A multi-scale model for the analysis of the inhomogeneity of elastic properties of DNA biofilm on microcantilevers

Zhang, Neng-Hui; Meng, Wei-Lie; Tan, Zefu

doi:10.1016/j.biomaterials.2012.11.023

Cited by 19 publications

(18 citation statements)

References 67 publications

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“…Furthermore, Figure 3c shows that the competition between the repulsive part and attractive part of free energy lead to the non-monotonic variation of elastic modulus. In addition, the magnitude of the elastic modulus of the DNA film in 0.1 M NaCl solution was about 0.1~100 MPa, which is similar to Zhang’s theoretical prediction [22], and slightly smaller than Legay’s (50 mM NaCl solution) [32], due to different salt concentrations and packing conditions as well as the inherent deficiency of AFM-based nano-indentation detection. What is more, our simulation showed a consistent monotonic trend with that of Domínguez’s theoretical predictions and approaches the order of their AFM experiment results [17].…”

Section: Resultssupporting

confidence: 78%

“…In this section, the adsorbed DNA film is treated as an elastomer. According to continuum mechanics, if the free energy of the self- or directed-assembled DNA film is derived, its elastic properties in a uniaxial compressive/tensile state can be easily obtained as [20] Enormalp=3η∂2Wnormalb/∂ε2|ε=0, σnormalp=3η∂Wnormalb/∂ε|ε=0 where E p is the elastic modulus, σ p is the surface stress, ε is the axial strain, η is the DNA packing density, and η=2/false(3d02false) for the hexagonal packing pattern, in which d 0 is the initial interaxial distance [21,22]; W b is the free energy per unit length between two parallel DNA cylinders. However, there is no a unified formula for the free energy of DNA solutions.…”

Section: Multiscale Analytical Modelmentioning

confidence: 99%

See 1 more Smart Citation

Anomalous Elastic Properties of Attraction-Dominated DNA Self-Assembled 2D Films and the Resultant Dynamic Biodetection Signals of Microbeam Sensors

Zhang

2019

Nanomaterials

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The condensation of DNA helices has been regularly found in cell nucleus, bacterial nucleoids, and viral capsids, and during its relevant biodetections the attractive interactions between DNA helices could not be neglected. In this letter, we theoretically characterize the elastic properties of double-stranded DNA (dsDNA) self-assembled 2D films and their multiscale correlations with the dynamic detection signals of DNA-microbeams. The comparison of attraction- and repulsion-dominated DNA films shows that the competition between attractive and repulsive micro-interactions endows dsDNA films in multivalent salt solutions with anomalous elastic properties such as tensile surface stresses and negative moduli; the occurrence of the tensile surface stress for the attraction-dominated DNA self-assembled film reveals the possible physical mechanism of the condensation found in organism. Furthermore, dynamic analyses of a hinged–hinged DNA-microbeam reveal non-monotonous frequency shifts due to attraction- or repulsion-dominated dsDNA adsorptions and dynamic instability occurrence during the detections of repulsion-dominated DNA films. This dynamic instability implies the existence of a sensitive interval of material parameters in which DNA adsorptions will induce a drastic natural frequency shift or a jump of vibration mode even with a tiny variation of the detection conditions. These new insights might provide us some potential guidance to achieve an ultra-highly sensitive biodetection method in the future.

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Section: Resultssupporting

confidence: 78%

Section: Multiscale Analytical Modelmentioning

confidence: 99%

Anomalous Elastic Properties of Attraction-Dominated DNA Self-Assembled 2D Films and the Resultant Dynamic Biodetection Signals of Microbeam Sensors

Zhang

2019

Nanomaterials

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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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“…Although the Parsegain's potential [10] was improved by Zhang et al with a soft cylinder model for dsDNA [13,14] to describe the flexibility of DNA film under different solution conditions, it still cannot be used to explain the adsorption-induced surface tension phenomenon [6][7][8][9] due to the lack of attraction interaction. Note that the assumption of cylinder model might be invalid for random coiled conformation of ssDNA with weak interactions [11] especially at the condition of low packing density.…”

Section: Introductionmentioning

confidence: 98%

Inverse piezoelectricity of single-stranded DNA film on microcantilever

Zhang

2015

IEEE Trans. Dielect. Electr. Insul.

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The paper aims to reveal the relation between the inverse piezoelectricity of singlestranded DNA (ssDNA) film and the origin and sign of the deflection of microcantilever produced by the DNA immobilization. By using Zhang's two-variable method for strain field of laminated beam and the linearized Poisson-Boltzmann equation for bioelectric potential of polyelectrolyte brush, an approximate model is presented to confirm the previous conjecture that the sign of the piezoelectric constant of ssDNA film might decide the sign of the surface stress. There is only one fitting parameter (piezoelectric stress constant) needed in the simplified model, which greatly reduces the difficulty of identifying the nanoscale electrical/mechanical properties of DNA film. Numerical fitting curves based-on the analytical models agree well with the pertinent experimental dada. The difference between the previous four-layered model and the present two-layered approximate model is also compared.

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A multi-scale model for the analysis of the inhomogeneity of elastic properties of DNA biofilm on microcantilevers

Cited by 19 publications

References 67 publications

Anomalous Elastic Properties of Attraction-Dominated DNA Self-Assembled 2D Films and the Resultant Dynamic Biodetection Signals of Microbeam Sensors

Anomalous Elastic Properties of Attraction-Dominated DNA Self-Assembled 2D Films and the Resultant Dynamic Biodetection Signals of Microbeam Sensors

Hydration Induced Stress on DNA Monolayers Grafted on Microcantilevers

Inverse piezoelectricity of single-stranded DNA film on microcantilever

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