Multiple label-free biodetection and quantitative DNA-binding assays on a nanomechanical cantilever array

McKendry, Rachel A.; Zhang, Jiayun; Arntz, Youri; Strunz, Torsten; Hegner, Martin; Lang, H.P.; Baller, Marko; Certa, Ulrich; Meyer, Ernst; Güntherodt, H.‐J.; Gerber, Christoph

doi:10.1073/pnas.152330199

Cited by 575 publications

(503 citation statements)

References 21 publications

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“…29) The direction of the difference requires more positive stress on the facets than on the spherical regions, resulting in a relative inward displacement of the facets upon thiol adsorption. Similar values of stress have been measured in micromechanical cantilever measurements 50,51) of stresses generated by applying thiols to micrometer-thick Si membranes coated on one side with Au. The specific Au-S bonding causes stress on the coated surface of the cantilever, causing it to bend.…”

Section: In-situ Thiolation Of Au Nanocrystalsupporting

confidence: 73%

Nanoparticle Structure by Coherent X-ray Diffraction

Robinson

2013

J. Phys. Soc. Jpn.

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This review examines the physical reasons why nanoparticles differ in structure from the bulk. Certain simple properties of nanoparticles are explained through these structural differences. A powerful method of measuring the three dimensional structure of nanoparticles, Coherent X-ray diffraction (CXD), is introduced. A key experiment is described that uses CXD to study the redistribution of strains on the surface of a Au nanocrystal. Some future perspectives are discussed in conclusion.

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Section: In-situ Thiolation Of Au Nanocrystalsupporting

confidence: 73%

Nanoparticle Structure by Coherent X-ray Diffraction

Robinson

2013

J. Phys. Soc. Jpn.

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“…In recent years a versatile platform for biodetection has been developed based on microfabricated arrays of silicon cantilevers 14,15,16,17,18,19,20,21 , each coated with a sensitive layer for molecular recognition, e.g. a gene specific oligonucleotide.…”

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confidence: 99%

Direct detection of a BRAF mutation in total RNA from melanoma cells using cantilever arrays

et al. 2013

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Malignant melanoma, the deadliest form of skin cancer, is characterised by a predominant mutation in the BRAF gene. Drugs that target tumours carrying this mutation have recently entered the clinic. Therefore patients are routinely screened for mutations in this gene to determine whether they can benefit from this type of treatment. The current gold standard for mutation screening uses real time polymerase chain reaction (PCR) and sequencing methods. Here we show that an assay based on microcantilever arrays can detect the mutation nanomechanically without amplification in total RNA samples isolated from melanoma cells. The assay is based on a BRAF specific oligonucleotide probe. We detected mutant BRAF at a concentration of 500 pM in a 50-fold excess of the wild-type sequence. The method was able to distinguish melanoma cells carrying the mutation from wild type cells using as little as 20 ng/µl of RNA material, without prior PCR amplification and use of labels.The identification of alterations in specific signalling pathways and recurrent oncogenic mutations in particular types of cancers has led in the past decade to the explosion of targeted therapy approaches. In cutaneous melanoma, a significant improvement in overall survival has been achieved by vemurafenib and similar drugs that selectively inhibit tumours carrying a mutated BRAF 2 gene 1,2 . Additional drugs for combination therapies with higher efficacies and fewer side effects are in clinical trials 3 . BRAF is one of three RAF genes (rapidly accelerated fibrosarcoma A, B and C) encoding cytoplasmic protein serine/threonine kinases belonging to the mitogen-activated protein kinase (MAPK) signal transduction cascade, a pathway controlling various cellular processes such as proliferation, migration and survival 4,5 . BRAF somatic mutations are present in half of cutaneous melanomas. Over 90% of the mutations are a single T to A transversion at position 1799 in the BRAF coding sequence (cT1799A), which converts a valine amino acid residue at position 600 in the protein to a glutamic acid (V600E). This mutation renders the protein constitutively active, resulting in a deregulated MAPK pathway 6 and thus uncontrolled cell growth and cancer. BRAF mutations are also present in other neoplasms, including hairy cell leukemias, thyroid and colon carcinomas 7,8,9 . As the presence of the cT1799A/V600E BRAF (hereafter BRAF V600E ) mutation determines eligibility to BRAF inhibitor treatment, molecular screening of tumour biopsies is now carried out routinely. with sensitivity comparable to COBAS TM , silicon nanowire field-effect transistors 12 and a threedimensional gold nanowire platform 13 . The latter technologies have only been shown to work using synthetic oligonucleotide targets, larger gene fragments or still rely on an initial PCR amplification. In particular, they have not been applied to the direct identification of a mutated messenger RNA (mRNA) sequence in total RNA (constituted primarily by ribosomal RNA and containing all mRNAs transcribed from gen...

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“…Early reports on experiments gave high immobilization densities in the range of 0.13-0.17 chains/nm 2 ; 12,27 the displacement predictions corresponding to these densities are compared to reported experimental measurements 5,6,11,12,23 in Table II. In order to simplify comparison across different experiments, the predicted and measured displacements in the table are multiplied with the square of the aspect ratio h l À Á 2 of the cantilever used in the experiment.…”

Section: Comparison Of Numerical Prediction With Experimental Rementioning

confidence: 87%

“…Since this work, cantilever deflection due to ssDNA hybridization has been utilized as a validation experiment for new techniques, and cantilever deflection signals up to $100 nm have been reported for those experiments. [9][10][11][12]23 Hansen et al 7 also demonstrated that hybridizationinduced cantilever deflection can be used to discriminate base-pair mismatches with 20-nt and 25-nt probe DNA molecules. They used 10 nt DNA oligonucleotides as complementary target molecules, which contain either one or two internal mismatches.…”

Section: Introductionmentioning

confidence: 99%

Cantilever deflection associated with hybridization of monomolecular DNA film

Zhao

Ganapathysubramanian

Shrotriya

2012

Journal of Applied Physics

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Recent experiments show that specific binding between a ligand and surface immobilized receptor, such as hybridization of single stranded DNA immobilized on a microcantilever surface, leads to cantilever deflection. The binding-induced deflection may be used as a method for detection of biomolecules, such as pathogens and biohazards. Mechanical deformation induced due to hybridization of surface-immobilized DNA strands is a commonly used system to demonstrate the efficacy of microcantilever sensors. To understand the mechanism underlying the cantilever deflections, a theoretical model that incorporates the influence of ligand/receptor complex surface distribution and empirical interchain potential is developed to predict the binding-induced deflections. The cantilever bending induced due to hybridization of DNA strands is predicted for different receptor immobilization densities, hybridization efficiencies, and spatial arrangements. Predicted deflections are compared with experimental reports to validate the modeling assumptions and identify the influence of various components on mechanical deformation. Comparison of numerical predictions and experimental results suggest that, at high immobilization densities, hybridization-induced mechanical deformation is determined, primarily by immobilization density and hybridization efficiency, whereas, at lower immobilization densities, spatial arrangement of hybridized chains need to be considered in determining the cantilever deflection. Recent experiments show that specific binding between a ligand and surface immobilized receptor, such as hybridization of single stranded DNA immobilized on a microcantilever surface, leads to cantilever deflection. The binding-induced deflection may be used as a method for detection of biomolecules, such as pathogens and biohazards. Mechanical deformation induced due to hybridization of surface-immobilized DNA strands is a commonly used system to demonstrate the efficacy of microcantilever sensors. To understand the mechanism underlying the cantilever deflections, a theoretical model that incorporates the influence of ligand/receptor complex surface distribution and empirical interchain potential is developed to predict the binding-induced deflections. The cantilever bending induced due to hybridization of DNA strands is predicted for different receptor immobilization densities, hybridization efficiencies, and spatial arrangements. Predicted deflections are compared with experimental reports to validate the modeling assumptions and identify the influence of various components on mechanical deformation. Comparison of numerical predictions and experimental results suggest that, at high immobilization densities, hybridization-induced mechanical deformation is determined, primarily by immobilization density and hybridization efficiency, whereas, at lower immobilization densities, spatial arrangement of hybridized chains need to be considered in determining the cantilever deflection. V C 2012 American Institute of Physics. [http://dx

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Multiple label-free biodetection and quantitative DNA-binding assays on a nanomechanical cantilever array

Cited by 575 publications

References 21 publications

Nanoparticle Structure by Coherent X-ray Diffraction

Nanoparticle Structure by Coherent X-ray Diffraction

Direct detection of a BRAF mutation in total RNA from melanoma cells using cantilever arrays

Cantilever deflection associated with hybridization of monomolecular DNA film

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