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López Marzo AM. Techniques for characterizing biofunctionalized surfaces for bioanalysis purposes. Biosens Bioelectron 2024; 263:116599. [PMID: 39111251 DOI: 10.1016/j.bios.2024.116599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 07/05/2024] [Accepted: 07/21/2024] [Indexed: 08/17/2024]
Abstract
Surface biofunctionalization is an essential stage in the preparation of any bioassay affecting its analytical performance. However, a complete characterization of the biofunctionalized surface, considering studies of coverage density, distribution and orientation of biomolecules, layer thickness, and target biorecognition efficiency, is not met most of the time. This review is a critical overview of the main techniques and strategies used for characterizing biofunctionalized surfaces and the process in between. Emphasis is given to scanning force microscopies as the most versatile and suitable tools to evaluate the quality of the biofunctionalized surfaces in real-time dynamic experiments, highlighting the helpful of atomic force microscopy, Kelvin probe force microscopy, electrochemical atomic force microscopy and photo-induced force microscopy. Other techniques such as optical and electronic microscopies, quartz crystal microbalance, X-ray photoelectron spectroscopy, contact angle, and electrochemical techniques, are also discussed regarding their advantages and disadvantages in addressing the whole characterization of the biomodified surface. Scarce reviews point out the importance of practicing an entire characterization of the biofunctionalized surfaces. This is the first review that embraces this topic discussing a wide variety of characterization tools applied in any bioanalysis platform developed to detect both clinical and environmental analytes. This survey provides information to the analysts on the applications, strengths, and weaknesses of the techniques discussed here to extract fruitful insights from them. The aim is to prompt and help the analysts to accomplish an entire assessment of the biofunctionalized surface, and profit from the information obtained to enhance the bioanalysis output.
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Affiliation(s)
- Adaris M López Marzo
- Institut de Ciencia de Materials de Barcelona (ICMAB-CSIC), Spain; Universitat Autònoma de Barcelona (UAB), Carrer dels Til·lers s/n, Campus de la UAB, 08193, Bellaterra, Spain.
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2
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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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3
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Adedeji Olulana AF, Choi D, Inverso V, Redhu SK, Vidonis M, Crevatin L, Nicholson AW, Castronovo M. Noncanonical DNA Cleavage by BamHI Endonuclease in Laterally Confined DNA Monolayers Is a Step Function of DNA Density and Sequence. Molecules 2022; 27:5262. [PMID: 36014501 PMCID: PMC9416302 DOI: 10.3390/molecules27165262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/04/2022] [Accepted: 08/15/2022] [Indexed: 11/17/2022] Open
Abstract
Cleavage of DNA at noncanonical recognition sequences by restriction endonucleases (star activity) in bulk solution can be promoted by global experimental parameters, including enzyme or substrate concentration, temperature, pH, or buffer composition. To study the effect of nanoscale confinement on the noncanonical behaviour of BamHI, which cleaves a single unique sequence of 6 bp, we used AFM nanografting to generate laterally confined DNA monolayers (LCDM) at different densities, either in the form of small patches, several microns in width, or complete monolayers of thiol-modified DNA on a gold surface. We focused on two 44-bp DNAs, each containing a noncanonical BamHI site differing by 2 bp from the cognate recognition sequence. Topographic AFM imaging was used to monitor end-point reactions by measuring the decrease in the LCDM height with respect to the surrounding reference surface. At low DNA densities, BamHI efficiently cleaves only its cognate sequence while at intermediate DNA densities, noncanonical sequence cleavage occurs, and can be controlled in a stepwise (on/off) fashion by varying the DNA density and restriction site sequence. This study shows that endonuclease action on noncanonical sites in confined nanoarchitectures can be modulated by varying local physical parameters, independent of global chemical parameters.
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Affiliation(s)
- Abimbola F. Adedeji Olulana
- Department of Physics, PhD School in Nanotechnology, University of Trieste, 34127 Trieste, Italy
- Department of Medical and Biological Sciences, University of Udine, 33100 Udine, Italy
- Regional Centre for Rare Diseases, University Hospital Udine, 33100 Udine, Italy
- School of Food Science and Nutrition, University of Leeds, Leeds LS2 9JT, UK
| | - Dianne Choi
- Department of Biology, Temple University, Philadelphia, PA 19122-6078, USA
| | - Vincent Inverso
- Department of Biology, Temple University, Philadelphia, PA 19122-6078, USA
| | - Shiv K. Redhu
- Department of Biology, Temple University, Philadelphia, PA 19122-6078, USA
| | - Marco Vidonis
- Department of Medical and Biological Sciences, University of Udine, 33100 Udine, Italy
- Department of Chemistry, University of Rome “Tor Vergata”, 00133 Rome, Italy
| | - Luca Crevatin
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Allen W. Nicholson
- Department of Biology, Temple University, Philadelphia, PA 19122-6078, USA
| | - Matteo Castronovo
- Department of Physics, PhD School in Nanotechnology, University of Trieste, 34127 Trieste, Italy
- Department of Medical and Biological Sciences, University of Udine, 33100 Udine, Italy
- Regional Centre for Rare Diseases, University Hospital Udine, 33100 Udine, Italy
- School of Food Science and Nutrition, University of Leeds, Leeds LS2 9JT, UK
- Department of Biology, Temple University, Philadelphia, PA 19122-6078, USA
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Kang D, Yu J, Xia F, Huang J, Zeng H, Tirrell M, Israelachvili J, Plaxco KW. Nanometer-Scale Force Profiles of Short Single- and Double-Stranded DNA Molecules on a Gold Surface Measured Using a Surface Forces Apparatus. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:13346-13352. [PMID: 34730362 PMCID: PMC8968159 DOI: 10.1021/acs.langmuir.1c01966] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Using a surface forces apparatus (SFA), we have studied the nanomechanical behavior of short single-stranded and partially and fully double-stranded DNA molecules attached via one end to a self-assembled monolayer on a gold surface. Our results confirm the previously proposed "mushroom-like" polymer structure for surface-attached, single-stranded DNA at low packing density and a "brush-like" structure for the same construct at higher density. At low density we observe a transition to "rigid rod" behavior upon addition of DNA complementary to the surface-attached single strand as the fraction of molecules that are double-stranded increases, with a concomitant increase in the SFA-observed thickness of the monolayer and the characteristic length of the observed repulsive forces. At higher densities, in contrast, this transition is effectively eliminated, presumably because the single-stranded state is already extended in its "brush" state. Taken together, these studies offer insights into the structure and physics of surface-attached short DNAs, providing new guidance for the rational design of DNA-modified functional surfaces.
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Affiliation(s)
- Di Kang
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Jing Yu
- School of Materials Science and Engineering, Nanyang Technological University, 639798 Singapore
| | - Fan Xia
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Jun Huang
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB T6G 2V4, Canada
| | - Hongbo Zeng
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB T6G 2V4, Canada
| | - Matthew Tirrell
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
- Center for Molecular Engineering, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Jacob Israelachvili
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Kevin W Plaxco
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, United States
- Interdepartmental Program in Biomolecular Science and Engineering, University of California, Santa Barbara, Santa Barbara, California 93106, United States
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5
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Computational Evolution of Beta-2-Microglobulin Binding Peptides for Nanopatterned Surface Sensors. Int J Mol Sci 2021; 22:ijms22020812. [PMID: 33467468 PMCID: PMC7831021 DOI: 10.3390/ijms22020812] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/24/2020] [Accepted: 01/04/2021] [Indexed: 11/17/2022] Open
Abstract
The bottom-up design of smart nanodevices largely depends on the accuracy by which each of the inherent nanometric components can be functionally designed with predictive methods. Here, we present a rationally designed, self-assembled nanochip capable of capturing a target protein by means of pre-selected binding sites. The sensing elements comprise computationally evolved peptides, designed to target an arbitrarily selected binding site on the surface of beta-2-Microglobulin (β2m), a globular protein that lacks well-defined pockets. The nanopatterned surface was generated by an atomic force microscopy (AFM)-based, tip force-driven nanolithography technique termed nanografting to construct laterally confined self-assembled nanopatches of single stranded (ss)DNA. These were subsequently associated with an ssDNA-peptide conjugate by means of DNA-directed immobilization, therefore allowing control of the peptide's spatial orientation. We characterized the sensitivity of such peptide-containing systems against β2m in solution by means of AFM-based differential topographic imaging and surface plasmon resonance (SPR) spectroscopy. Our results show that the confined peptides are capable of specifically capturing β2m from the surface-liquid interface with micromolar affinity, hence providing a viable proof-of-concept for our approach to peptide design.
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6
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Zhao H, Ye D, Mao X, Li F, Xu J, Li M, Zuo X. Stepping gating of ion channels on nanoelectrode via DNA hybridization for label-free DNA detection. Biosens Bioelectron 2019; 133:141-146. [PMID: 30925363 DOI: 10.1016/j.bios.2019.03.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/10/2019] [Accepted: 03/17/2019] [Indexed: 12/21/2022]
Abstract
Natural ion channels on cell membrane can gate the transport of ions and molecules by the conformational alteration of transmembrane proteins to regulate the normal physiological activities of cells. Inspired by the similarity of the conformation change under specific stimuli, here we introduce an ion channel gating model on a single nanoelectrode by anchoring DNA-gated switches on the very nanotip of gold nanoelectrode to mimic the response-to-stimulus behaviors of ion channels on bio-membranes. The surface-tethered DNA ion channels can be switched on by the Watson-Crick base pairing, which can alter the conformation of the tethered DNA from lying state to upright state. And these conformational alterations of the anchored DNA switches can effectively gate the transport of potassium ferricyanide onto the electrode interface. By continuously initiating the gates with DNA of different concentrations, we achieved the stepping gating of ion channels on a single nanoelectrode. Further, we demonstrated that the ion gating system on nanoelectrode showed excellent sensing performance. For example, the response kinetic was very fast with the signal saturation time of ~1 min, the reproducibility of the OFF/ON switch was robust enough to sustain for two cycles, and simultaneously, the specificity was high enough to distinguish complementary DNA and noncomplementary DNA. When used for label-free DNA detection, the limit of detection can be as low as 10 pM. This study provides a promising avenue to achieve label free and real-time detection of multiple biomolecules.
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Affiliation(s)
- Haipei Zhao
- NEST Lab, Department of Chemistry, College of Sciences, Shanghai University, Shanghai 200444, China; Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Dekai Ye
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Xiuhai Mao
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Fan Li
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Jiaqiang Xu
- NEST Lab, Department of Chemistry, College of Sciences, Shanghai University, Shanghai 200444, China.
| | - Min Li
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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7
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Pinto G, Parisse P, Solano I, Canepa P, Canepa M, Casalis L, Cavalleri O. Functionalizing gold with single strand DNA: novel insight into optical properties via combined spectroscopic ellipsometry and nanolithography measurements. SOFT MATTER 2019; 15:2463-2468. [PMID: 30810150 DOI: 10.1039/c8sm02589d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We have studied the self-assembly of 22-base oligonucleotides bound by a short alkyl thiol linker (C6-ssDNA) on flat Au films. The self-assembled monolayer (SAM) was modified by addition of a spacer (mercaptohexanol, MCH). Molecular depositions were monitored in situ by spectroscopic ellipsometry (SE). SAMs were characterized in a liquid environment by coupling SE (difference spectra method) with Atomic Force Microscope (AFM) measurements. We exploited the biofilm thickness obtained by AFM nanolithography and imaging to solve the refractive index/thickness correlation in optical measurements on ultrathin molecular layers. The combined SE/AFM analysis provided reliable estimates of the thickness and the refractive index of the biofilm in the NIR region (650-1300 nm) and revealed new aspects of DNA molecular organization: exposure to MCH leads to an increase of both film thickness and refractive index, which points to a reorganization of C6-ssDNA film. We show that the contribution of the thiol/Au interface has to be included in the optical model to obtain a more reliable determination of the refractive index of the biofilm in a liquid. The careful, correlative characterization of the mixed C6-ssDNA/MCH SAM represents a key step towards the optimization of a robust detection scheme based on helix-helix hybridization.
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Affiliation(s)
- Giulia Pinto
- OPTMATLAB, Department of Physics, University of Genova, via Dodecaneso 33, 16146 Genova, Italy.
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8
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Speyer K, Pastorino C. Pressure responsive gating in nanochannels coated by semiflexible polymer brushes. SOFT MATTER 2019; 15:937-946. [PMID: 30644495 DOI: 10.1039/c8sm02388c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We study by coarse-grained molecular-dynamics simulations the liquid flow in a slit channel with the inner walls coated by semiflexible polymer brushes. The distance between walls is close enough such that polymers grafted to opposing walls interact among each other and form bundles across the channel in poor solvent conditions. The solvent is simulated explicitly, including particles that fill the interior of the channel. The system is studied in equilibrium and under flow, by applying a constant body force on each particle of the system. A non-linear relation between external force and flow rate is observed, for a particular set of parameters. This non-linear response is linked to a morphological change of the polymer brushes. For large enough forces, the bundle structures formed across the channel break as the chains lean in the direction of the flow, and clear the middle of the channel. This morphological alteration of the polymer configurations translates in a sudden increase in the flow rate, acting as a pressure-responsive gate. The relation between flow and external force is investigated for various parameters, such as grafting density, quality of the solvent and polymer bending rigidity. We observe a non-monotonic dependence of the flow as a function of the polymer rigidity, and find an optimum value for the persistence length. We also find that the force threshold at which the morphological changes happen in the polymer brush, depends linearly on the grafting density. These findings can lead to new flow control techniques in micro and nano-fluidic devices.
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Affiliation(s)
- K Speyer
- Departamento de Física de la Materia Condensada, Centro Atómico Constituyentes, CNEA, Av. Gral. Paz 1499, 1650 Pcia. de Buenos Aires, Argentina.
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9
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Bizzotto D, Burgess IJ, Doneux T, Sagara T, Yu HZ. Beyond Simple Cartoons: Challenges in Characterizing Electrochemical Biosensor Interfaces. ACS Sens 2018; 3:5-12. [PMID: 29282982 DOI: 10.1021/acssensors.7b00840] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Design and development of surface-based biosensors is challenging given the multidisciplinary nature of this enterprise, which is certainly the case for electrochemical biosensors. Self-assembly approaches are used to modify the surface with capture probes along with electrochemical methods for detection. Complex surface structures are created to improve the probe-target interaction. These multicomponent surface structures are usually idealized in schematic representations. Many rely on the analytical performance of the sensor surface as an indication of the quality of the surface modification strategy. While directly linked to the eventual device, arguments for pursuing a more extensive characterization of the molecular environments at the surface are presented as a path to understanding how to make electrochemical sensors that are more robust, reliable with improved sensitivity. This is a complex task that is most often accomplished using methods that only report the average characteristics of the surface. Less often applied are methods that are sensitive to the probe (or adsorbate) present in nonideal configurations (e.g., aggregates, clusters, nonspecifically adsorbed). Though these structures may compose a small fraction of the overall modified surface, they have an uncertain impact on sensor performance and reliability. Addressing this issue requires application of imaging methods over a variety of length scales (e.g., optical microscopy and/or scanning probe microscopy) that provide valuable insight into the diversity of surface structures and molecular environments present at the sensing interface. Furthermore, using in situ analytical methods, while complex, can be more relevant to the sensing environment. Reliable measurements of the nature and extent of these features are required to assess the impact of these nonideal configurations on the sensing process. The development and use of methods that can characterize complex surface based biosensors is arguably required, highlighting the need for a multidisciplinary approach toward the preparation and analysis of the biosensor surface. In many ways, representing the surface without reliance on overly simplified cartoons will highlight these important considerations for improving sensor characteristics.
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Affiliation(s)
- Dan Bizzotto
- Department
of Chemistry, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Ian J. Burgess
- Department
of Chemistry, University of Saskatchewan, Saskatoon, SK S7N 5A2, Canada
| | - Thomas Doneux
- Chimie
Analytique et Chimie des Interfaces, Faculté des Sciences, Université libre de Bruxelles (ULB), 1050 Bruxelles, Belgium
| | - Takamasa Sagara
- Division
of Chemistry and Materials Science, Graduate School of Engineering, Nagasaki University, Nagasaki, Nagasaki 852-8131, Japan
| | - Hua-Zhong Yu
- Department
of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
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10
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Gil PS, Lacks DJ, Parisse P, Casalis L, Nkoua Ngavouka MD. Single-stranded DNA oligomer brush structure is dominated by intramolecular interactions mediated by the ion environment. SOFT MATTER 2018; 14:9675-9680. [PMID: 30460961 DOI: 10.1039/c8sm01743c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Single-stranded DNA (ssDNA) brushes, in which ssDNA oligomers are tethered to surfaces in dense monolayers, are being investigated for potential biosensing applications.
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Affiliation(s)
- Phwey S. Gil
- Department of Chemical and Biomolecular Engineering
- Case Western Reserve University
- OH 441060 Cleveland
- USA
| | - Daniel J. Lacks
- Department of Chemical and Biomolecular Engineering
- Case Western Reserve University
- OH 441060 Cleveland
- USA
| | - Pietro Parisse
- INSTM-ST Unit
- Italy
- Elettra-Sincrotrone Trieste
- S.C.p.A
- Italy
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11
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Solano I, Parisse P, Gramazio F, Ianeselli L, Medagli B, Cavalleri O, Casalis L, Canepa M. Atomic Force Microscopy and Spectroscopic Ellipsometry combined analysis of Small Ubiquitin-like Modifier adsorption on functional monolayers. APPLIED SURFACE SCIENCE 2017. [DOI: 10.1016/j.apsusc.2016.10.195] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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12
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Ambrosetti E, Paoletti P, Bosco A, Parisse P, Scaini D, Tagliabue E, de Marco A, Casalis L. Quantification of Circulating Cancer Biomarkers via Sensitive Topographic Measurements on Single Binder Nanoarrays. ACS OMEGA 2017; 2:2618-2629. [PMID: 30023671 PMCID: PMC6044866 DOI: 10.1021/acsomega.7b00284] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 04/28/2017] [Indexed: 01/10/2023]
Abstract
Early detection of cancer plays a crucial role in disease prognosis. It requires the recognition and quantification of low amounts of specific molecular biomarkers, either free or transported inside nanovesicles, through the development of novel sensitive diagnostic technologies. In this context, we have developed a nanoarray platform for the noninvasive quantification of cancer biomarkers circulating in the bloodstream. The assay is based on molecular manipulation to create functional spots of surface-immobilized binders and differential topography measurements. It is label-free and requires just a single binder per antigen, and when it is implemented with fluorescence labeling/readout, it can be used for epitope mapping. As a benchmark, we focused on the plasma release of Her2 extracellular domain (ECD), a proposed biomarker for the progression of Her2-positive tumors and response to anticancer therapies. By employing robust, easily engineered camelid nanobodies as binders, we measured ECD-Her2 concentrations in the range of the actual clinical cutoff value for Her2-positive breast cancer. The specificity for Her2 detection was preserved when it was measured in parallel with other potential biomarkers, demonstrating a forthcoming implementation of this approach for multiplexing analysis. Prospectively, this nanorarray platform may be customized to allow for the detection of promising new classes of circulating biomarkers, such as exosomes and microvesicles.
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Affiliation(s)
- Elena Ambrosetti
- NanoInnovation
Lab, Elettra-Sincrotone S.C.p.A., ss 14 km 163.5 in Area Science Park, 34149 Basovizza-Trieste, Italy
- PhD
School in Nanotechnology, University of
Trieste, Piazzale Europa
1, 34127 Trieste, Italy
- INSTM−ST Unit, ss 14 km 163.5
in Area Science Park, 34149 Basovizza-Trieste, Italy
| | - Pamela Paoletti
- NanoInnovation
Lab, Elettra-Sincrotone S.C.p.A., ss 14 km 163.5 in Area Science Park, 34149 Basovizza-Trieste, Italy
- International
School for Advanced Studies (SISSA), Via Bonomea 265, 34136 Trieste, Italy
| | - Alessandro Bosco
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles väg, 17177 Stockholm, Sweden
| | - Pietro Parisse
- NanoInnovation
Lab, Elettra-Sincrotone S.C.p.A., ss 14 km 163.5 in Area Science Park, 34149 Basovizza-Trieste, Italy
| | - Denis Scaini
- NanoInnovation
Lab, Elettra-Sincrotone S.C.p.A., ss 14 km 163.5 in Area Science Park, 34149 Basovizza-Trieste, Italy
- PhD
School in Nanotechnology, University of
Trieste, Piazzale Europa
1, 34127 Trieste, Italy
| | - Elda Tagliabue
- Department
of Experimental Oncology and Molecular Medicine, Fondazione IRCCS−Istituto Nazionale dei Tumori, Via Amadeo 42, 20133 Milano, Italy
| | - Ario de Marco
- Center
for Biomedical Sciences and Engineering, University of Nova Gorica, Dvorec Lanthieri, Glavni Trg 8, 5271 Vipava, Slovenia
| | - Loredana Casalis
- NanoInnovation
Lab, Elettra-Sincrotone S.C.p.A., ss 14 km 163.5 in Area Science Park, 34149 Basovizza-Trieste, Italy
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13
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Rotella C, Doni G, Bosco A, Castronovo M, De Vita A, Casalis L, Pavan GM, Parisse P. Site accessibility tailors DNA cleavage by restriction enzymes in DNA confined monolayers. NANOSCALE 2017; 9:6399-6405. [PMID: 28453019 DOI: 10.1039/c7nr00966f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Density-tunable nanografted monolayers (NAMs) of short oligonucleotide sequences on gold surfaces show novel properties that make them suitable for advanced biosensing applications, and in particular to study the effects of crowding and confinement on biomolecular interactions. Here, combining atomic force microscopy nanolithography, topography measurements and coarse-grained molecular dynamics simulations, we investigated restriction enzyme reaction mechanisms within confined DNA brushes highlighting the role played by the DNA sequence conformation and restriction site position along the chain, respectively, in determining the accessibility of the enzyme, and its consequent cleavage efficiency.
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Affiliation(s)
- Chiara Rotella
- Elettra Sincrotrone Trieste, s.s. 14 km 163.5 in Area Science Park, Trieste, Italy.
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15
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Ngavouka MDN, Capaldo P, Ambrosetti E, Scoles G, Casalis L, Parisse P. Mismatch detection in DNA monolayers by atomic force microscopy and electrochemical impedance spectroscopy. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2016; 7:220-227. [PMID: 26977379 PMCID: PMC4778512 DOI: 10.3762/bjnano.7.20] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 01/25/2016] [Indexed: 01/10/2023]
Abstract
Background: DNA hybridization is at the basis of most current technologies for genotyping and sequencing, due to the unique properties of DNA base-pairing that guarantee a high grade of selectivity. Nonetheless the presence of single base mismatches or not perfectly matched sequences can affect the response of the devices and the major challenge is, nowadays, to distinguish a mismatch of a single base and, at the same time, unequivocally differentiate devices read-out of fully and partially matching sequences. Results: We present here two platforms based on different sensing strategies, to detect mismatched and/or perfectly matched complementary DNA strands hybridization into ssDNA oligonucleotide monolayers. The first platform exploits atomic force microscopy-based nanolithography to create ssDNA nano-arrays on gold surfaces. AFM topography measurements then monitor the variation of height of the nanostructures upon biorecognition and then follow annealing at different temperatures. This strategy allowed us to clearly detect the presence of mismatches. The second strategy exploits the change in capacitance at the interface between an ssDNA-functionalized gold electrode and the solution due to the hybridization process in a miniaturized electrochemical cell. Through electrochemical impedance spectroscopy measurements on extended ssDNA self-assembled monolayers we followed in real-time the variation of capacitance, being able to distinguish, through the difference in hybridization kinetics, not only the presence of single, double or triple mismatches in the complementary sequence, but also the position of the mismatched base pair with respect to the electrode surface. Conclusion: We demonstrate here two platforms based on different sensing strategies as sensitive and selective tools to discriminate mismatches. Our assays are ready for parallelization and can be used in the detection and quantification of single nucleotide mismatches in microRNAs or in genomic DNA.
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Affiliation(s)
- Maryse D Nkoua Ngavouka
- Elettra-Sincrotrone Trieste S.C.p.A., s.s. 14 km 163.5 in Area Science Park, Basovizza, Trieste, Italy.,INSTM - ST Unit, s.s. 14 km 163.5 in Area Science Park, Basovizza, Trieste, Italy.,University of Trieste, Via Valerio 9, Trieste, Italy
| | - Pietro Capaldo
- Elettra-Sincrotrone Trieste S.C.p.A., s.s. 14 km 163.5 in Area Science Park, Basovizza, Trieste, Italy.,University of Trieste, Via Valerio 9, Trieste, Italy
| | - Elena Ambrosetti
- Elettra-Sincrotrone Trieste S.C.p.A., s.s. 14 km 163.5 in Area Science Park, Basovizza, Trieste, Italy.,INSTM - ST Unit, s.s. 14 km 163.5 in Area Science Park, Basovizza, Trieste, Italy.,University of Trieste, Via Valerio 9, Trieste, Italy
| | - Giacinto Scoles
- Department of Medical and Biological Sciences, University of Udine, Udine, Italy
| | - Loredana Casalis
- Elettra-Sincrotrone Trieste S.C.p.A., s.s. 14 km 163.5 in Area Science Park, Basovizza, Trieste, Italy.,INSTM - ST Unit, s.s. 14 km 163.5 in Area Science Park, Basovizza, Trieste, Italy
| | - Pietro Parisse
- Elettra-Sincrotrone Trieste S.C.p.A., s.s. 14 km 163.5 in Area Science Park, Basovizza, Trieste, Italy.,INSTM - ST Unit, s.s. 14 km 163.5 in Area Science Park, Basovizza, Trieste, Italy
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16
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Zhang TB, Zhang CL, Dong ZL, Guan YF. Determination of base binding strength and base stacking interaction of DNA duplex using atomic force microscope. Sci Rep 2015; 5:9143. [PMID: 25772017 PMCID: PMC4360479 DOI: 10.1038/srep09143] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 02/19/2015] [Indexed: 01/23/2023] Open
Abstract
As one of the most crucial properties of DNA, the structural stability and the mechanical strength are attracting a great attention. Here, we take advantage of high force resolution and high special resolution of Atom Force Microscope and investigate the mechanical force of DNA duplexes. To evaluate the base pair hydrogen bond strength and base stacking force in DNA strands, we designed two modes (unzipping and stretching) for the measurement rupture forces. Employing k-means clustering algorithm, the ruptured force are clustered and the mean values are estimated. We assessed the influence of experimental parameters and performed the force evaluation for DNA duplexes of pure dG/dC and dA/dT base pairs. The base binding strength of single dG/dC and single dA/dT were estimated to be 20.0 ± 0.2 pN and 14.0 ± 0.3 pN, respectively, and the base stacking interaction was estimated to be 2.0 ± 0.1 pN. Our results provide valuable information about the quantitative evaluation of the mechanical properties of the DNA duplexes.
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Affiliation(s)
- Tian-biao Zhang
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang, China. 110001
| | - Chang-lin Zhang
- State Key Laboratory of Robotics, Shenyang Institute of Automatics, Chinese Academy of Sciences, Shenyang, China. 110016
| | - Zai-li Dong
- State Key Laboratory of Robotics, Shenyang Institute of Automatics, Chinese Academy of Sciences, Shenyang, China. 110016
| | - Yi-fu Guan
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang, China. 110001
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17
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Solano I, Parisse P, Gramazio F, Cavalleri O, Bracco G, Castronovo M, Casalis L, Canepa M. Spectroscopic ellipsometry meets AFM nanolithography: about hydration of bio-inert oligo(ethylene glycol)-terminated self assembled monolayers on gold. Phys Chem Chem Phys 2015; 17:28774-81. [PMID: 26445913 DOI: 10.1039/c5cp04028k] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
An accurate thickness determination provides insight into the complex vertical morphology of OEG-terminated SAMs.
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Affiliation(s)
- Ilaria Solano
- Dipartimento di Fisica
- Università di Genova and CNISM
- Genova
- Italy
| | | | | | | | | | - Matteo Castronovo
- Department of Medical and Biological Sciences – University of Udine
- Udine
- Italy
| | | | - Maurizio Canepa
- Dipartimento di Fisica
- Università di Genova and CNISM
- Genova
- Italy
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18
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Nkoua Ngavouka MD, Bosco A, Casalis L, Parisse P. Determination of Average Internucleotide Distance in Variable Density ssDNA Nanobrushes in the Presence of Different Cations Species. Macromolecules 2014. [DOI: 10.1021/ma501712a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Maryse D. Nkoua Ngavouka
- PhD
School in Nanotechnology and Nanoscience, University of Trieste, Piazzale Europa 1, 34127, Trieste, Italy
- Elettra-Sincrotrone
Trieste, S.C.p.A., Strada Statale 14-km
163,5 in AREA Science Park, I-34149, Basovizza Trieste, Italy
| | - Alessandro Bosco
- Elettra-Sincrotrone
Trieste, S.C.p.A., Strada Statale 14-km
163,5 in AREA Science Park, I-34149, Basovizza Trieste, Italy
| | - Loredana Casalis
- Elettra-Sincrotrone
Trieste, S.C.p.A., Strada Statale 14-km
163,5 in AREA Science Park, I-34149, Basovizza Trieste, Italy
- INSTM-ST Unit, Strada Statale 14-km 163,5 in AREA Science Park, I-34149, Basovizza Trieste, Italy
| | - Pietro Parisse
- INSTM-ST Unit, Strada Statale 14-km 163,5 in AREA Science Park, I-34149, Basovizza Trieste, Italy
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19
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Domínguez CM, Kosaka PM, Mokry G, Pini V, Malvar O, del Rey M, Ramos D, San Paulo A, Tamayo J, Calleja M. Hydration induced stress on DNA monolayers grafted on microcantilevers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:10962-10969. [PMID: 25148575 DOI: 10.1021/la501865h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
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 h, while quantification is a major challenge.
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Affiliation(s)
- Carmen M Domínguez
- Instituto de Microelectrónica de Madrid, IMM-CNM (CSIC), 28760 Tres Cantos, Spain
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20
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Idili A, Amodio A, Vidonis M, Feinberg-Somerson J, Castronovo M, Ricci F. Folding-upon-binding and signal-on electrochemical DNA sensor with high affinity and specificity. Anal Chem 2014; 86:9013-9. [PMID: 24947124 PMCID: PMC4165453 DOI: 10.1021/ac501418g] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Here we investigate a novel signal-on
electrochemical DNA sensor
based on the use of a clamp-like DNA probe that binds a complementary
target sequence through two distinct and sequential events, which
lead to the formation of a triplex DNA structure. We demonstrate that
this target-binding mechanism can improve both the affinity
and specificity of recognition as opposed to classic probes solely
based on Watson–Crick recognition. By using electrochemical
signaling to report the conformational change, we demonstrate a signal-on
E-DNA sensor with up to 400% signal gain upon target binding. Moreover,
we were able to detect with nanomolar affinity a perfectly matched
target as short as 10 bases (KD = 0.39
nM). Finally, thanks to the molecular “double-check”
provided by the concomitant Watson–Crick and Hoogsteen base
pairings involved in target recognition, our sensor provides excellent
discrimination efficiency toward a single-base mismatched target.
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Affiliation(s)
- Andrea Idili
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome, Tor Vergata , Via della Ricerca Scientifica 1, 00133 Rome, Italy
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21
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A DNA-based nano-immunoassay for the label-free detection of glial fibrillary acidic protein in multicell lysates. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2014; 11:293-300. [PMID: 24780311 DOI: 10.1016/j.nano.2014.04.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 03/27/2014] [Accepted: 04/15/2014] [Indexed: 12/12/2022]
Abstract
UNLABELLED We have developed a quantitative approach to eventually enable precise and multiplexing protein analysis of very small systems, down to a single or a few cells. Through DNA-directed immobilization of DNA-protein conjugates we immobilized antibodies specific for a certain protein of interest, on a complementary DNA nanoarray fabricated by means of nanografting, a nanolithography technique based on atomic force microscopy (AFM). The proof of concept was realized for glial fibrillary acidic protein (GFAP), a biomarker crucial in cell's differentiation of astrocytes, and functional to grade classification of gliomas, the most common of primary malignant brain tumors. The efficiency of the nano-immuno sensing was tested by obtaining the immobilization of purified recombinant GFAP protein at different concentration in a standard solution then in a cellular lysate. A comparison of sensitivity between our technique and conventional ELISA assays is provided at the end of the paper. FROM THE CLINICAL EDITOR This team developed a quantitative approach to enable precise and multiplexing protein analysis of very small systems, down to a single or a few cells, demonstrating the utility of this DNA-based nano-immunoassay in the detection of GFAP.
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22
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Digital imprinting of RNA recognition and processing on a self-assembled nucleic acid matrix. Sci Rep 2014; 3:2550. [PMID: 23989631 PMCID: PMC3757352 DOI: 10.1038/srep02550] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 08/08/2013] [Indexed: 11/08/2022] Open
Abstract
The accelerating progress of research in nanomedicine and nanobiotechnology has included initiatives to develop highly-sensitive, high-throughput methods to detect biomarkers at the single-cell level. Current sensing approaches, however, typically involve integrative instrumentation that necessarily must balance sensitivity with rapidity in optimizing biomarker detection quality. We show here that laterally-confined, self-assembled monolayers of a short, double-stranded(ds)[RNA-DNA] chimera enable permanent digital detection of dsRNA-specific inputs. The action of ribonuclease III and the binding of an inactive, dsRNA-binding mutant can be permanently recorded by the input-responsive action of a restriction endonuclease that cleaves an ancillary reporter site within the dsDNA segment. The resulting irreversible height change of the arrayed ds[RNA-DNA], as measured by atomic force microscopy, provides a distinct digital output for each dsRNA-specific input. These findings provide the basis for developing imprinting-based bio-nanosensors, and reveal the versatility of AFM as a tool for characterizing the behaviour of highly-crowded biomolecules at the nanoscale.
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23
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Gan T, Zhou X, Ma C, Liu X, Xie Z, Zhang G, Zheng Z. Liquid-mediated three-dimensional scanning probe nanosculpting. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2013; 9:2851-2856. [PMID: 23554330 DOI: 10.1002/smll.201300238] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Indexed: 06/02/2023]
Abstract
3D functional polymer brushes are fabricated by liquid-mediated scanning probe nanosculpting (LSPN). Surface-tethered functional polymer brushes, which are immersed in their good solvent, are mechanically cleaved away from the substrate by the AFM tip at high forces, and immediately imaged in situ with the same AFM tip at low applied forces.
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Affiliation(s)
- Tiansheng Gan
- Faculty of Materials Science and Engineering, South China University of Technology, Guangzhou 510640, PR China
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24
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Josephs EA, Ye T. Nanoscale spatial distribution of thiolated DNA on model nucleic acid sensor surfaces. ACS NANO 2013; 7:3653-3660. [PMID: 23540444 DOI: 10.1021/nn400659m] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The nanoscale arrangement of the DNA probe molecules on sensor surfaces has a profound impact on molecular recognition and signaling reactions on DNA biosensors and microarrays. Using electrochemical atomic force microscopy, we have directly determined the nanoscale spatial distribution of thiolated DNA that are attached to gold via different methods. We discovered significant heterogeneity in the probe density and limited stability for DNA monolayers prepared by the backfilling method, that is, first exposing the surface to thiolated DNA then "backfilling" with a passivating alkanethiol. On the other hand, the monolayers prepared by "inserting" thiolated DNA into a preformed alkanethiol monolayer lead to a more uniformly distributed layer of DNA. With high-resolution images of single DNA molecules on the surface, we have introduced spatial statistics to characterize the nanoscale arrangement of DNA probes. The randomness of the spatial distribution has been characterized. By determining the local densities surrounding individual molecules, we observed subpopulations of probes with dramatically different levels of "probe crowding". We anticipate that the novel application of spatial statistics to DNA monolayers can enable a framework to understand heterogeneity in probe spatial distributions, interprobe interactions, and ultimately probe activity on sensor surfaces.
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Affiliation(s)
- Eric A Josephs
- School of Engineering, University of California, Merced, California 95343, United States
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25
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Doni G, Nkoua Ngavouka MD, Barducci A, Parisse P, De Vita A, Scoles G, Casalis L, Pavan GM. Structural and energetic basis for hybridization limits in high-density DNA monolayers. NANOSCALE 2013; 5:9988-93. [PMID: 23996015 DOI: 10.1039/c3nr01799k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Giovanni Doni
- Department of Physics, King's College London, London WC2R 2LS, UK
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