{Pt(en)(L)}(4)](4+) (en=ethylenediamine; 2: LH=5-chloro-2-hydroxypyrimidine (5-Cl-Hpymo); 3: LH=5-bromo-2-hydroxypyrimidine (5-Br-Hpymo); 4: LH=5-iodo-2-hydroxypyrimidine (5-I-Hpymo)) have been obtained from the reaction between cis-protected square-planar [Pt(en)(H(2)O)(2)](2+) metal entities and LH in aqueous media. Additionally, the binding properties of 2, 3, 4 and their congener [{Pt(en)(L)}(4)](4+) (1: LH=2-hydroxypyrimidine (Hpymo)) with calf thymus-DNA (ct-DNA) have been studied by using different techniques including circular and linear dichroism (CD and LD, respectively) and UV-visible absorbance spectroscopies, gel electrophoresis, fluorescence competitive-binding studies and atomic force microscopy (AFM). The results are consistent with significant non-covalent interactions taking place between the polynuclear cyclic species and ct-DNA. Moreover, gel electrophoresis, linear dichroism titrations and AFM images of ct-DNA with metallacalixarenes show ct-DNA coiling at low metallacalixarene concentrations and upon subsequent increments in metallacalixarene concentration ct-DNA can be seen to uncoil with concomitant formation of long and inflexible ct-DNA structures.
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Affiliation(s)
- Miguel A Galindo
- Departamento de Química Inorgánica Universidad de Granada, Av. Fuentenueva s/n, 18071 Granada, Spain
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Kienberger F, Costa LT, Zhu R, Kada G, Reithmayer M, Chtcheglova L, Rankl C, Pacheco ABF, Thalhammer S, Pastushenko V, Heckl WM, Blaas D, Hinterdorfer P. Dynamic force microscopy imaging of plasmid DNA and viral RNA. Biomaterials 2007; 28:2403-11. [PMID: 17291581 DOI: 10.1016/j.biomaterials.2007.01.025] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2006] [Accepted: 01/05/2007] [Indexed: 11/23/2022]
Abstract
Plasmid DNA and viral RNA were imaged in a liquid environment by dynamic force microscopy (DFM) and fine structures of DNA with heights of 1.82+/-0.66 nm were obtained in topographical images. In simultaneously acquired phase images, DNA could be imaged with better contrast at lower imaging forces. By splitting the cantilever oscillation signal into lower and upper parts, the contribution of the adhesion between tip and sample to the topographical images was eliminated, resulting in better signal-to-noise ratio. DFM of the single stranded RNA genome of a human rhinovirus showed loops protruding from a condensed RNA core, 20-50 nm in height. The mechanical rigidity of the RNA was determined by single molecule pulling experiments. From fitting RNA stretching curves to the Worm-Like-Chain (WLC) model a persistence length of 1.0+/-0.17 nm was obtained.
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Affiliation(s)
- Ferry Kienberger
- Institute for Biophysics, Johannes Kepler University of Linz, Altenbergerstrasse 69, A-4040 Linz, Austria
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37
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Klomparens KL, Heckman JW. Transmission electron microscopy and scanning probe microscopy. METHODS OF BIOCHEMICAL ANALYSIS 2006; 37:73-115. [PMID: 7508542 DOI: 10.1002/9780470110584.ch2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- K L Klomparens
- Center for Electron Optics, Michigan State University, East Lansing
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38
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Srinivasan C, Lee J, Papadimitrakopoulos F, Silbart LK, Zhao M, Burgess DJ. Labeling and intracellular tracking of functionally active plasmid DNA with semiconductor quantum dots. Mol Ther 2006; 14:192-201. [PMID: 16698322 DOI: 10.1016/j.ymthe.2006.03.010] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2005] [Revised: 03/07/2006] [Accepted: 03/10/2006] [Indexed: 01/28/2023] Open
Abstract
Semiconductor nanocrystal quantum dots (QDs) allow long-term imaging in the cellular environment with high photostability. QD biolabeling techniques have previously been developed for tagging proteins and peptides as well as oligonucleotides. In this contribution, QD-decorated plasmid DNA was utilized for the first time for long-term intracellular and intranuclear tracking studies. Conjugation of plasmid DNA with phospholipid-coated QDs was accomplished using a peptide nucleic acid (PNA)-N-succinimidyl-3-(2-pyridylthio) propionate linker. Gel electrophoresis and confocal and atomic force microscopy (AFM) were used to confirm the structure of QD-DNA conjugates. AFM imaging also revealed that multiple QDs were attached in a cluster at the PNA-reactive site of the plasmid DNA. These QD-DNA conjugates were capable of expressing the reporter protein, enhanced green fluorescent protein, following transfection in Chinese hamster ovary (CHO-K1) cells with an efficiency of ca. 62%, which was comparable to the control (unconjugated) plasmid DNA.
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Affiliation(s)
- Charudharshini Srinivasan
- Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Unit 3092, Storrs, 06269, USA
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39
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Gigliotti B, Sakizzie B, Bethune DS, Shelby RM, Cha JN. Sequence-independent helical wrapping of single-walled carbon nanotubes by long genomic DNA. NANO LETTERS 2006; 6:159-64. [PMID: 16464027 DOI: 10.1021/nl0518775] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Because of their nanometer sizes and molecular recognition capabilities, biological systems have garnered much attention as vehicles for the directed assembly of nanoscale materials.(1-6) One of the greatest challenges of this research has been to successfully interface biological systems with electronic materials, such as semiconductors and metals. As a means to address some of these issues, Sarikaya, Belcher, and others have used a combinatorial technique called phage display(7-9) to discover new families of peptides that showed binding affinities to various substrates. More recently, Zheng and co-workers used combinatorial DNA libraries to isolate short DNA oligomers (30-90 bases) that could disperse single-walled carbon nanotubes (SWCNT) in water.(10) Through a systematic analysis, they found that short oligonucleotides having repeating sequences of gunanines and thymines (dGdT)(n) could wrap in a helical manner around a CNT with periodic pitch.(11) Although helix formation around SWCNTs having regular pitches is an effective method for dispersing and separating CNTs, the need for specific repeating sequences limits use to non-natural DNA that must be synthesized with optimal lengths of less than 150 bases. In contrast, we demonstrate here that long genomic single-stranded DNA (>>100 bases) of a completely random sequence of bases can be used to disperse CNTs efficiently through the single-stranded DNA's (ssDNA) ability to form tight helices around the CNTs with distinct periodic pitches. Although this process occurs irrespective of the DNA sequence, we show that this process is highly dependent on the removal of complementary strands. We also demonstrate that although the helix pitch-to-pitch distances remain constant down the length of a single CNT, the distances are variable from one DNA-CNT to another. Finally, we report initial work that shows that methods developed to align long dsDNA can be applied in a similar fashion to produce highly dense arrays of aligned ssDNA-CNT hybrids.
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Affiliation(s)
- Brittany Gigliotti
- IBM Almaden Research Center, 650 Harry Road, San Jose, California 95120, USA
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40
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Wu A, Yu L, Li Z, Yang H, Wang E. Atomic force microscope investigation of large-circle DNA molecules. Anal Biochem 2004; 325:293-300. [PMID: 14751264 DOI: 10.1016/j.ab.2003.11.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A circular bacterial artificial chromosome of 148.9kbp on human chromosome 3 has been extended and fixed on bare mica substrates using a developed fluid capillary flow method in evaporating liquid drops. Extended circular DNA molecules were imaged with an atomic force microscope (AFM) under ambient conditions. The measured total lengths of the whole DNA molecules were in agreement with sequencing analysis data with an error range of +/-3.6%. This work is important groundwork for probing single nucleotide polymorphisms in the human genome, mapping genomic DNA, manipulating biomolecular nanotechnology, and studying the interaction of DNA-protein complexes investigated by AFM.
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Affiliation(s)
- Aiguo Wu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 130022, Jilin, China
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41
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Wu A, Li Z, Wang E. DNA Network Structures on Various Solid Substrates Investigated by Atomic Force Microscopy. ANAL SCI 2004; 20:1083-6. [PMID: 15293407 DOI: 10.2116/analsci.20.1083] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We have fabricated DNA network structures on glass and sapphire substrates. As a comparison, we also formed the network structure on mica substrate. For titanate strontium substrate, however, DNA network can not be obtained even if it is wet-treated by Na2HPO4 solution to make it hydrophilic. We also discuss the factors that affect the DNA networks formed on various substrates.
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Affiliation(s)
- Aiguo Wu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, China
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42
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Abstract
The measured height of DNA molecules adsorbed on a mica substrate by scanning probe microscopy is always less than the theoretical diameter. In this paper we show that, when imaged in ambient conditions, the molecules are usually immersed in the salt layer used to adsorb them to the substrate. This layer distorts the measurement of DNA height and is the main source of error but not the only one. We have performed different experiments to study this problem using two scanning force techniques: non-contact tapping mode in air and jumping mode in aqueous solution, where the dehydration phenomena is minimized. Height measurements of DNA in air using tapping mode reveal a height of 0.7+/-0.2nm. This value increases up to 1.5+/-0.2nm when the salt layer, in which the molecules are embedded, is removed. Jumping experiments in water give a value of 1.4+/-0.3nm when the maximum applied force is 300pN and 1.8+/-0.2nm at very low forces, which confirms the removal of the salt layer. Still, in all our experiments, the measured height of the DNA is less than the theoretical value. Our results show that although the salt layer present is important, some sample deformation due to either the loading force of the tip or the interaction with the substrate is also present.
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Affiliation(s)
- F Moreno-Herrero
- Laboratorio de Nuevas Microscopías, Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, 28049, Madrid, Spain.
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43
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Zuccheri G, Samorì B. Scanning force microscopy studies on the structure and dynamics of single DNA molecules. Methods Cell Biol 2003; 68:357-95. [PMID: 12053739 DOI: 10.1016/s0091-679x(02)68018-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
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44
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Abstract
The assembly of synthetic, controllable molecules is one of the goals in nanotechnology. The primary objective of this contribution is to selectively immobilize DNA on gold via electric potential control. The self-assembly monolayer (SAM) was prepared with 2-aminoethanethiol (AET) on the gold electrode. A new approach based on electric potential was firstly used to control DNA immobilization covalently onto the SAM with the activation of 1-ethyl-3(3-dimethyl-aminopropyl)-carbodiimide (EDC) and N-hydroxysulfosuccinimide (NHS) in low ionic strength solution. The influence of electric potential on DNA immobilization was investigated by means of cyclic voltammogram, A.C. impedance, auger electron spectrometer as well as atomic force microscope (AFM) on template-stripped gold surface. The result proves that controlled potential can affect the course of DNA immobilization. More negative potential can restrain the DNA immobilization, while the more positive potential can accelerate the DNA immobilization. It is of great significance for the control of DNA self-assembly and will find wide application in the fields of DNA-based devices.
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Affiliation(s)
- Cunwang Ge
- National Laboratory of Molecular and Biomolecular Electronics, Southeast University, Nanjing 210096, People's Republic of China.
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45
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Affiliation(s)
- Volker Oberle
- Department of Membrane Cell Biology, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
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46
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Onoa GB, Moreno V. Study of the modifications caused by cisplatin, transplatin, and Pd(II) and Pt(II) mepirizole derivatives on pBR322 DNA by atomic force microscopy. Int J Pharm 2002; 245:55-65. [PMID: 12270242 DOI: 10.1016/s0378-5173(02)00332-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Modifications of the structure of pBR322 DNA caused by interaction with cisplatin, transplatin and Pd(II) and Pt(II) mepirizole derivatives were studied. The compounds were incubated with the plasmid DNA for 24 h at 37 degrees C and then observed with an atomic force microscope. Circular DNA was used because the small tertiary structural changes are easy to monitor. Likewise, its superhelical nature mimics DNA better than certain forms of intracellular DNA such as chromatin. AFM images clearly reveal that the complexes induce changes in the topological forms of fully relaxed pBR322 DNA. Most of the compounds produce a more compact DNA structure with modified writhing number. Analysis of gel migration of the relaxed pBR322 DNA incubated with the platinum complexes provides complementary information, which is in good agreement with AFM results.
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Affiliation(s)
- G B Onoa
- Departament de Química Inorgànica, Universitat de Barcelona, Avgda Diagonal 647, 08028 Barcelona, Spain.
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47
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Fay MJ, Walter NG, Burke JM. Imaging of single hairpin ribozymes in solution by atomic force microscopy. RNA (NEW YORK, N.Y.) 2001; 7:887-95. [PMID: 11421363 PMCID: PMC1370136 DOI: 10.1017/s1355838201002473] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The hairpin ribozyme is a short endonucleolytic RNA motif isolated from a family of related plant virus satellite RNAs. It consists of two independently folding domains, each comprising two Watson-Crick helices flanking a conserved internal loop. The domains need to physically interact (dock) for catalysis of site-specific cleavage and ligation reactions. Using tapping-mode atomic force microscopy in aqueous buffer solution, we were able to produce high quality images of individual hairpin ribozyme molecules with extended terminal helices. Three RNA constructs with either the essential cleavage site guanosine or a detrimental adenosine substitution and with or without a 6-nt insertion to confer flexibility to the interdomain hinge show structural differences that correlate with their ability to form the active docked conformation. The observed contour lengths and shapes are consistent with previous bulk-solution measurements of the transient electric dichroism decays for the same RNA constructs. The active docked construct appears as an asymmetrically docked conformation that might be an indication of a more complicated docking event than a simple collapse around the interdomain hinge.
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Affiliation(s)
- M J Fay
- Markey Center for Molecular Genetics, Department of Microbiology and Molecular Genetics, The University of Vermont, Burlington 05405, USA
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48
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Smith BL. The importance of molecular structure and conformation: learning with scanning probe microscopy. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2001; 74:93-113. [PMID: 11106808 DOI: 10.1016/s0079-6107(00)00016-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Molecular structure holds a key to understanding Nature's intricate design mechanisms and blueprints. If we can understand her blueprints and basic materials, perhaps we can begin to mimic her beautiful products more cost effectively and with less detrimental environmental consequences. Higher resolution instrumentation has allowed us to study single molecules. Indeed, many stellar contributions to the field have come forth in the last couple of years. We can measure the forces required to unravel individual domains of biological molecules such as titin or DNA to a few picoNewtons resolution. This review will attempt to provide a general overview of the field of single molecule analysis using scanning force microscopy.
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Affiliation(s)
- B L Smith
- Department of Physics and Marine Science Institute, University of California, Santa Barbara, CA 93106, USA.
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49
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Zuccheri G, Bergia A, Gallinella G, Musiani M, Samorì B. Scanning force microscopy study on a single-stranded DNA: the genome of parvovirus B19. Chembiochem 2001; 2:199-204. [PMID: 11828445 DOI: 10.1002/1439-7633(20010302)2:3<199::aid-cbic199>3.0.co;2-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The genome of parvovirus B19 is a 5600-base-long single-stranded DNA molecule with peculiar sequence symmetries. Both complementary forms of this single-stranded DNA are contained in distinct virions and they hybridize intermolecularly to double-stranded DNA if extracted from the capsids with traditional methods, thus losing some of their native structural features. A scanning force microscopy analysis of these double-stranded DNA molecules after thermal denaturation and renaturation gave us the chance to study the possible states that this DNA can assume in both its single-stranded and double-stranded forms. A novel but still poorly reproducible in situ lysis experiment that we have conducted on single virions with the scanning force microscope made it possible to image the totally unpaired state that the single-stranded DNA molecule most likely assumes inside the viral particle. Structural considerations on single molecules offer the opportunity for the formulation of plausible hypotheses on the interaction between the DNA and the viral structural proteins that could prove important for the DNA packaging in the capsid and, possibly, the viral infection mechanisms.
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Affiliation(s)
- G Zuccheri
- Department of Biochemistry G. Moruzzi, University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
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50
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Umemura K, Ishikawa M, Kuroda R. Controlled immobilization of DNA molecules using chemical modification of mica surfaces for atomic force microscopy: characterization in air. Anal Biochem 2001; 290:232-7. [PMID: 11237324 DOI: 10.1006/abio.2001.4996] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Immobilization of biomolecules on surfaces while keeping the maximum conformational flexibility of the molecules is one of the most important techniques for atomic force microscopy imaging. We have developed two methods of controlling adsorption of DNA molecules on mica surfaces. The first method is the use of a mica surface modified with diluted 3-aminopropyltriethoxysilane (APS). Here we named this a "diluted APS-treated mica (AP-mica)" technique. The second method is the use of a mica surface modified with mixed self-assembled monolayers of organosilanes. In both of the techniques, the number of DNA molecules immobilized on a mica surface was controlled. Further, a conformational change of circular DNA, from a supercoiled to a relaxed form was observed for the molecules immobilized on a diluted AP-mica surface, when 254-nm UV light was irradiated. This observation demonstrated that flexibility of circular DNA molecules was kept on a diluted AP-mica surface.
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Affiliation(s)
- K Umemura
- Joint Research Center for Atom Technology--Angstrom Technology Partnership, 1-1-4, Higashi, Tsukuba, Ibaraki 305-0046, Japan
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