An energy model for nanomechanical deflection of cantilever-DNA chip

Zhang, Neng-Hui; Shan, Jin-Ying

doi:10.1016/j.jmps.2007.12.003

Cited by 41 publications

(43 citation statements)

References 27 publications

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“…34 Previous theoretical works reveal that small amounts of disorder in the DNA monolayer can affect cantilever deflection. 28,[42][43][44] Moreover, Kosaka et al 19 , proved the heterogeneity of highly packed DNA monolayers on gold obtained by selfassembly. We speculate that the observed variations in the value of ΔS from sample to sample, for the same sequence and incubation conditions, could arise due to slight probe density differences or inhomogeneities.…”

Section: Resultsmentioning

confidence: 99%

Hydration Induced Stress on DNA Monolayers Grafted on Microcantilevers

et al. 2014

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Surface tethered single-stranded DNA films are relevant biorecognition layers for oligonucleotide sequence identification. Also, hydration induced effects on these films have proven useful for the nanomechanical detection of DNA hybridization. Here, we apply nanomechanical sensors and atomic force microscopy to characterize in air and upon varying relative humidity conditions the swelling and deswelling of grafted single stranded and double stranded DNA films. The combination of these techniques validates a two-step hybridization process, where complementary strands first bind to the surface tethered single stranded DNA probes and then slowly proceed to a fully zipped configuration. Our results also demonstrate that, despite the slow hybridization kinetics observed for grafted DNA onto microcantilever surfaces, ex-situ sequence identification does not require hybridization times typically longer than 1 hour, while quantification is a major challenge.. 2

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Section: Resultsmentioning

confidence: 99%

Hydration Induced Stress on DNA Monolayers Grafted on Microcantilevers

et al. 2014

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“…In addition, a microcantilever-based DNA sensor typically is a multilayered structure, including a DNA-, Si-or SiNx-, Au-, Cr-or Ti-layer in a buffer solution environment. Recently, some theoretical methods have been presented to understand this mechanical behavior, such as liquid crystal theory [10,11], flexoelectric membrane theory [12], surface energy [13] and classical density functional theory [14].…”

Section: Introductionmentioning

confidence: 99%

Effect of Conformational Entropy on the Nanomechanics of Microcantilever-Based Single-Stranded DNA Sensors

Tan

Zhang

2014

Entropy

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An entropy-controlled bending mechanism is presented to study the nanomechanics of microcantilever-based single-stranded DNA (ssDNA) sensors. First; the conformational free energy of the ssDNA layer is given with an improved scaling theory of thermal blobs considering the curvature effect; and the mechanical energy of the non-biological layer is described by Zhang's two-variable method for laminated beams. Then; an analytical model for static deflections of ssDNA microcantilevers is formulated by the principle of minimum energy. The comparisons of deflections predicted by the proposed model; Utz-Begley's model and Hagan's model are also examined. Numerical results show that the conformational entropy effect on microcantilever deflections cannot be ignored; especially at the conditions of high packing density or long chain systems; and the variation of deflection predicted by the proposed analytical model not only accords with that observed in the related experiments qualitatively; but also appears quantitatively closer to the experimental values than that by the preexisting models. In order to improve the sensitivity of static-mode biosensors; it should be as small as possible to reduce the substrate stiffness.

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“…In recent years, microcantilever-based biosensors have attracted much attention (Fritz et al 2000;Wu et al 2001;Hagan et al 2002;Liu et al 2003;Alvarez et al 2004;Hansen and Thundat 2005;Stachowiak et al 2006;Zhang et al 2007;Zhang and Shan 2008;Finot et al 2008;Fritz 2008;Zhang and Chen 2009a;). The low-cost sensors not only exhibit fast response, high sensitivity, and suitability for parallelization into arrays, but also provide common platforms for label-free analyses, such as DNA hybridization, antigen-antibody binding, and drug discovery.…”

Section: Introductionmentioning

confidence: 99%

“…Based on Strey's empirical potential (Strey et al 1997(Strey et al , 1999 for a double-stranded DNA (dsDNA) systems, Hagan et al (2002) provided a theoretical framework for such microcantilever-dsDNA chips (corresponding to detection process) and showed that the dominant contribution to hybridization deflections comes from hydration forces. Using an alternative two-variable method (Zhang and Xing 2006;Zhang et al 2007;Zhang and Chen 2008, 2009b, 2010 for laminated cantilever beams, Zhang et al formulated a four-layer energy model for microcantilever-dsDNA chips (Zhang and Shan 2008) and investigated stochastic effect (Zhang and Shan 2008), hybridization exothermic effect ) as well as compressive elastic modulus (Zhang and Chen 2009a) of dsDNA-biolayer. In the process of modeling ssDNA chips (corresponding to packing process), Hagan et al (2002) pointed out that there is relatively little information about the segment-segment interactions in ssDNA, and therefore estimated the ssDNA free energy by utilizing several methods commonly used to examine polymer brushes, e.g., scaling laws, self-consistent-field methods, and Monte Carlo simulations.…”

Section: Introductionmentioning

confidence: 99%

“…Different from previous nanomechanical models (Hagan et al 2002;Zhang and Chen 2009a;Zhang and Shan 2008), hybridization exothermic models ) for dsDNA, and piezoelectric models for ssDNA ), this article is aimed to predict nanomechanical deflections of ssDNA chips induced by counterion osmotic pressure during packing process. First, Hagan's model for a cylindrical polyelectrolyte brush system based on Poisson- Boltzmann distribution hypothesis is employed to estimate the counterion osmotic energy in the ssDNA-biolayer with weak interactions.…”

Section: Introductionmentioning

confidence: 99%

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Nanomechanical behaviors of microcantilever-based single-stranded DNA chips induced by counterion osmotic effects

Zhang

Shan

2010

Biomech Model Mechanobiol

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Experiments show that deflections of microcantilever-DNA chip can be induced by many factors, such as grafting density, hybridization efficiency, concentration, length and sequence of DNA molecules, buffer salt concentration, time, and temperature variation. However, there are few theoretical works on microcantilever-DNA chips. The present paper is aimed to study the influence of counterion effects of single-stranded DNA (ssDNA) polyelectrolyte solution on the nanomechanical behaviors of microcantilever-based ssDNA chips during packing process. First, the effect of osmotic pressure induced by ingress of counterions into DNA brush structures is studied with Hagan's model for a cylindrical polyelectrolyte brush system on the basis of Poisson-Boltzmann distribution hypothesis. Second, Zhang's two-variable method for a laminated cantilever is used to formulate a four-layer energy model for ssDNA chips with weak interactions. Third, the influence of grafting density, ssDNA chain length, and salt concentration on packing deflection is investigated using the principle of minimum energy. The predictive tendency is qualitatively similar to those observed in some related ssDNA chip experiments. The difference between the four-layer model and the simplified two-layer model for ssDNA chips is also discussed.

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An energy model for nanomechanical deflection of cantilever-DNA chip

Cited by 41 publications

References 27 publications

Hydration Induced Stress on DNA Monolayers Grafted on Microcantilevers

Hydration Induced Stress on DNA Monolayers Grafted on Microcantilevers

Effect of Conformational Entropy on the Nanomechanics of Microcantilever-Based Single-Stranded DNA Sensors

Nanomechanical behaviors of microcantilever-based single-stranded DNA chips induced by counterion osmotic effects

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