Kinetic Measurements of DNA Hybridization on an Oligonucleotide-Immobilized 27-MHz Quartz Crystal Microbalance

Okahata, Yoshio; Kawase, Masanori; Niikura, Kenichi; Ohtake, Fuyuka; Furusawa, Hiroyuki; Ebara, Yasuhito

doi:10.1021/ac970584w

Cited by 412 publications

(342 citation statements)

References 55 publications

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“…Finally, it is worth noting that probe association can also explain suppression of surface K values relative to those in solution found in other physical studies of solid phase hybridization (5,18,26,27).…”

Section: Hybridization At Low Conversion: Electrostatics and The Onsementioning

confidence: 73%

“…A variety of aids to enhance hybridization performance is used, including surfactants and blocking agents to control nonspecific adsorption, washing procedures to develop contrast between fully and partially complementary sequences, and variation of assay parameters such as ionic strength or temperature. Physical studies (9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27) aim to distill down this complexity into scenarios where specific features of surface hybridization are brought out; for example, the impact of probe surface coverage on target hybridization (17,20,22,23,28).…”

mentioning

confidence: 99%

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DNA surface hybridization regimes

Gong

Levicky²

2008

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

219

282

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Surface hybridization reactions, in which sequence-specific recognition occurs between immobilized and solution nucleic acids, are routinely carried out to quantify and interpret genomic information. Although hybridization is fairly well understood in bulk solution, the greater complexity of an interfacial environment presents new challenges to a fundamental understanding, and hence application, of these assays. At a surface, molecular interactions are amplified by the two-dimensional nature of the immobilized layer, which focuses the nucleic acid charge and concentration to levels not encountered in solution, and which impacts the hybridization behavior in unique ways. This study finds that, at low ionic strengths, an electrostatic balance between the concentration of immobilized oligonucleotide charge and solution ionic strength governs the onset of hybridization. As ionic strength increases, the importance of electrostatics diminishes and the hybridization behavior becomes more complex. Suppression of hybridization affinity constants relative to solution values, and their weakened dependence on the concentration of DNA counterions, indicate that the immobilized strands form complexes that compete with hybridization to analyte strands. Moreover, an unusual regime is observed in which the surface coverage of immobilized oligonucleotides does not significantly influence the hybridization behavior, despite physical closeness and hence compulsory interactions between sites. These results are interpreted and summarized in a diagram of hybridization regimes that maps specific behaviors to experimental ranges of ionic strength and probe coverage.biosensor ͉ ferrocene ͉ ionic strength ͉ microarray ͉ probe coverage S olid-phase or ''surface'' hybridization is the foundation of modern microarray and biosensing technologies widely used in applied genomics for genotyping, drug discovery, gene expression profiling, and related applications based on measurement of genomic information (1, 2). These tools function through detection of interactions between nucleic acids immobilized on a solid support, or ''probes,'' with analyte ''target'' nucleic acids present in solution. Binding, or hybridization, between probes and targets to form an immobilized duplex takes place based on the degree of complementarity between the probe and target base sequences. The tremendous growth in applications of surface hybridization has been mirrorred by increased emphasis on experimental and fundamental aspects of the assays that directly impact measurement and interpretation of data (3, 4).As summarized in several recent reviews (5-8), physical studies under simplified experimental conditions have begun to unravel the rich phenomenology that occurs in diagnostic assays. Applications typically operate away from equilibrium and are faced with a highly diverse pool of target sequences competing for the probe sites. A variety of aids to enhance hybridization performance is used, including surfactants and blocking agents to control nonspecific adsorp...

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Section: Hybridization At Low Conversion: Electrostatics and The Onsementioning

confidence: 73%

mentioning

confidence: 99%

DNA surface hybridization regimes

Gong

Levicky²

2008

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

219

282

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“…The 27 MHz QCM is highly sensitive and quantitative enough to detect various molecular recognitions on DNA molecules, such as DNA-DNA hybridization, 41 sequence specific binding of bZIP peptide to dsDNA, 42 and a series of DNA polymerase reactions such as the binding process of enzyme, the elongation rate and the release of the enzyme from the completely polymerized DNA). 43 Since the QCM is a mass-measuring device, we can apply it widely to detect various host-guest interactions: adsorption of bitter or odor substances to lipid membrane, 22 peptide-DNA interactions, 44 intercalation of antibiotics to DNA strands, and in vitro selection of DNA binding to host molecules.…”

Section: Resultsmentioning

confidence: 99%

A Highly Sensitive 27 MHz Quartz-Crystal Microbalance as a Device for Kinetic Measurements of Molecular Recognition on DNA Strands

et al. 2000

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DNA-DNA hybridization and DNA-protein or enzyme interactions are essential steps in biomolecular recognitions. These interactions have been conventionally studied by gel mobility shift assay. This technique gives us only qualitative information, we must label enzymes radioactive or fluorescent molecules, and it takes a relatively long time to analyze the results. Here we introduce a new tool of a highly sensitive 27 MHz quartz-crystal microbalance (QCM), in which the resonance frequency decreases linearly with the increase of mass on the electrode area at the nanogram level. Thus, when a host molecule is immobilized on a QCM, the binding behavior and its kinetics can be monitored from frequency changes due to the guest binding in aqueous solution. The results are also compared with those from a surface plasmon resonance sensor.

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“…In this work, we hypothesize that the kinetics of particle reorganization in superlattices can be explained by examining the kinetics of free oligonucleotides. Specifically, we propose to explain reorganization kinetics based upon how the rates of hybridization (k on ) and dehybridization (k off ) change as a function of design variables including temperature, nucleobase sequence, oligonucleotide density, and solution ionic strength (18)(19)(20).…”

Section: Significancementioning

confidence: 99%

“…Changing the solution salt concentration has multiple effects on reorganization because it affects both C 0 k on and k off (Fig. 5A, Inset) (18,20). Specifically, raising the salt concentration is expected to increase k on because the additional charge screening minimizes the repulsion between negatively charged DNA strands, and it is also expected to lower k off because the increased counterion concentration will help to stabilize the linkages once formed.…”

Section: Significancementioning

confidence: 99%

Importance of the DNA “bond” in programmable nanoparticle crystallization

Macfarlane

Thaner

Brown

et al. 2014

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

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If a solution of DNA-coated nanoparticles is allowed to crystallize, the thermodynamic structure can be predicted by a set of structural design rules analogous to Pauling's rules for ionic crystallization. The details of the crystallization process, however, have proved more difficult to characterize as they depend on a complex interplay of many factors. Here, we report that this crystallization process is dictated by the individual DNA bonds and that the effect of changing structural or environmental conditions can be understood by considering the effect of these parameters on free oligonucleotides. Specifically, we observed the reorganization of nanoparticle superlattices using time-resolved synchrotron small-angle X-ray scattering in systems with different DNA sequences, salt concentrations, and densities of DNA linkers on the surface of the nanoparticles. The agreement between bulk crystallization and the behavior of free oligonucleotides may bear important consequences for constructing novel classes of crystals and incorporating new interparticle bonds in a rational manner.DNA materials | self assembly | nanostructure M aterials scientists have accomplished much by studying the way atoms and molecules crystallize. In these systems, however, the identity of the atom and its bonding behavior cannot be independently controlled, limiting our ability to tune material properties at will. In contrast, when a nanoparticle is modified with a dense shell of upright, oriented DNA, it can behave as a programmable atom equivalent (PAE) (1, 2) that can be used to synthesize diverse crystal structures with independent control over composition, scale, and lattice symmetry (3-14). The thermodynamic product of this crystallization process has been extensively studied by both experimental and theoretical means, and thus a series of design rules has been proposed and validated with a simple geometric model known as the complementary contact model (CCM). These rules allow one to predict the thermodynamically favored structure as the arrangement of particles that maximizes complementary contacts and therefore DNA hybridization (2, 6). These efforts have been very successful in predicting the thermodynamically favored product; recent studies have even demonstrated that PAEs can form single-crystal Wulff polyhedra that are analogous to those formed in atomic systems with the same crystallographic symmetry (15). However, the fact that there is a crystalline thermodynamic product does not mean that any choice of DNA and nanoparticles will result in crystalline systems in practice (3, 4). For example, crystallization has been observed for a relatively narrow class of PAEs (16) and in a manner that is primarily dependent upon the length of the DNA linker and temperature at which assembly occurs (8). Thus, absent from our understanding of these systems is a connection between the crystallization process and the properties of the DNA bonds that form the foundation of these structures.Here, we study the crystallization process and find t...

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Kinetic Measurements of DNA Hybridization on an Oligonucleotide-Immobilized 27-MHz Quartz Crystal Microbalance

Cited by 412 publications

References 55 publications

DNA surface hybridization regimes

DNA surface hybridization regimes

A Highly Sensitive 27 MHz Quartz-Crystal Microbalance as a Device for Kinetic Measurements of Molecular Recognition on DNA Strands

Importance of the DNA “bond” in programmable nanoparticle crystallization

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