| 1. |
- Fernandez, Yuri A. Diaz, 1978, et al.
(author)
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Research Update: Progress in synthesis of nanoparticle dimers by self-assembly
- 2014
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In: APL Materials. - : AIP Publishing. - 2166-532X. ; 2:1
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Journal article (peer-reviewed)abstract
- This article highlights recent advances in the controlled self-assembly of nanoparticles to produce dimeric nanoparticle structures. The relevance of this emergent field is discussed in terms of recent applications in plasmonics and chemical catalysis. The concept of bond-valence applied to nanoparticles will be discussed, emphasizing some general approaches that have been successfully used to build these structures. Further, the asymmetric functionalization of nanoparticles surfaces as a path to drive selective aggregation, the use of biomolecules to self-assemble nanoparticles into dimers in solution, and the confinement of aggregates in small cavities are discussed.
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| 2. |
- Sun, Lu, 1982, et al.
(author)
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Characterization of self-assembled DNA concatemers from synthetic oligonucleotides
- 2014
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In: Computational and Structural Biotechnology Journal. - : Elsevier BV. - 2001-0370. ; 11:18, s. 66-72
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Journal article (peer-reviewed)abstract
- Studies of DNA–ligand interaction on a single molecule level provide opportunities to understand individual behavior of molecules. Construction of DNA molecules with repetitive copies of the same segments of sequences linked in series could be helpful for enhancing the interaction possibility for sequence-specific binding ligand to DNA. Here we report on the use of synthetic oligonucleotides to self-assembly into duplex DNA concatemeric molecules. Two strands of synthetic oligonucleotides used here were designed with 50-mer in length and the sequences are semi-complimentary so to hybridize spontaneously into concatemers of double stranded DNA. In order to optimize the length of the concatemers the oligonucleotides were incubated at different oligomer concentrations, ionic strengths and temperatures for different durations. Increasing the salt concentration to 200 mM NaCl was found to be the major optimizing factor because at this enhanced ionic strength the concatemers formed most quickly and the other parameters had no detectable effect. The size and shape of formed DNA concatemers were studied by gel electrophoresis in agarose, polyacrylamide gels and by AFM. Our results show that linear DNA constructs up to several hundred base pairs were formed and could be separated from a substantial fraction of non-linear constructs.
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| 3. |
- Sun, Lu, 1982
(author)
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Concatemerization of Synthetic Oligonucleotides
- 2014
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Doctoral thesis (other academic/artistic)abstract
- DNA nanotechnology has become an important research field because of its advantages in high predictability and accuracy of base-paring recognition. For example, the DNA concatemer, one of the simplest DNA constructs in shape, has been used to enhance signals in biosensing. In this thesis, concatemers were designed and characterized towards sequence-specific target amplifiers for single molecule mechanical studies. The project firstly focuses on exploring how to obtain concatemers of satisfactory length by self-assembly in bulk. Concatemers formed in solution by mixing of the different components were characterized by gel electrophoresis and AFM. Experimental results show that the concatemer yield could be increased primarily by increasing the ionic strength, and linear concatemers of expected length could be separated from mixed sizes and shapes. As an alternative, a platform for concatemer formation based on a planar surface was investigated by immobilizing and sequentially hybridizing oligonucleotides to concatemers. This method was further improved by involving click-reaction to link the nicks on backbones of the concatemers. QCM-D and SPR were utilized to monitor the step-by-step construction process. Gel electrophoresis shows that concatemers with desired length were successfully formed in a controllable manner. Furthermore, the surface-based concatemer formation platform was applied to study DNA-ligand interaction using QCM-D and SPR. We selected three ligands, known to bind to DNA: spermidine, spermine and RAD51. We observed that polyamines condense the DNA layers; by contrast, RAD51 induces an extension of the DNA layer. This study provides some guidelines for QCM-D and SPR-based characterization of changes in the properties of DNA films (e.g., thickness, viscoelastic properties) on sensor surfaces. It is interesting to correlate these changes to structural and mechanical changes induced in single DNA molecules upon ligand binding. The biosensing approach provides rapid access to kinetic data of DNA-ligand interactions, which is typically useful in various screening applications.
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| 4. |
- Sun, Lu, 1982
(author)
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Concatemerization of Synthetic Oligonucleotides, Assembly on Surface and Ligand Interactions
- 2014
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Doctoral thesis (other academic/artistic)abstract
- DNA nanotechnology has become an important research field because of its advantages in high predictability and accuracy of base-paring recognition. DNA concatemer, one of the simplest DNA constructs in shape, have been found as efficient signal amplifiers in several biosensors for different applications. In this thesis, formation of concatemers as sequence-specific target amplifier for single molecular mechanical study was constructed and characterized. The research work firstly focuses on exploring to obtain concatemers in satisfactory length by self-assembled method via varying incubation conditions. Formed concatemers were characterized by gel electrophoresis and AFM. Experimental results show that the efficiency of forming concatemers could be optimized primarily by increasing ionic strength. Moreover, linear concatemers with expected length could be separated from mixed sizes and shapes.In the second part, an attempt of establishing a platform on planar surface is investigated by immobilizing and sequentially hybridizing oligonucleotides to concatemers. This method is further improved by involving click-reaction to link the nicks on the backbones. QCM-D and SPR were utilized to monitor the step by step construction process. Gel electrophoresis shows that concatemers with desired length were successfully formed in a controllable manner. Finally, we apply the concatemer formation platform to study DNA-ligand interaction using QCM-D. We selected three ligands to bind to DNA: spermidine, spermine and RAD51. We observe that polyamines condense the DNA layers; by contrast, RAD51 induces an extension of the DNA layer. This study provides some guidelines for a QCM-D biosensor based on ligand-induced structural changes of DNA films.
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| 5. |
- Sun, Lu, 1982, et al.
(author)
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Construction and Modeling of Concatemeric DNA Multilayers on a Planar Surface as Monitored by QCM-D and SPR
- 2014
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In: Langmuir. - : American Chemical Society (ACS). - 1520-5827 .- 0743-7463. ; 30:28, s. 8432-8441
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Journal article (peer-reviewed)abstract
- The sequential hybridization of a 534 base pair DNA concatemer layer was monitored by QCM-D and SPR, and the QCM-D data were analyzed by Voigt viscoelastic models. The results show that Voigt-based modeling gives a good description of the experimental data but only if shear viscosity and elasticity are allowed to depend on the shear frequency. The derived layer thickness, shear viscosity and elasticity of the growing film give a representation of the DNA film in agreement with known bulk properties of DNA, and reveal a maximum in film viscosity when the molecules in the layer contain 75 base pairs. The experimental data during construction of a 3084 bp DNA concatemer layer were compared to predictions of the QCM-D response of a 1 mu m thick film of rod-like polymers. A predicted nonmonotonous variation of dissipation with frequency (added mass) is in qualitative agreement with the experiments, but with a quantitative disagreement which likely reflects that the flexibility of such long DNA molecules is not included in the model.
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| 6. |
- Sun, Lu, 1982, et al.
(author)
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Sensing Conformational Changes in DNA upon Ligand Binding Using QCM-D. Polyamine Condensation and Rad51 Extension of DNA Layers
- 2014
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In: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 118:41, s. 11895-11904
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Journal article (peer-reviewed)abstract
- Biosensors, in which binding of ligands is detected through changes in the optical or electrochemical properties of a DNA layer confined to the sensor surface, are important tools for investigating DNA interactions. Here, we investigate if conformational changes induced in surface-attached DNA molecules upon ligand binding can be monitored by the quartz crystal microbalance with dissipation (QCM-D) technique. DNA duplexes containing 59–184 base pairs were formed on QCM-D crystals by stepwise assembly of synthetic oligonucleotides of designed base sequences. The DNA films were exposed to the cationic polyamines spermidine and spermine, known to condense DNA molecules in bulk experiments, or to the recombination protein Rad51, known to extend the DNA helix. The binding and dissociation of the ligands to the DNA films were monitored in real time by measurements of the shifts in resonance frequency (Δf) and in dissipation (ΔD). The QCM-D data were analyzed using a Voigt-based model for the viscoelastic properties of polymer films in order to evaluate how the ligands affect thickness and shear viscosity of the DNA layer. Binding of spermine shrinks all DNA layers and increases their viscosity in a reversible fashion, and so does spermidine, but to a smaller extent, in agreement with its lower positive charge. SPR was used to measure the amount of bound polyamines, and when combined with QCM-D, the data indicate that the layer condensation leads to a small release of water from the highly hydrated DNA films. The binding of Rad51 increases the effective layer thickness of a 59bp film, more than expected from the know 50% DNA helix extension. The combined results provide guidelines for a QCM-D biosensor based on ligand-induced structural changes in DNA films. The QCM-D approach provides high discrimination between ligands affecting the thickness and the structural properties of the DNA layer differently. The reversibility of the film deformation allows comparative studies of two or more analytes using the same DNA layer as demonstrated here by spermine and spermidine.
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