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Rotondi SMC, Canepa P, Angeli E, Canepa M, Cavalleri O. DNA Sensing Platforms: Novel Insights into Molecular Grafting Using Low Perturbative AFM Imaging. SENSORS (BASEL, SWITZERLAND) 2023; 23:s23094557. [PMID: 37177760 PMCID: PMC10181596 DOI: 10.3390/s23094557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/01/2023] [Accepted: 05/06/2023] [Indexed: 05/15/2023]
Abstract
By using AFM as a nanografting tool, we grafted micrometer-sized DNA platforms into inert alkanethiol SAMs. Tuning the grafting conditions (surface density of grafting lines and scan rate) allowed us to tailor the molecular density of the DNA platforms. Following the nanografting process, AFM was operated in the low perturbative Quantitative Imaging (QI) mode. The analysis of QI AFM images showed the coexistence of molecular domains of different heights, and thus different densities, within the grafted areas, which were not previously reported using contact AFM imaging. Thinner domains corresponded to low-density DNA regions characterized by loosely packed, randomly oriented DNA strands, while thicker domains corresponded to regions with more densely grafted DNA. Grafting with densely spaced and slow scans increased the size of the high-density domains, resulting in an overall increase in patch height. The structure of the grafted DNA was compared to self-assembled DNA, which was assessed through nanoshaving experiments. Exposing the DNA patches to the target sequence produced an increase in the patch height, indicating that hybridization was accomplished. The relative height increase of the DNA patches upon hybridization was higher in the case of lower density patches due to hybridization leading to a larger molecular reorganization. Low density DNA patches were therefore the most suitable for targeting oligonucleotide sequences.
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Affiliation(s)
| | - Paolo Canepa
- Dipartimento di Fisica and Optmatlab, Università di Genova, Via Dodecaneso 33, 16146 Genova, Italy
| | - Elena Angeli
- Dipartimento di Fisica, Università di Genova, Via Dodecaneso 33, 16146 Genova, Italy
| | - Maurizio Canepa
- Dipartimento di Fisica and Optmatlab, Università di Genova, Via Dodecaneso 33, 16146 Genova, Italy
- INFN, Sezione di Genova, Via Dodecaneso 33, 16146 Genova, Italy
| | - Ornella Cavalleri
- Dipartimento di Fisica and Optmatlab, Università di Genova, Via Dodecaneso 33, 16146 Genova, Italy
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2
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Fu R, Li Q, Wang R, Xue N, Lin X, Su Y, Jiang K, Jin X, Lin R, Gan W, Lu Y, Huang G. An interferometric imaging biosensor using weighted spectrum analysis to confirm DNA monolayer films with attogram sensitivity. Talanta 2017; 181:224-231. [PMID: 29426505 DOI: 10.1016/j.talanta.2017.12.066] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 12/13/2017] [Accepted: 12/21/2017] [Indexed: 11/28/2022]
Abstract
Interferometric imaging biosensors are powerful and convenient tools for confirming the existence of DNA monolayer films on silicon microarray platforms. However, their accuracy and sensitivity need further improvement because DNA molecules contribute to an inconspicuous interferometric signal both in thickness and size. Such weaknesses result in poor performance of these biosensors for low DNA content analyses and point mutation tests. In this paper, an interferometric imaging biosensor with weighted spectrum analysis is presented to confirm DNA monolayer films. The interferometric signal of DNA molecules can be extracted and then quantitative detection results for DNA microarrays can be reconstructed. With the proposed strategy, the relative error of thickness detection was reduced from 88.94% to merely 4.15%. The mass sensitivity per unit area of the proposed biosensor reached 20 attograms (ag). Therefore, the sample consumption per unit area of the target DNA content was only 62.5 zeptomoles (zm), with the volume of 0.25 picolitres (pL). Compared with the fluorescence resonance energy transfer (FRET), the measurement veracity of the interferometric imaging biosensor with weighted spectrum analysis is free to the changes in spotting concentration and DNA length. The detection range was more than 1µm. Moreover, single nucleotide mismatch could be pointed out combined with specific DNA ligation. A mutation experiment for lung cancer detection proved the high selectivity and accurate analysis capability of the presented biosensor.
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Affiliation(s)
- Rongxin Fu
- Department of Biomedical Engineering, the School of Medicine, Tsinghua University, Beijing 100084, China
| | - Qi Li
- Department of Biomedical Engineering, the School of Medicine, Tsinghua University, Beijing 100084, China
| | - Ruliang Wang
- Department of Biomedical Engineering, the School of Medicine, Tsinghua University, Beijing 100084, China
| | - Ning Xue
- Department of Biomedical Engineering, the School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xue Lin
- Department of Biomedical Engineering, the School of Medicine, Tsinghua University, Beijing 100084, China
| | - Ya Su
- Department of Biomedical Engineering, the School of Medicine, Tsinghua University, Beijing 100084, China
| | - Kai Jiang
- Department of Biomedical Engineering, the School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xiangyu Jin
- Department of Biomedical Engineering, the School of Medicine, Tsinghua University, Beijing 100084, China
| | - Rongzan Lin
- Department of Biomedical Engineering, the School of Medicine, Tsinghua University, Beijing 100084, China
| | - Wupeng Gan
- National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, China
| | - Ying Lu
- Department of Biomedical Engineering, the School of Medicine, Tsinghua University, Beijing 100084, China
| | - Guoliang Huang
- Department of Biomedical Engineering, the School of Medicine, Tsinghua University, Beijing 100084, China; National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, China.
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van Grinsven B, Eersels K, Peeters M, Losada-Pérez P, Vandenryt T, Cleij TJ, Wagner P. The heat-transfer method: a versatile low-cost, label-free, fast, and user-friendly readout platform for biosensor applications. ACS APPLIED MATERIALS & INTERFACES 2014; 6:13309-13318. [PMID: 25105260 DOI: 10.1021/am503667s] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In recent years, biosensors have become increasingly important in various scientific domains including medicine, biology, and pharmacology, resulting in an increased demand for fast and effective readout techniques. In this Spotlight on Applications, we report on the recently developed heat-transfer method (HTM) and illustrate the use of the technique by zooming in on four established bio(mimetic) sensor applications: (i) mutation analysis in DNA sequences, (ii) cancer cell identification through surface-imprinted polymers, (iii) detection of neurotransmitters with molecularly imprinted polymers, and (iv) phase-transition analysis in lipid vesicle layers. The methodology is based on changes in heat-transfer resistance at a functionalized solid-liquid interface. To this extent, the device applies a temperature gradient over this interface and monitors the temperature underneath and above the functionalized chip in time. The heat-transfer resistance can be obtained by dividing this temperature gradient by the power needed to achieve a programmed temperature. The low-cost, fast, label-free and user-friendly nature of the technology in combination with a high degree of specificity, selectivity, and sensitivity makes HTM a promising sensor technology.
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Affiliation(s)
- Bart van Grinsven
- Maastricht Science Programme, Maastricht University , PO Box 616, 6200 MD Maastricht, The Netherlands
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4
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van Grinsven B, Vanden Bon N, Strauven H, Grieten L, Murib M, Monroy KLJ, Janssens SD, Haenen K, Schöning MJ, Vermeeren V, Ameloot M, Michiels L, Thoelen R, De Ceuninck W, Wagner P. Heat-transfer resistance at solid-liquid interfaces: a tool for the detection of single-nucleotide polymorphisms in DNA. ACS NANO 2012; 6:2712-21. [PMID: 22356595 DOI: 10.1021/nn300147e] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
In this article, we report on the heat-transfer resistance at interfaces as a novel, denaturation-based method to detect single-nucleotide polymorphisms in DNA. We observed that a molecular brush of double-stranded DNA grafted onto synthetic diamond surfaces does not notably affect the heat-transfer resistance at the solid-to-liquid interface. In contrast to this, molecular brushes of single-stranded DNA cause, surprisingly, a substantially higher heat-transfer resistance and behave like a thermally insulating layer. This effect can be utilized to identify ds-DNA melting temperatures via the switching from low- to high heat-transfer resistance. The melting temperatures identified with this method for different DNA duplexes (29 base pairs without and with built-in mutations) correlate nicely with data calculated by modeling. The method is fast, label-free (without the need for fluorescent or radioactive markers), allows for repetitive measurements, and can also be extended toward array formats. Reference measurements by confocal fluorescence microscopy and impedance spectroscopy confirm that the switching of heat-transfer resistance upon denaturation is indeed related to the thermal on-chip denaturation of DNA.
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Affiliation(s)
- Bart van Grinsven
- Institute for Materials Research IMO, IMOMEC, Hasselt University, Wetenschapspark 1, B-3590 Diepenbeek, Belgium.
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5
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Affiliation(s)
- Emil Paleček
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, 612
65 Brno, Czech Republic
| | - Martin Bartošík
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, 612
65 Brno, Czech Republic
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6
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Papadakis G, Tsortos A, Bender F, Ferapontova EE, Gizeli E. Direct Detection of DNA Conformation in Hybridization Processes. Anal Chem 2012; 84:1854-61. [DOI: 10.1021/ac202515p] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- George Papadakis
- Institute of Molecular Biology
and Biotechnology, Foundation for Research and Technology Hellas, 100 N. Plastira, Vassilika Vouton, 70013 Heraklion,
Greece
| | - Achilleas Tsortos
- Institute of Molecular Biology
and Biotechnology, Foundation for Research and Technology Hellas, 100 N. Plastira, Vassilika Vouton, 70013 Heraklion,
Greece
| | - Florian Bender
- Institute of Molecular Biology
and Biotechnology, Foundation for Research and Technology Hellas, 100 N. Plastira, Vassilika Vouton, 70013 Heraklion,
Greece
- Department of
Electrical and
Computer Engineering, Marquette University, 1515 West Wisconsin Avenue, Milwaukee, Wisconsin 53233, United
States
| | - Elena E. Ferapontova
- Danish National Research
Foundation:
Center for DNA Nanotechnology, and Department of Chemistry and iNANO, Aarhus University, Ny Munkegade 1521, DK-8000 Aarhus
C, Denmark
| | - Electra Gizeli
- Institute of Molecular Biology
and Biotechnology, Foundation for Research and Technology Hellas, 100 N. Plastira, Vassilika Vouton, 70013 Heraklion,
Greece
- Department of Biology, University of Crete, Vassilika Vouton, 71409, Heraklion,
Greece
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7
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Wenmackers S, Vanpoucke DEP. Models and simulations in material science: two cases without error bars. STAT NEERL 2012. [DOI: 10.1111/j.1467-9574.2011.00519.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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8
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Drew ME, Konicek AR, Jaroenapibal P, Carpick RW, Yamakoshi Y. Nanocrystalline diamond AFM tips for chemical force spectroscopy: fabrication and photochemical functionalization. ACTA ACUST UNITED AC 2012. [DOI: 10.1039/c2jm16209a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Ambia-Garrido J, Vainrub A, Montgomery Pettitt B. Free energy considerations for nucleic acids with dangling ends near a surface: a coarse grained approach. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2011; 23:325101. [PMID: 21743128 PMCID: PMC3191199 DOI: 10.1088/0953-8984/23/32/325101] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
A coarse grained model for the thermodynamics of nucleic acid hybridization near surfaces has been extended and parameterized to consider the contribution of unpaired dangling ends. The parameters of the model differ when representing a double stranded DNA section or a single stranded DNA section. The thermodynamic effects of the possibility of different dangling end combinations were considered in the presence of different types of surfaces. Configurational sampling was achieved by the Metropolis Monte Carlo method. To gain a more complete picture of the free energy changes, an estimation of the conformational entropy was included. We find a strong thermodynamic effect for dangling mismatches due to sequence requirements when they are nearer the surface as opposed to being held away from the surface.
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Affiliation(s)
- J Ambia-Garrido
- Department of Physics, University of Houston, Houston, TX, USA
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10
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van Grinsven B, Vanden Bon N, Grieten L, Murib M, Janssens SD, Haenen K, Schneider E, Ingebrandt S, Schöning MJ, Vermeeren V, Ameloot M, Michiels L, Thoelen R, De Ceuninck W, Wagner P. Rapid assessment of the stability of DNA duplexes by impedimetric real-time monitoring of chemically induced denaturation. LAB ON A CHIP 2011; 11:1656-1663. [PMID: 21448492 DOI: 10.1039/c1lc20027e] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
In this article, we report on the electronic monitoring of DNA denaturation by NaOH using electrochemical impedance spectroscopy in combination with fluorescence imaging as a reference technique. The probe DNA consisting of a 36-mer fragment was covalently immobilized on nanocrystalline-diamond electrodes and hybridized with different types of 29-mer target DNA (complementary, single-nucleotide defects at two different positions, and a non-complementary random sequence). The mathematical separation of the impedimetric signals into the time constant for NaOH exposure and the intrinsic denaturation-time constants gives clear evidence that the denaturation times reflect the intrinsic stability of the DNA duplexes. The intrinsic time constants correlate with calculated DNA-melting temperatures. The impedimetric method requires minimal instrumentation, is label-free and fast with a typical time scale of minutes and is highly reproducible. The sensor electrodes can be used repetitively. These elements suggest that the monitoring of chemically induced denaturation at room temperature is an interesting approach to measure DNA duplex stability as an alternative to thermal denaturation at elevated temperatures, used in DNA-melting experiments and single nucleotide polymorphism (SNP) analysis.
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Affiliation(s)
- B van Grinsven
- Hasselt University, Institute for Materials Research, Wetenschapspark 1, B-3590, Diepenbeek, Belgium.
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11
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Ambia-Garrido J, Vainrub A, Pettitt BM. A model for Structure and Thermodynamics of ssDNA and dsDNA Near a Surface: a Coarse Grained Approach. COMPUTER PHYSICS COMMUNICATIONS 2010; 181:2001-2007. [PMID: 20957064 PMCID: PMC2955266 DOI: 10.1016/j.cpc.2010.08.029] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
New methods based on surfaces or beads have allowed measurement of properties of single DNA molecules in very accurate ways. Theoretical coarse grained models have been developed to understand the behavior of single stranded and double stranded DNA. These models have been shown to be accurate and relatively simple for very short systems of 6-8 base pairs near surfaces. Comparatively less is known about the influence of a surface on the secondary structures of longer molecules important to many technologies. Surface fields due to either applied potentials and/or dielectric boundaries are not in current surface mounted coarse grained models. To gain insight into longer and surface mounted sequences we parameterized a discretized worm-like chain model. Each link is considered a sphere of 6 base pairs in length for dsDNA, and 1.5 bases for ssDNA (requiring an always even number of spheres). For this demonstration of the model, the chain is tethered to a surface by a fixed length, non-interacting 0.536 nm linker. Configurational sampling was achieved via Monte-Carlo simulation. Our model successfully reproduces end to end distance averages from experimental results, in agreement with polymer theory and all atom simulations. Our average tilt results are also in agreement with all atom simulations for the case of dense systems.
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Affiliation(s)
- J Ambia-Garrido
- Department of Physics and Department of Chemistry, University of Houston, Houston, Texas
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12
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Liu Y, Sun K. Protein functionalized nanodiamond arrays. NANOSCALE RESEARCH LETTERS 2010; 5:1045-50. [PMID: 20672037 PMCID: PMC2894344 DOI: 10.1007/s11671-010-9600-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Accepted: 04/01/2010] [Indexed: 05/29/2023]
Abstract
Various nanoscale elements are currently being explored for bio-applications, such as in bio-images, bio-detection, and bio-sensors. Among them, nanodiamonds possess remarkable features such as low bio-cytotoxicity, good optical property in fluorescent and Raman spectra, and good photostability for bio-applications. In this work, we devise techniques to position functionalized nanodiamonds on self-assembled monolayer (SAMs) arrays adsorbed on silicon and ITO substrates surface using electron beam lithography techniques. The nanodiamond arrays were functionalized with lysozyme to target a certain biomolecule or protein specifically. The optical properties of the nanodiamond-protein complex arrays were characterized by a high throughput confocal microscope. The synthesized nanodiamond-lysozyme complex arrays were found to still retain their functionality in interacting with E. coli.
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Affiliation(s)
- Yl Liu
- Department of Applied Chemistry, National Chiao Tung University, 30010, Hsinchu, Taiwan.
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Puleo DA, Bizios R. Investigating Protein Adsorption via Spectroscopic Ellipsometry. BIOLOGICAL INTERACTIONS ON MATERIALS SURFACES 2009. [PMCID: PMC7121108 DOI: 10.1007/978-0-387-98161-1_2] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In this chapter, the basic concepts behind ellipsometry and spectroscopic ellipsometry are discussed along with some instrument details. Ellipsometry is an optical technique that measures changes in the reflectance and phase difference between the parallel (RP) and perpendicular (RS) components of a polarized light beam upon reflection from a surface. Aside from providing a simple, sensitive, and nondestructive way to analyze thin films, ellipsometry allows dynamic studies of film growth (thickness and optical constants) with a time resolution that is relevant to biomedical research. The present chapter intends to introduce ellipsometry as an emerging but highly promising technique, that is useful to elucidate the interactions of proteins with solid surfaces. In this regard, particular emphasis is placed on experimental details related to the development of biomedically relevant conjugated surfaces. Results from our group related to adsorption of proteins to nanostructured materials, as well as results published by other research groups, are discussed to illustrate the advantages and limitations of the technique.
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Relative Specificity of the Hybridization Process on DNA Chips: Direct Comparison of Four Interfacial Architectures Investigated by Surface Plasmon Resonance. E-JOURNAL OF SURFACE SCIENCE AND NANOTECHNOLOGY 2009. [DOI: 10.1380/ejssnt.2009.777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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