Disorder in DNA-Linked Gold Nanoparticle Assemblies

Abstract

We report experimental observations on the effect of disorder on the phase behavior of DNA-linked nanoparticle assemblies. Variation in DNA linker lengths results in different melting temperatures of the DNA-linked nanoparticle assemblies. We observed an unusual trend of a nonmonotonic "zigzag" pattern in the melting temperature as a function of DNA linker length. Linker DNA resulting in unequal DNA duplex lengths introduces disorder and lowers the melting temperature of the nanoparticle system. Comparison with free DNA thermodynamics shows that such an anomalous zigzag pattern does not exist for free DNA duplex melting, which suggests that the disorder introduced by unequal DNA duplex lengths results in this unusual collective behavior of DNA-linked nanoparticle assemblies.DNA-linked nanoparticle assemblies are a novel system in which gold nanoparticles are chemically affixed to known DNA sequences to create DNA "probes" with the capability to self-assemble into aggregates [1][2][3][4][5]. The interaction potential between these colloids are tunable and controllable, which makes these multicomponent complex fluids particularly suitable for studying the link between the interaction potential and phase behavior [6,7]. Similar colloidal phase transitions have also been used to detect the protein interactions at membrane surfaces [8]. On the other hand, the dynamics of DNA melting and hybridization in DNA replication and transcription is also a subject of intense investigation [9,10].The change in optical property upon aggregation makes DNA-linked nanoparticle systems a potential tool in future DNA detection technology [11,12]. DNA detection is important in medical research for applications such as detection of genetic diseases, RNA profiling, and biodefense [13][14][15][16][17]. The DNA-linked nanoparticle detection systems utilize the sequencedependent hybridization of DNA for accuracy and the optical properties of colloidal gold for sensitivity to create a DNA detection method that changes color upon the introduction of a specific DNA sequence. Study of these DNA-gold nanoparticle assemblies is warranted to gain a fundamental understanding of DNA hybridization in confined geometries, as well as to probe the potential of this and similar systems for practical applications in biotechnology [18,19].Much like other colloidal suspensions [20][21][22], the DNA-gold nanoparticle system has been shown to exhibit interesting phase behavior. The assembly melting temperature is dependent upon parameters such as particle size, DNA composition, and electrolyte concentrations [1,2]. Recent theory has sought to explain these observations [6,23,24]. More study is necessary to fully understand the underlying mechanisms affecting the phase behavior of this system.Here we report experimental observations of the effects of disorder on the melting temperature of the DNA-linked nanoparticle assemblies [2,3]. The basic building block is illustrated in Fig. 1. Disorder in the DNA duplex length was introduced by choosing linker...

Assembly of DNA-Functionalized Gold Nanoparticles with Gaps and Overhangs in Linker DNA

“…25,39 Such properties are often studied using a configuration shown in Figure 1A, where two AuNPs are functionalized with different DNA sequences and they can be assembled by a linker DNA. 25,40,41 Such a design is highly programmable because the size and shape of each AuNP and the DNA sequence can all be changed as long as certain DNA base pairing interactions are maintained. 42 With this model system, many important parameters have been characterized, including the effect of particle size, salt concentration, melting example, a single adenine base insertion was identified to be important for crystallization of DNAfunctionalized AuNPs.…”

Toward Fast and Quantitative Modification of Large Gold Nanoparticles by Thiolated DNA: Scaling of Nanoscale Forces, Kinetics, and the Need for Thiol Reduction

“…7 Since the structural and molecular recognition property of DNA is coupled to the optical and electric property of AuNPs, this conjugate is also useful for answering fundamental nanoscale problems. [8][9][10][11][12][13] Since its first report in 1996, many aspects of this conjugate have been extensively studied, including structure, 14,15 assembly kinetics, 16 thermodynamics, 17,18 melting property, 13,19 electrophoresis, 20,21 and DNA conformation. 22,23 Attaching thiolated DNA to AuNPs to achieve a stable conjugate is the first step for all downstream applications.…”

Melting transition of directly linked gold nanoparticle DNA assembly

“…Previous work relies on a linker DNA [7,8,9,10], and it has been suggested that entropic cooperativity plays an important role in the sharp phase transition of such DNA-linked nanoparticle assembly systems. On the other hand, most simulations do not explicitly incorporate linker DNA [11], and the results cannot be directly compared to experimental data.…”