Surface and bulk dissolution properties, and selectivity of DNA-linked nanoparticle assemblies

Lukatsky, David B.; Frenkel, Daan

doi:10.1063/1.1906210

Cited by 33 publications

(32 citation statements)

References 59 publications

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“…These materials have found use in sensing applications, in part because they exhibit much narrower melting transitions (thermal dehybridization) than occur for the same duplexes in solution (15). This behavior, which also contrasts with the normal melting curves that are observed when DNA links microparticles, has been the subject of several theoretical studies (15)(16)(17)(18)(19)(20)(21)(22), and some general principles that can produce this behavior have been established. A limitation in modeling this process is that the simulation of DNA melting at the atomic scale is not feasible, even for a 10-bp duplex such as that illustrated in Fig.…”

Section: Structural and Thermal Propertiesmentioning

confidence: 94%

Using theory and computation to model nanoscale properties

Schatz

2007

Proc. Natl. Acad. Sci. U.S.A.

102

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This article provides an overview of the use of theory and computation to describe the structural, thermodynamic, mechanical, and optical properties of nanoscale materials. Nanoscience provides important opportunities for theory and computation to lead in the discovery process because the experimental tools often provide an incomplete picture of the structure and/or function of nanomaterials, and theory can often fill in missing features crucial to understanding what is being measured. However, there are important challenges to using theory as well, as the systems of interest are usually too large, and the time scales too long, for a purely atomistic level theory to be useful. At the same time, continuum theories that are appropriate for describing larger-scale (micrometer) phenomena are often not accurate for describing the nanoscale. Despite these challenges, there has been important progress in a number of areas, and there are exciting opportunities that we can look forward to as the capabilities of computational facilities continue to expand. Some specific applications that are discussed in this paper include: self-assembly of supramolecular structures, the thermal properties of nanoscale molecular systems (DNA melting and nanoscale water meniscus formation), the mechanical properties of carbon nanotubes and diamond crystals, and the optical properties of silver and gold nanoparticles. molecular dynamics ͉ nanomaterials ͉ nanoparticle ͉ plasmon ͉ self-assembly N anoscience deals with the behavior of matter on length scales where a large number of atoms play a role, but where the system is still small enough that the material does not behave like bulk matter. For example, a 5-nm gold particle, which contains on the order of 10 5 atoms, absorbs light strongly at 520 nm, whereas bulk gold is reflective at this wavelength and small clusters of gold atoms have absorption at shorter wavelengths. The special properties associated with nanoscale systems like this have provided both challenges and opportunities for the use of theory and computation to play a role in the discovery process. The challenges arise from the fact that most theories that describe the properties of matter by using first-principles approaches in which all atoms (and even all electrons in these atoms) are explicitly described are close to or (more often) beyond their capability to describe such systems, even using the largest computer available. At the same time, continuum theories, which play such a useful role for micrometer-scale systems, are sometimes incapable of describing nanoscale properties due to incomplete incorporation of the underlying physics in the size-dependent materials parameters. However, the opportunities for theory to play a role are significant, as nanoscience often provides the smallest systems that are amenable to study using methods that involve macroscopic manipulation of nanoscale structures. Thus, it is possible to measure the structure and thermal properties of a single supramolecular assembly, observe the thermal ...

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Section: Structural and Thermal Propertiesmentioning

confidence: 94%

Using theory and computation to model nanoscale properties

Schatz

2007

Proc. Natl. Acad. Sci. U.S.A.

102

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“…DNA-decorated colloids potentially exhibit extremely rich behaviour, since, in addition to modifying base sequencing, the colloidal properties also can be altered. This tremendous number of possible choices makes DNA-linked assemblies one of the most versatile and promising new soft-matter materials and thus calls for theoretical [8][9][10] and numerical studies of these systems.…”

mentioning

confidence: 99%

Model for assembly and gelation of four-armed DNA dendrimers

Starr¹,

Sciortino²

2006

J. Phys.: Condens. Matter

107

153

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We introduce and numerically study a model designed to mimic the bulk behavior of a system composed of single-stranded DNA dendrimers. Complementarity of the base sequences of different strands results in the formation of strong cooperative intermolecular links. We find that in an extremely narrow temperature range the system forms a large-scale, low-density disordered network via a thermo-reversible gel transition. By controlling the strand length, the gel transition temperature can be made arbitrarily close to the percolation transition, in contrast with recent model systems of physical gelation. This study helps the understanding of self-assembly in this class of new biomaterials and provides an excellent bridge between physical and chemical gels.

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“…Therefore we expect that our tags present higher biocompatibility than SERS tags marked with potentially toxic, Raman-active organic dyes. Moreover, our fabrication strategy for the assembly of AuNPs differs from most of the reported techniques which involve crosslinking molecules, like alkanethiols [19,20], surfactants [21], specific proteins [22], and oligonucleotides [23] and most often destabilizing species like salt or ethanol [24], which might further interfere with the intrinsic particles signal. Herein thiol-modified PEG, a nontoxic, hydrophilic polymer, commonly used to improve particles stability, biocompatibility, and their systemic retention [25], is used for multiple purposes: to link the particles between them and stabilize the formed nanoensembles.…”

Section: Journal Of Nanotechnologymentioning

confidence: 96%

Designing Gold Nanoparticle-Ensembles as Surface Enhanced Raman Scattering Tags inside Human Retinal Cells

Boca

Rugină

Pintea

et al. 2012

Journal of Nanotechnology

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Apart from the traditional development of surface-enhanced raman scattering (SERS) substrates for ultrasensitive spectroscopic analysis, an increasing interest is given nowadays to the design of the so-called SERS nanotags which integrate multiple SERS applications into single plasmonic nanoparticles. The fabrication of SERS tags is still a challenging task due to the complicated fabrication process. Typically, SERS tags are hybrid nanoconstructs consisting in a unique plasmonic nanoobject encoded with specific reporter molecules and enveloped in a protective shell that provides both biocompatibility and targeting function. Herein, we produce effective SERS tags consisting in small aggregates of gold nanoparticles (mainly dimers and trimers) which are captured from solution and then transferred into cells to perform as individual plasmonic nanostructures. Actually the small aggregates formed under controlled conditions are stabilized in solution by interlocking into a polymeric envelope made of thiol-modified poly(ethylene) glycol (PEG-SH). No further encoding operation is necessary in our case since part of ascorbic acid used as reducing agent remains attached in the interparticle junctions, providing persistent and strong SERS signal when the fabricated tags are internalized by human retinal cells. Our studies demonstrate a promising potential of new SERS-active nanoparticles to serve as effective reporters for biomedical tracing and imaging.

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Surface and bulk dissolution properties, and selectivity of DNA-linked nanoparticle assemblies

Cited by 33 publications

References 59 publications

Using theory and computation to model nanoscale properties

Using theory and computation to model nanoscale properties

Model for assembly and gelation of four-armed DNA dendrimers

Designing Gold Nanoparticle-Ensembles as Surface Enhanced Raman Scattering Tags inside Human Retinal Cells

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