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Piccirilli F, Vondracek H, Silvestrini L, Parisse P, Spinozzi F, Vaccari L, Toma A, Aglieri V, Casalis L, Piccionello AP, Mariani P, Birarda G, Ortore MG. Dimeric and monomeric conformation of SARS-CoV-2 main protease: New technical approaches based on IR radiation. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 322:124772. [PMID: 39003826 DOI: 10.1016/j.saa.2024.124772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 06/11/2024] [Accepted: 07/02/2024] [Indexed: 07/16/2024]
Abstract
The main proteases Mpro are a group of highly conserved cysteine hydrolases in β-coronaviruses. They have been demonstrated to play an unavoidable role in viral replication, and consequently they have been suggested as key targets for treating coronavirus-caused infectious diseases, mainly from the COVID-19 epidemic. Since the most functional form for Mpro enzymatic activity is associated to its homodimer, compounds inhibiting dimerization should also inhibit catalytic activity. We show how PIR-SEIRA (Plasmonic Internal Reflection-Surface Enhanced InfraRed Absorption) spectroscopy can be a noteworthy technique to study proteins subtle structural variations associated to inhibitor binding. Nanoantennas arrays can selectively confine and enhance electromagnetic field via localized plasmonic resonances, thus promoting ultrasensitive detection of biomolecules in close proximity of nanoantenna arrays and enabling the effective investigation of protein monolayers. By adopting this approach, reflection measurements conducted under back illumination of nanoantennas allow to probe anchored protein monolayers, with minimum contribution of environmental buffer molecules. PIR-SEIRA spectroscopy on Mpro was carried out by ad hoc designed devices, resonating in the spectral region of Amide I and Amide II bands. We evaluated here the structure of anchored monomers and dimers in different buffered environment and in presence of a newly designed Mpro inhibitor. Experimental results show that dimerization is not associated to relevant backbone rearrangements of the protein at secondary structure level, and even if the compound inhibits the dimerization, it is not effective at breaking preformed dimers.
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Affiliation(s)
| | - Hendrik Vondracek
- Elettra-Synchrotron Trieste S.C.p.A., Strada Statale 14, Basovizza, Trieste, I-34149, Italy
| | - Lucia Silvestrini
- Department of Life and Environmental Sciences, Marche Polytechnic University, via brecce bianche, Ancona, I-60131, Italy
| | - Pietro Parisse
- Elettra-Synchrotron Trieste S.C.p.A., Strada Statale 14, Basovizza, Trieste, I-34149, Italy; CNR - Istituto Officina dei Materiali, s.s. 14 km 163.5 in Area Science Park, 34149 Basovizza, Trieste, Italy
| | - Francesco Spinozzi
- Department of Life and Environmental Sciences, Marche Polytechnic University, via brecce bianche, Ancona, I-60131, Italy
| | - Lisa Vaccari
- Elettra-Synchrotron Trieste S.C.p.A., Strada Statale 14, Basovizza, Trieste, I-34149, Italy
| | - Andrea Toma
- Fondazione Istituto Italiano di Tecnologia, via Morego 30, Genova, I- 16163, Italy
| | - Vincenzo Aglieri
- Fondazione Istituto Italiano di Tecnologia, via Morego 30, Genova, I- 16163, Italy
| | - Loredana Casalis
- Elettra-Synchrotron Trieste S.C.p.A., Strada Statale 14, Basovizza, Trieste, I-34149, Italy
| | - Antonio Palumbo Piccionello
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche, viale delle scienze, Palermo, I-90133, Italy
| | - Paolo Mariani
- Department of Life and Environmental Sciences, Marche Polytechnic University, via brecce bianche, Ancona, I-60131, Italy
| | - Giovanni Birarda
- Elettra-Synchrotron Trieste S.C.p.A., Strada Statale 14, Basovizza, Trieste, I-34149, Italy.
| | - Maria Grazia Ortore
- Department of Life and Environmental Sciences, Marche Polytechnic University, via brecce bianche, Ancona, I-60131, Italy.
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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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Noncanonical DNA Cleavage by BamHI Endonuclease in Laterally Confined DNA Monolayers Is a Step Function of DNA Density and Sequence. Molecules 2022; 27:molecules27165262. [PMID: 36014501 PMCID: PMC9416302 DOI: 10.3390/molecules27165262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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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4
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An electrophoresis approach with online thermal lens detection to monitoring DNA surface coatings on gold nanoparticles. Microchem J 2022. [DOI: 10.1016/j.microc.2021.106961] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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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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Warner CN, Hunter ZD, Carte DD, Skidmore TJ, Vint ES, Day BS. Structure and Function Analysis of DNA Monolayers Created from Self-Assembling DNA-Dendron Conjugates. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:5428-5434. [PMID: 32336098 DOI: 10.1021/acs.langmuir.0c00340] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Short sequences of DNA immobilized on gold surfaces can be used to capture an array of target molecules because of their high level of specificity. Depending on the nature of the target molecules, the proper density and distribution of the immobilized DNA molecules are fundamental to the quality of the sensor. With the aim to control the packing density and minimize the heterogeneity of the surfaces, DNA-dendron conjugate molecules were synthesized in solution and used to make self-assembled monolayers of single-stranded DNA surfaces on gold. The headgroups used were polyamido amine dendrons (cleaved cystamine core dendrimers) of generations two through five. The structural composition of these self-assembled monolayers was characterized using grazing angle Fourier-transform infrared and X-ray photoelectron spectroscopies. Surface plasmon resonance was used to measure surface densities of the probe monolayers and each monolayer's ability to capture fully complementary DNA strands from solution. The surface density of the probe monolayers was found to decrease with increasing dendron generation number, while the hybridization efficiency increased with increasing dendron generation number.
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Affiliation(s)
- Christian N Warner
- Department of Chemistry, Marshall University, Huntington, West Virginia 25755, United States
| | - Zachary D Hunter
- Department of Chemistry, Marshall University, Huntington, West Virginia 25755, United States
| | - Destiny D Carte
- Department of Chemistry, Marshall University, Huntington, West Virginia 25755, United States
| | - Tyler J Skidmore
- Department of Chemistry, Marshall University, Huntington, West Virginia 25755, United States
| | - Erik S Vint
- Department of Chemistry, Marshall University, Huntington, West Virginia 25755, United States
| | - B Scott Day
- Department of Chemistry, Marshall University, Huntington, West Virginia 25755, United States
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7
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Choi Y, Schmidt C, Tinnefeld P, Bald I, Rödiger S. A new reporter design based on DNA origami nanostructures for quantification of short oligonucleotides using microbeads. Sci Rep 2019; 9:4769. [PMID: 30886341 PMCID: PMC6423227 DOI: 10.1038/s41598-019-41136-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 02/28/2019] [Indexed: 01/05/2023] Open
Abstract
The DNA origami technique has great potential for the development of brighter and more sensitive reporters for fluorescence based detection schemes such as a microbead-based assay in diagnostic applications. The nanostructures can be programmed to include multiple dye molecules to enhance the measured signal as well as multiple probe strands to increase the binding strength of the target oligonucleotide to these nanostructures. Here we present a proof-of-concept study to quantify short oligonucleotides by developing a novel DNA origami based reporter system, combined with planar microbead assays. Analysis of the assays using the VideoScan digital imaging platform showed DNA origami to be a more suitable reporter candidate for quantification of the target oligonucleotides at lower concentrations than a conventional reporter that consists of one dye molecule attached to a single stranded DNA. Efforts have been made to conduct multiplexed analysis of different targets as well as to enhance fluorescence signals obtained from the reporters. We therefore believe that the quantification of short oligonucleotides that exist in low copy numbers is achieved in a better way with the DNA origami nanostructures as reporters.
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Affiliation(s)
- Youngeun Choi
- University of Potsdam, Department of Chemistry, Physical Chemistry, 14476, Potsdam, Germany.,BAM Federal Institute for Materials Research and Testing, 12489, Berlin, Germany
| | - Carsten Schmidt
- Brandenbrug University of Technology Cottbus-Senftenberg, Institute of Biotechnology, 01968, Senftenberg, Germany
| | - Philip Tinnefeld
- Department Chemie and Center for NanoScience, Ludwig-Maximilians-Universitaet Muenchen, Butenandtstr, 5-13 Haus E, 81377, Muenchen, Germany
| | - Ilko Bald
- University of Potsdam, Department of Chemistry, Physical Chemistry, 14476, Potsdam, Germany. .,BAM Federal Institute for Materials Research and Testing, 12489, Berlin, Germany.
| | - Stefan Rödiger
- Brandenbrug University of Technology Cottbus-Senftenberg, Institute of Biotechnology, 01968, Senftenberg, Germany.
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8
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Gu Q, Nanney W, Cao HH, Wang H, Ye T. Single Molecule Profiling of Molecular Recognition at a Model Electrochemical Biosensor. J Am Chem Soc 2018; 140:14134-14143. [PMID: 30293418 DOI: 10.1021/jacs.8b07325] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The spatial arrangement of target and probe molecules on the biosensor is a key aspect of the biointerface structure that ultimately determines the properties of interfacial molecular recognition and the performance of the biosensor. However, the spatial patterns of single molecules on practical biosensors have been unknown, making it difficult to rationally engineer biosensors. Here, we have used high-resolution atomic force microscopy to map closely spaced individual probes as well as discrete hybridization events on a functioning electrochemical DNA sensor surface. We also applied spatial statistical methods to characterize the spatial patterns at the single molecule level. We observed the emergence of heterogeneous spatiotemporal patterns of surface hybridization of hairpin probes. The clustering of target capture suggests that hybridization may be enhanced by proximity of probes and targets that are about 10 nm away. The unexpected enhancement was rationalized by the complex interplay between the nanoscale spatial organization of probe molecules, the conformational changes of the probe molecules, and target binding. Such molecular level knowledge may allow one to tailor the spatial patterns of the biosensor surfaces to improve the sensitivity and reproducibility.
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9
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Qi L, Tian H, Yu HZ. Binary Thiolate DNA/Ferrocenyl Self-Assembled Monolayers on Gold: A Versatile Platform for Probing Biosensing Interfaces. Anal Chem 2018; 90:9174-9181. [PMID: 29938496 DOI: 10.1021/acs.analchem.8b01655] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The properties of DNA self-assembled monolayers (SAMs) have strong influences on the interfacial DNA-analyte binding behavior, which further affect the performance of biosensors built upon. In this work, we prepared binary thiolate DNA/6-ferrocenyl-1-hexanethiol (FcC6SH) SAMs on gold (DNA/FcC6S-Au) for convenient electrochemical characterization and subsequent data analysis. Our cyclic voltammetric (CV) studies confirmed that the redox responses of surface-tethered Fc and electrostatically bound [Ru(NH3)6]3+ are capable of providing quantitative information regarding the DNA film properties, including the surface density, structural heterogeneity, and molecular orientation under different preparation and measurement conditions. With the binary thiolate DNA/FcC6S-Au SAM prepared in the conventional post-assembly exchange protocol as a trial system, we are demonstrating the capability of introducing redox-active thiols as passivating and labeling reagents for preparing many other DNA-based biosensing interfaces via varied assembly steps and under different measurement conditions.
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Affiliation(s)
- Lin Qi
- Department of Chemistry , Simon Fraser University , Burnaby , British Columbia V5A 1S6 , Canada
| | - Huihui Tian
- Department of Chemistry , Simon Fraser University , Burnaby , British Columbia V5A 1S6 , Canada.,National Center for Nanoscience and Technology , Beijing 100190 , P.R. China
| | - Hua-Zhong Yu
- Department of Chemistry , Simon Fraser University , Burnaby , British Columbia 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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Hao X, Josephs EA, Gu Q, Ye T. Molecular conformations of DNA targets captured by model nanoarrays. NANOSCALE 2017; 9:13419-13424. [PMID: 28875997 DOI: 10.1039/c7nr04715k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
An open question in single molecule nanoarrays is how the chemical and morphological heterogeneities of the solid support affect the properties of biomacromolecules. We generated arrays that allowed individually-resolvable DNA molecules to interact with tailored surface heterogeneities and revealed how molecular conformations are impacted by surface interactions.
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Affiliation(s)
- X Hao
- Chemistry and Chemical Biology, University of California, Merced, California 95343, USA.
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12
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Ensafi AA, Gorgabi-Khorzoughi M, Rezaei B, Jafari-Asl M. Electrochemical behavior of polyoxometalates decorated on poly diallyl dimethyl ammonium chloride-MWCNTs: A highly selective electrochemical sensor for determination of guanine and adenine. J Taiwan Inst Chem Eng 2017. [DOI: 10.1016/j.jtice.2017.06.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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13
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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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14
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Surface-Enhanced Raman Spectroscopy Label-free Detection of DNA Complementary PolyA and PolyT Polybases on Ag/TiO2
Platform. ChemistrySelect 2016. [DOI: 10.1002/slct.201600521] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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15
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16
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Capaldo P, Alfarano SR, Ianeselli L, Zilio SD, Bosco A, Parisse P, Casalis L. Circulating Disease Biomarker Detection in Complex Matrices: Real-Time, In Situ Measurements of DNA/miRNA Hybridization via Electrochemical Impedance Spectroscopy. ACS Sens 2016. [DOI: 10.1021/acssensors.6b00262] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Pietro Capaldo
- Elettra-Sincrotrone Trieste S.C.p.A., Area
Science Park, Strada Statale 14 km 163.5, 34149 Basovizza, Trieste, Italy
| | | | - Luca Ianeselli
- Elettra-Sincrotrone Trieste S.C.p.A., Area
Science Park, Strada Statale 14 km 163.5, 34149 Basovizza, Trieste, Italy
| | - Simone Dal Zilio
- CNR-IOM, Laboratorio TASC, Area
Science Park, Strada Statale 14 km 163.5, 34149 Basovizza, Trieste, Italy
| | - Alessandro Bosco
- Elettra-Sincrotrone Trieste S.C.p.A., Area
Science Park, Strada Statale 14 km 163.5, 34149 Basovizza, Trieste, Italy
| | - Pietro Parisse
- Elettra-Sincrotrone Trieste S.C.p.A., Area
Science Park, Strada Statale 14 km 163.5, 34149 Basovizza, Trieste, Italy
- INSTM-ST Unit, Area Science Park,
Strada Statale 14 km 163.5, 34149 Basovizza, Trieste, Italy
| | - Loredana Casalis
- Elettra-Sincrotrone Trieste S.C.p.A., Area
Science Park, Strada Statale 14 km 163.5, 34149 Basovizza, Trieste, Italy
- INSTM-ST Unit, Area Science Park,
Strada Statale 14 km 163.5, 34149 Basovizza, Trieste, Italy
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17
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Izadi Z, Sheikh-Zeinoddin M, Ensafi AA, Soleimanian-Zad S. Fabrication of an electrochemical DNA-based biosensor for Bacillus cereus detection in milk and infant formula. Biosens Bioelectron 2016; 80:582-589. [DOI: 10.1016/j.bios.2016.02.032] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 01/23/2016] [Accepted: 02/10/2016] [Indexed: 11/25/2022]
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18
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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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19
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Bano F, Sluysmans D, Wislez A, Duwez AS. Unraveling the complexity of the interactions of DNA nucleotides with gold by single molecule force spectroscopy. NANOSCALE 2015; 7:19528-19533. [PMID: 26538184 DOI: 10.1039/c5nr05695k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Addressing the effect of different environmental factors on the adsorption of DNA to solid supports is critical for the development of robust miniaturized devices for applications ranging from biosensors to next generation molecular technology. Most of the time, thiol-based chemistry is used to anchor DNA on gold - a substrate commonly used in nanotechnology - and little is known about the direct interaction between DNA and gold. So far there have been no systematic studies on the direct adsorption behavior of the deoxyribonucleotides (i.e., a nitrogenous base, a deoxyribose sugar, and a phosphate group) and on the factors that govern the DNA-gold bond strength. Here, using single molecule force spectroscopy, we investigated the interaction of the four individual nucleotides, adenine, guanine, cytosine, and thymine, with gold. Experiments were performed in three salinity conditions and two surface dwell times to reveal the factors that influence nucleotide-Au bond strength. Force data show that, at physiological ionic strength, adenine-Au interactions are stronger, asymmetrical and independent of surface dwell time as compared to cytosine-Au and guanine-Au interactions. We suggest that in these conditions only adenine is able to chemisorb on gold. A decrease of the ionic strength significantly increases the bond strength for all nucleotides. We show that moderate ionic strength along with longer surface dwell period suggest weak chemisorption also for cytosine and guanine.
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Affiliation(s)
- Fouzia Bano
- University of Liège, Department of Chemistry, B6a Sart-Tilman, 4000 Liège, Belgium.
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20
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Zhang X, Daaboul GG, Spuhler PS, Freedman DS, Yurt A, Ahn S, Avci O, Ünlü MS. Nanoscale characterization of DNA conformation using dual-color fluorescence axial localization and label-free biosensing. Analyst 2015; 139:6440-9. [PMID: 25340741 DOI: 10.1039/c4an01425a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Quantitative determination of the density and conformation of DNA molecules tethered to the surface can help optimize and understand DNA nanosensors and nanodevices, which use conformational or motional changes of surface-immobilized DNA for detection or actuation. We present an interferometric sensing platform that combines (i) dual-color fluorescence spectroscopy for precise axial co-localization of two fluorophores attached at different nucleotides of surface-immobilized DNA molecules and (ii) independent label-free quantification of biomolecule surface density at the same site. Using this platform, we examined the conformation of DNA molecules immobilized on a three-dimensional polymeric surface and demonstrated simultaneous detection of DNA conformational change and binding in real-time. These results demonstrate that independent quantification of both surface density and molecular nanoscale conformation constitutes a versatile approach for nanoscale solid-biochemical interface investigations and molecular binding assays.
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Affiliation(s)
- Xirui Zhang
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215, USA.
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21
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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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22
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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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23
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Corvaglia S, Sanavio B, Hong Enriquez RP, Sorce B, Bosco A, Scaini D, Sabella S, Pompa PP, Scoles G, Casalis L. Atomic force microscopy based nanoassay: a new method to study α-Synuclein-dopamine bioaffinity interactions. Sci Rep 2014; 4:5366. [PMID: 24947141 PMCID: PMC4064358 DOI: 10.1038/srep05366] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 05/28/2014] [Indexed: 12/25/2022] Open
Abstract
Intrinsically Disordered Proteins (IDPs) are characterized by the lack of well-defined 3-D structure and show high conformational plasticity. For this reason, they are a strong challenge for the traditional characterization of structure, supramolecular assembly and biorecognition phenomena. We show here how the fine tuning of protein orientation on a surface turns useful in the reliable testing of biorecognition interactions of IDPs, in particular α-Synuclein. We exploited atomic force microscopy (AFM) for the selective, nanoscale confinement of α-Synuclein on gold to study the early stages of α-Synuclein aggregation and the effect of small molecules, like dopamine, on the aggregation process. Capitalizing on the high sensitivity of AFM topographic height measurements we determined, for the first time in the literature, the dissociation constant of dopamine-α-Synuclein adducts.
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Affiliation(s)
- Stefania Corvaglia
- NanoInnovation Laboratory, Elettra Sincrotrone Trieste S.C.p.A., S.S.14 Km 163.5, 34149 Basovizza, Trieste, Italy
- Life Science Department, University of Trieste, via Giorgieri 1, I-34127 Trieste, Italy
| | - Barbara Sanavio
- NanoInnovation Laboratory, Elettra Sincrotrone Trieste S.C.p.A., S.S.14 Km 163.5, 34149 Basovizza, Trieste, Italy
- Department of Biological and Medical Science, University of Udine, Ospedale della Misericordia, Piazzale Santa Maria della Misericordia, 15 -33100 Udine, Italy
- Current address: Fondazione I.R.C.C.S. Istituto Neurologico Carlo Besta, IFOM-IEO-campus, via Adamello, 16, 20139 Milan, Italy
| | - Rolando P. Hong Enriquez
- Department of Biological and Medical Science, University of Udine, Ospedale della Misericordia, Piazzale Santa Maria della Misericordia, 15 -33100 Udine, Italy
| | - Barbara Sorce
- Center for Bio-Molecular Nanotechnologies@UniLe, Istituto Italiano di Tecnologia, Via Barsanti-73010 Arnesano, Lecce, Italy
- Current address: ETH Zürich, Department of Biosystems Science and Engineering, 4058 Basel, Switzerland
| | - Alessandro Bosco
- NanoInnovation Laboratory, Elettra Sincrotrone Trieste S.C.p.A., S.S.14 Km 163.5, 34149 Basovizza, Trieste, Italy
| | - Denis Scaini
- NanoInnovation Laboratory, Elettra Sincrotrone Trieste S.C.p.A., S.S.14 Km 163.5, 34149 Basovizza, Trieste, Italy
- Life Science Department, University of Trieste, via Giorgieri 1, I-34127 Trieste, Italy
| | - Stefania Sabella
- Center for Bio-Molecular Nanotechnologies@UniLe, Istituto Italiano di Tecnologia, Via Barsanti-73010 Arnesano, Lecce, Italy
| | - Pier Paolo Pompa
- Center for Bio-Molecular Nanotechnologies@UniLe, Istituto Italiano di Tecnologia, Via Barsanti-73010 Arnesano, Lecce, Italy
| | - Giacinto Scoles
- NanoInnovation Laboratory, Elettra Sincrotrone Trieste S.C.p.A., S.S.14 Km 163.5, 34149 Basovizza, Trieste, Italy
- Department of Biological and Medical Science, University of Udine, Ospedale della Misericordia, Piazzale Santa Maria della Misericordia, 15 -33100 Udine, Italy
| | - Loredana Casalis
- NanoInnovation Laboratory, Elettra Sincrotrone Trieste S.C.p.A., S.S.14 Km 163.5, 34149 Basovizza, Trieste, Italy
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24
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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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25
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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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26
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Wongkaew P, Poosittisak S. Diagnosis of Sugarcane White Leaf Disease Using the Highly Sensitive DNA Based Voltammetric Electrochemical Determination. ACTA ACUST UNITED AC 2014. [DOI: 10.4236/ajps.2014.515240] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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27
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Ianeselli L, Grenci G, Callegari C, Tormen M, Casalis L. Development of stable and reproducible biosensors based on electrochemical impedance spectroscopy: three-electrode versus two-electrode setup. Biosens Bioelectron 2013; 55:1-6. [PMID: 24355458 DOI: 10.1016/j.bios.2013.11.067] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 11/25/2013] [Indexed: 01/05/2023]
Abstract
This work focuses on the development of electrochemical impedance biosensors based on capacitance readout, for the detection of biomolecules in small sample volumes. We performed electrochemical impedance spectroscopy (EIS) measurements of DNA hybridization in electrochemical cells with microfabricated gold electrodes. The time stability of the device was tested in two different configurations: two microelectrodes in a microfluidic channel; two microelectrodes plus a reference electrode in an electrochemical cell. Our results demonstrate that the three-electrode setup is more stable, more reproducible, and suitable for real-time measurements. In the last part of the work we perform a test study of DNA hybridization in real time, and we show that the three-electrode configuration can measure the process in situ and in real time.
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Affiliation(s)
| | - Gianluca Grenci
- CNR-IOM, Laboratorio TASC, Area Science Park, Basovizza, Strada Statale 14 km 163.5, Trieste I-34149, Italy
| | - Carlo Callegari
- Elettra-Sincrotrone Trieste S.C.p.A., S.S. 14 km 163.5, In Area Science Park, Basovizza, Trieste 34149, Italy
| | - Massimo Tormen
- CNR-IOM, Laboratorio TASC, Area Science Park, Basovizza, Strada Statale 14 km 163.5, Trieste I-34149, Italy
| | - Loredana Casalis
- Elettra-Sincrotrone Trieste S.C.p.A., S.S. 14 km 163.5, In Area Science Park, Basovizza, Trieste 34149, Italy.
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28
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Howorka S. DNA nanoarchitectonics: assembled DNA at interfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:7344-7353. [PMID: 23373872 DOI: 10.1021/la3045785] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
DNA is a powerful biomaterial for creating rationally designed and functionally enhanced nanostructures. DNA nanoarchitectures positioned at substrate interfaces can offer unique advantages leading to improved surface properties relevant to biosensing, nanotechnology, materials science, and cell biology. This Perspective highlights the benefits and challenges of using assembled DNA as a nanoscale building block for interfacial layers and surveys their applications in three areas: homogeneous dense surface coatings, bottom-up nanopatterning, and 3D nanoparticle lattices. Possible future research developments are discussed at the end of the Perspective.
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Affiliation(s)
- Stefan Howorka
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London, England, United Kingdom.
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29
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Johnson-Buck A, Nangreave J, Jiang S, Yan H, Walter NG. Multifactorial modulation of binding and dissociation kinetics on two-dimensional DNA nanostructures. NANO LETTERS 2013; 13:2754-9. [PMID: 23701430 DOI: 10.1021/nl400976s] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We use single-particle fluorescence resonance energy transfer (FRET) to show that organizing oligonucleotide probes into patterned two-dimensional arrays on DNA origami nanopegboards significantly alters the kinetics and thermodynamics of their hybridization with complementary targets in solution. By systematically varying the spacing of probes, we demonstrate that the rate of dissociation of a target is reduced by an order of magnitude in the densest probe arrays. The rate of target binding is reduced less dramatically, but to a greater extent than reported previously for one-dimensional probe arrays. By additionally varying target sequence and buffer composition, we provide evidence for two distinct mechanisms for the markedly slowed dissociation: direct hopping of targets between adjacent sequence-matched probes and nonsequence-specific, salt-bridged, and thus attractive electrostatic interactions with the DNA origami pegboard. This kinetic behavior varies little between individual copies of a given array design and will have significant impact on hybridization measurements and overall performance of DNA nanodevices as well as microarrays.
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Affiliation(s)
- Alexander Johnson-Buck
- Department of Chemistry, Single Molecule Analysis Group, 930 N. University Avenue, University of Michigan, Ann Arbor, Michigan 48109-1055, USA
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30
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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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31
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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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32
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Federici S, Oliviero G, Maiolo D, Depero LE, Colombo I, Bergese P. On the thermodynamics of biomolecule surface transformations. J Colloid Interface Sci 2012; 375:1-11. [DOI: 10.1016/j.jcis.2012.02.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 02/03/2012] [Accepted: 02/04/2012] [Indexed: 02/06/2023]
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33
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Bosco A, Bano F, Parisse P, Casalis L, DeSimone A, Micheletti C. Hybridization in nanostructured DNA monolayers probed by AFM: theory versus experiment. NANOSCALE 2012; 4:1734-41. [PMID: 22301788 DOI: 10.1039/c2nr11662f] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Nanografted monolayers (NAMs) of DNA show novel physico-chemical properties that make them ideally suited for advanced biosensing applications. In comparison with alternative solid-phase techniques for diagnostic DNA detection, NAMs have the advantage of combining a small size with a high homogeneity of the DNA surface coverage. These two properties favour the extreme miniaturization and ultrasensitivity in high-throughput biosensing devices. The systematic use of NAMs for quantitative DNA (and protein) detection has so far suffered from the lack of a control on key fabrication parameters, such as the ss- or ds-DNA surface coverage. Here we report on a combined experimental-computational study that allows us to estimate the surface density of the grafted DNA by analyzing the sample mechanical response, that is the DNA patch height vs. applied tip load curves. It is shown that the same analysis scheme can be used to detect the occurrence of hybridization with complementary strands in solution and estimate its efficiency. Thanks to these quantitative relationships it is possible to use a single AFM-based setup to: (i) fabricate a DNA NAM, (ii) control the DNA surface coverage, and (iii) characterize its level of hybridization helping the design of NAMs with pre-determined fabrication parameters.
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Affiliation(s)
- Alessandro Bosco
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, I-34136, Trieste, Italy
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34
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Liang J, Castronovo M, Scoles G. DNA as Invisible Ink for AFM Nanolithography. J Am Chem Soc 2011; 134:39-42. [DOI: 10.1021/ja2076845] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jian Liang
- Department of Biology, Temple University, 1900 North 12th Street, Philadelphia,
Pennsylvania 19122, United States
| | - Matteo Castronovo
- Department of Biology, Temple University, 1900 North 12th Street, Philadelphia,
Pennsylvania 19122, United States
- Experimental and Clinical Pharmacology
Unit, CRO-National Center Institute, Via
Franco Gallini 2, I-33081 Aviano Pordenone, Italy
| | - Giacinto Scoles
- Department of Biology, Temple University, 1900 North 12th Street, Philadelphia,
Pennsylvania 19122, United States
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35
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Melli M, Scoles G, Lazzarino M. Fast detection of biomolecules in diffusion-limited regime using micromechanical pillars. ACS NANO 2011; 5:7928-7935. [PMID: 21955070 DOI: 10.1021/nn202224g] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We have developed a micromechanical sensor based on vertically oriented oscillating beams, in which contrary to what is normally done (for example with oscillating cantilevers) the sensitive area is located at the free end of the oscillator. In the micropillar geometry used here, analyte adsorption is confined only to the tip of the micropillar, thus reducing the volume from which the analyte molecules must diffuse to saturate the surface to a sphere of radius more than 2 orders of magnitude smaller than the corresponding linear distance valid for adsorption on a macroscopic surface. Hence the absorption rate is 3 orders of magnitude faster than on a typical 200 × 20 square micrometer cantilever. Pillar oscillations are detected by means of an optical lever method, but the geometry is suitable for multiplexing with compact integrated detection. We demonstrate our technology by investigating the formation of a single-strand DNA self-assembled monolayer (SAM) consisting of less than 10(6) DNA molecules and by measuring their hybridization efficiency. We show that the binding rate is 1000 times faster than on a "macroscopic" surface. We also show that the hybridization of a SAM of maximum density DNA is 40% or 4 times the value reported in the literature. These results suggest that the lower values previously reported in the literature can be attributed to incomplete saturation of the surface due to the slower adsorption rate on the "macroscopic" surfaces used.
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Affiliation(s)
- Mauro Melli
- CNR-IOM, Laboratorio TASC-Area Science Park Basovizza-ss 14 km 163.5 34149 Trieste, Italy
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36
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Day BS, Fiegland LR, Vint ES, Shen W, Morris JR, Norton ML. Thiolated dendrimers as multi-point binding headgroups for DNA immobilization on gold. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:12434-12442. [PMID: 21916426 DOI: 10.1021/la202444s] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The synthesis of multithiolated DNA molecules that can be used to produce self-assembled monolayers of single-stranded DNA oligonucleotides on gold substrates is described. Generation 3 polyamidoamine (PAMAM) dendrimers were conjugated to DNA oligomers and functionalized with ~30 protected thiol groups. The protected thiol groups-thioacetate groups-allowed the dendrimer-DNA constructs to be stored in a buffer solution for at least 2 months before deprotection without any observable decrease in their ability to assemble into functional layers. The monolayers formed using these multithiolated DNA probe strands demonstrate target capture efficiencies comparable to those of analogous monolayers assembled with DNA functionalized with single thiol groups. A functional advantage of using dendrimer headgroups is the resistance to probe strand loss in prolonged exposure to buffer solutions at a high temperature (95 °C).
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Affiliation(s)
- B Scott Day
- Department of Chemistry, Marshall University, Huntington, West Virginia 25755, USA.
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Shircliff RA, Martin IT, Pankow JW, Fennell J, Stradins P, Ghirardi ML, Cowley SW, Branz HM. High-resolution X-ray photoelectron spectroscopy of mixed silane monolayers for DNA attachment. ACS APPLIED MATERIALS & INTERFACES 2011; 3:3285-3292. [PMID: 21797205 DOI: 10.1021/am200604q] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The amine density of 3-aminopropyldimethylethoxysilane (APDMES) films on silica is controlled to determine its effect on DNA probe density and subsequent DNA hybridization. The amine density is tailored by controlling the surface reaction time of (1) APDMES, or (2) n-propyldimethylchlorosilane (PDMCS, which is not amine terminated) and then reacting it with APDMES to form a mixed monolayer. High-resolution X-ray photoelectron spectroscopy (XPS) is used to quantify silane surface coverage of both pure and mixed monolayers on silica; the XPS data demonstrate control of amine density in both pure APDMES and PDMCS/APDMES mixed monolayers. A linear correlation between the atomic concentration of N atoms from the amine and Si atoms from the APDMES in pure APDMES films allows us to calculate the PDMCS/APDMES ratio in the mixed monolayers. Fluorescence from attached DNA probes and from hybridized DNA decreases as the percentage of APDMES in the mixed monolayer is decreased by dilution with PDMCS.
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Affiliation(s)
- Rebecca A Shircliff
- Chemistry and Geochemistry Department, Colorado School of Mines, Golden, Colorado 80401, United States
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Brown TT, Lejeune ZM, Liu K, Hardin S, Li JR, Rupnik K, Garno JC. Automated scanning probe lithography with n-alkanethiol self assembled monolayers on Au(111): Application for teaching undergraduate laboratories. ACTA ACUST UNITED AC 2011; 16:112-25. [PMID: 21483651 DOI: 10.1016/j.jala.2010.06.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2010] [Indexed: 10/19/2022]
Abstract
Controllers for scanning probe instruments can be programmed for automated lithography to generate desired surface arrangements of nanopatterns of organic thin films, such as n-alkanethiol self-assembled monolayers (SAMs). In this report, atomic force microscopy (AFM) methods of lithography known as nanoshaving and nanografting are used to write nanopatterns within organic thin films. Commercial instruments provide software to control the length, direction, speed, and applied force of the scanning motion of the tip. For nanoshaving, higher forces are applied to an AFM tip to selectively remove regions of the matrix monolayer, exposing bare areas of the gold substrate. Nanografting is accomplished by force-induced displacement of molecules of a matrix SAM, followed immediately by the surface self-assembly of n-alkanethiol molecules from solution. Advancements in AFM automation enable rapid protocols for nanolithography, which can be accomplished within the tight time restraints of undergraduate laboratories. Example experiments with scanning probe lithography (SPL) will be described in this report that were accomplished by undergraduate students during laboratory course activities and research internships in the chemistry department of Louisiana State University. Students were introduced to principles of surface analysis and gained "hands-on" experience with nanoscale chemistry.
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Affiliation(s)
- Treva T Brown
- Chemistry Department and the Center for BioModular Multi-Scale Systems, 232 Choppin Hall, Louisiana State University, Baton Rouge, LA 70803
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39
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Oliviero G, Federici S, Colombi P, Bergese P. On the difference of equilibrium constants of DNA hybridization in bulk solution and at the solid-solution interface. J Mol Recognit 2011; 24:182-7. [DOI: 10.1002/jmr.1019] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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40
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Castronovo M, Scaini D. The atomic force microscopy as a lithographic tool: nanografting of DNA nanostructures for biosensing applications. Methods Mol Biol 2011; 749:209-221. [PMID: 21674375 DOI: 10.1007/978-1-61779-142-0_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Current in vitro techniques cannot accurately identify small differences in concentration in samples containing few molecules in single or few cells. Nanotechnology overcomes these limitations with the possibility of measuring protein amounts down to a hundred molecules and subnanomolar concentrations and in nanoliter to picoliter volumes. The nanoscale approach, therefore, permits measurements in samples consisting of single or few cells. Atomic force microscopy (AFM) nanografting can be utilized to prepare DNA nanopatches of different sizes (from few hundreds of nanometers to few microns in size) onto which DNA-antibody conjugates can be anchored through DNA-directed immobilization. AFM height measurements are used to assess the binding of the proteins as well as their subsequent interaction with other components, such as specific proteins from the serum. Recent results have contributed to demonstrate that nanografted patch arrays are well suited for application in biosensing and could enable the fabrication of multifeature protein nanoarrays.
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Affiliation(s)
- Matteo Castronovo
- Department of Biology, MONALISA Laboratory, College of Science and Technology, Temple University, Philadelphia, PA, USA.
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Castronovo M, Lucesoli A, Parisse P, Kurnikova A, Malhotra A, Grassi M, Grassi G, Scaggiante B, Casalis L, Scoles G. Two-dimensional enzyme diffusion in laterally confined DNA monolayers. Nat Commun 2011; 2:297. [PMID: 21540839 DOI: 10.1038/ncomms1296] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Accepted: 03/30/2011] [Indexed: 02/08/2023] Open
Abstract
Addressing the effects of confinement and crowding on biomolecular function may provide insight into molecular mechanisms within living organisms, and may promote the development of novel biotechnology tools. Here, using molecular manipulation methods, we investigate restriction enzyme reactions with double-stranded (ds)DNA oligomers confined in relatively large (and flat) brushy matrices of monolayer patches of controlled, variable density. We show that enzymes from the contacting solution cannot access the dsDNAs from the top-matrix interface, and instead enter at the matrix sides to diffuse two-dimensionally in the gap between top- and bottom-matrix interfaces. This is achieved by limiting lateral access with a barrier made of high-density molecules that arrest enzyme diffusion. We put forward, as a possible explanation, a simple and general model that relates these data to the steric hindrance in the matrix, and we briefly discuss the implications and applications of this strikingly new phenomenon.
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Affiliation(s)
- Matteo Castronovo
- Department of Biology, Temple University, 1900 North 12th Street, Philadelphia, Philadelphia 19122, USA.
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42
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Jiang KR, Huang JL, Chen CC, Su HJ, Wu JC. Effect of co-axially hybridized gene targets on hybridization efficiency of microarrayed DNA probes. J Taiwan Inst Chem Eng 2011; 42:5-12. [PMID: 32362954 PMCID: PMC7185593 DOI: 10.1016/j.jtice.2010.04.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2009] [Revised: 04/19/2010] [Accepted: 04/25/2010] [Indexed: 11/25/2022]
Abstract
The effect of relative size of two co-axially hybridized gene targets on the hybridization efficiency was studied for two DNA probe configurations and various probe concentrations. Each of two sets of microarrayed probes contained a pair of DNA probes and a pair of their complementary samples labeled with two distinct fluorescent dyes. The sequence of each probe is especially designed so that two targets are simultaneously complementary to two adjacent sections of the probe. The molecular steric effect on the hybridization efficiency is investigated by comparing the dye signals between configurations of one-target and two-target hybridization scenarios. The results show that a low probe concentration gives better hybridization efficiency and the first-hybridization conducted by a shorter-size DNA target improves the hybridization efficiency of the second target coupling onto the same probe.
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Affiliation(s)
- Kai Ren Jiang
- Chemical Engineering Department, Chung Yuan Christian University, Chung Li, Tao Yuan 32023, Taiwan
| | - Jie-Len Huang
- Biomedical Engineering Center, Industrial Technology Research Institute, Chu Tung, Hsin Chu 31040, Taiwan
| | - Chia-Chun Chen
- Biomedical Engineering Center, Industrial Technology Research Institute, Chu Tung, Hsin Chu 31040, Taiwan
| | - Hung-Ju Su
- Biomedical Engineering Center, Industrial Technology Research Institute, Chu Tung, Hsin Chu 31040, Taiwan
| | - Jui-Chuang Wu
- Chemical Engineering Department, Chung Yuan Christian University, Chung Li, Tao Yuan 32023, Taiwan
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43
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Cederquist KB, Keating CD. Hybridization efficiency of molecular beacons bound to gold nanowires: effect of surface coverage and target length. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:18273-80. [PMID: 21038880 PMCID: PMC2994276 DOI: 10.1021/la1031703] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Revised: 10/13/2010] [Indexed: 05/22/2023]
Abstract
Surface-bound nucleic acid probes designed to adopt specific secondary structures are becoming increasingly important in a range of biosensing applications but remain less well characterized than traditional single-stranded probes, which are typically designed to avoid secondary structure. We report the hybridization efficiency for surface-immobilized hairpin DNA probes. Our probes are molecular beacons, carrying a 3' dye moiety and a 5' thiol for attachment to gold nanowires, which serve as both scaffolds for probe attachment and quenchers. Hybridization efficiency was dependent on probe surface coverage, reaching a maximum of ∼90% at intermediate coverages of (1-2) × 10(12) probes/cm(2) and dropping to ≤20% at higher or lower coverages. Fluorescence intensity did not track with the number of target molecules bound, and was highest for high probe coverage despite the lower bound targets per square centimeter. Backfilling with short thiolated oligoethylene glycol spacers increased hybridization efficiency at low hairpin probe coverages (∼(3-4) × 10(11) probes/cm(2)), but not at higher probe coverages (1 × 10(12)/cm(2)). We also evaluated the effect of target length by adding up to 50 nonhybridizing nucleotides to the 3' or 5' end of the complementary target sequence. Additional nucleotides on the 3' end of the complementary target sequence (i.e., the end near the nanowire surface) had a much greater impact on hybridization efficiency as compared to nucleotides added to the 5' end. This work provides guidance in designing sensors in which surface-bound probes designed to adopt secondary structures are used to detect target sequences from solution.
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Affiliation(s)
- Kristin B. Cederquist
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Christine D. Keating
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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44
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Sanavio B, Scaini D, Grunwald C, Legname G, Scoles G, Casalis L. Oriented immobilization of prion protein demonstrated via precise interfacial nanostructure measurements. ACS NANO 2010; 4:6607-6616. [PMID: 20958083 DOI: 10.1021/nn101872w] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Nanopatterning of biomolecules on functionalized surfaces offers an excellent route for ultrasensitive protein immobilization, for interaction measurements, and for the fabrication of devices such as protein nanoarrays. An improved understanding of the physics and chemistry underlying the device properties and the recognition process is necessary for performance optimization. This is especially important for the recognition and immobilization of intrinsically disordered proteins (IDPs), like the prion protein (PrP), a partial IDP, whose folding and stability may be influenced by local environment and confinement. Atomic force microscopy allows for both highly controllable nanolithography and for sensitive and accurate direct detection, via precise topographic measurements on ultraflat surfaces, of protein interactions in a liquid environment, thus different environmental parameters affecting the biorecognition phenomenon can be investigated in situ. Using nanografting, a tip-induced lithographic technique, and an affinity immobilization strategy based on two different histidine tagged antibodies, with high nM affinity for two different regions of PrP, we successfully demonstrated the immobilization of recombinant mouse PrP onto nanostructured surfaces, in two different orientations. Clear discrimination of the two molecular orientations was shown by differential height (i.e., topographic) measurements, allowing for the estimation of binding parameters and the full characterization of the nanoscale biorecognition process. Our work opens the way to several high sensitivity diagnostic applications and, by controlling PrP orientation, allows for the investigation of unconventional interactions with partially folded proteins, and may serve as a platform for protein misfolding and refolding studies on PrP and other thermodynamically unstable, fibril forming, proteins.
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Affiliation(s)
- Barbara Sanavio
- SISSA/ELETTRA NanoInnovation Laboratory, Sincrotrone Trieste S.C.p.A., S.S.14 Km 163.5, 34149 Basovizza, Trieste, Italy
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45
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Wong IY, Melosh NA. An electrostatic model for DNA surface hybridization. Biophys J 2010; 98:2954-63. [PMID: 20550908 DOI: 10.1016/j.bpj.2010.03.017] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Revised: 02/23/2010] [Accepted: 03/09/2010] [Indexed: 10/19/2022] Open
Abstract
DNA hybridization at surfaces is a crucial process for biomolecular detection, genotyping, and gene expression analysis. However, hybridization density and kinetics can be strongly inhibited by electric fields from the negatively charged DNA as the reaction proceeds. Here, we develop an electrostatic model to optimize hybridization density and kinetics as a function of DNA surface density, salt concentrations, and applied voltages. The electrostatic repulsion from a DNA surface layer is calculated numerically and incorporated into a modified Langmuir scheme, allowing kinetic suppression of hybridization. At the low DNA probe densities typically used in assays (<10(13)/cm(2)), electrostatics effects are largely screened and hybridization is completed with fast kinetics. However, higher hybridization densities can be achieved at intermediate DNA surface densities, albeit with slower kinetics. The application of positive voltages circumvents issues resulting from the very high DNA probe density, allowing highly enhanced hybridization densities and accelerated kinetics, and validating recent experimental measurements.
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Affiliation(s)
- Ian Y Wong
- Geballe Laboratory for Advanced Materials, Department of Materials Science and Engineering, Stanford University, Stanford, California, USA
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46
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te Riet J, Smit T, Gerritsen JW, Cambi A, Elemans JAAW, Figdor CG, Speller S. Molecular friction as a tool to identify functionalized alkanethiols. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:6357-6366. [PMID: 20225883 DOI: 10.1021/la9038057] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
By using the nanografting method, well-defined nanoscale patches of alkanethiols were constructed in a self-assembled monolayer (SAM) matrix on an atomically flat gold (Au(111)) surface. A series of nanografted patches, composed of alkanethiols with different end groups (-CH(3), -CF(3), -OH, -SH, -COOH, and -NH(2)), were analyzed in detail by a combination of atomic force microscopy (AFM) height and quantitative lateral friction measurements. By constructing a series of nanografted patches of methyl-terminated thiols with various chain lengths, it was shown that the absolute friction of the nanografted patches was always smaller than that of the surrounding SAM matrix, demonstrating that, because of the spatially confined self-assembly during nanografting, SAMs show less defects. In addition, the friction gradually increased for decreasing alkane chain length as expected, although a subtle odd-even effect was observed. The study of thiols with functionalized end groups (-CF(3), -OH, -SH, -COOH, and -NH(2)) gave specific insights in orientation, packing, and structure of the molecules in the SAMs. Depending on the thiol end groups, these nanografted patches exhibited large and specific differences in lateral friction force, which offers the unique possibility to use the friction as a molecular recognition tool for thiol-based self-assembled monolayers.
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Affiliation(s)
- Joost te Riet
- Department of Scanning Probe Microscopy, Institute for Molecules and Materials, Radboud University Nijmegen, P.O. Box 9010, 6500GL Nijmegen, The Netherlands
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Han WH, Liao JM, Chen KL, Wu SM, Chiang YW, Lo ST, Chen CL, Chiang CM. Enhanced Recognition of Single-Base Mismatch Using Locked Nucleic Acid-Integrated Hairpin DNA Probes Revealed by Atomic Force Microscopy Nanolithography. Anal Chem 2010; 82:2395-400. [DOI: 10.1021/ac902665c] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Wen-Hsin Han
- Department of Chemistry, Center for Nanoscience and Nanotechnology, National Sun Yat-Sen University, Kaohsiung, Taiwan 80424
| | - Jun-Min Liao
- Department of Chemistry, Center for Nanoscience and Nanotechnology, National Sun Yat-Sen University, Kaohsiung, Taiwan 80424
| | - Kuan-Liang Chen
- Department of Chemistry, Center for Nanoscience and Nanotechnology, National Sun Yat-Sen University, Kaohsiung, Taiwan 80424
| | - Shin-Mou Wu
- Department of Chemistry, Center for Nanoscience and Nanotechnology, National Sun Yat-Sen University, Kaohsiung, Taiwan 80424
| | - Yi-Wen Chiang
- Department of Chemistry, Center for Nanoscience and Nanotechnology, National Sun Yat-Sen University, Kaohsiung, Taiwan 80424
| | - Shu-Ting Lo
- Department of Chemistry, Center for Nanoscience and Nanotechnology, National Sun Yat-Sen University, Kaohsiung, Taiwan 80424
| | - Cheng-Lung Chen
- Department of Chemistry, Center for Nanoscience and Nanotechnology, National Sun Yat-Sen University, Kaohsiung, Taiwan 80424
| | - Chao-Ming Chiang
- Department of Chemistry, Center for Nanoscience and Nanotechnology, National Sun Yat-Sen University, Kaohsiung, Taiwan 80424
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48
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DNA nanomechanics allows direct digital detection of complementary DNA and microRNA targets. Nature 2009; 462:1075-8. [PMID: 20010806 DOI: 10.1038/nature08626] [Citation(s) in RCA: 127] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2009] [Accepted: 10/30/2009] [Indexed: 12/18/2022]
Abstract
Techniques to detect and quantify DNA and RNA molecules in biological samples have had a central role in genomics research. Over the past decade, several techniques have been developed to improve detection performance and reduce the cost of genetic analysis. In particular, significant advances in label-free methods have been reported. Yet detection of DNA molecules at concentrations below the femtomolar level requires amplified detection schemes. Here we report a unique nanomechanical response of hybridized DNA and RNA molecules that serves as an intrinsic molecular label. Nanomechanical measurements on a microarray surface have sufficient background signal rejection to allow direct detection and counting of hybridized molecules. The digital response of the sensor provides a large dynamic range that is critical for gene expression profiling. We have measured differential expressions of microRNAs in tumour samples; such measurements have been shown to help discriminate between the tissue origins of metastatic tumours. Two hundred picograms of total RNA is found to be sufficient for this analysis. In addition, the limit of detection in pure samples is found to be one attomolar. These results suggest that nanomechanical read-out of microarrays promises attomolar-level sensitivity and large dynamic range for the analysis of gene expression, while eliminating biochemical manipulations, amplification and labelling.
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49
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Pinnick VT, Verkhoturov SV, Kaledin L, Bisrat Y, Schweikert EA. Molecular Identification of Individual Nano-Objects. Anal Chem 2009; 81:7527-31. [DOI: 10.1021/ac9014337] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Veronica T. Pinnick
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255, Argonide Corporation, 291 Power Court, Sanford, Florida 32771-1943, and Materials Characterization Facility, Texas A&M University, College Station, Texas 77843
| | - Stanislav V. Verkhoturov
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255, Argonide Corporation, 291 Power Court, Sanford, Florida 32771-1943, and Materials Characterization Facility, Texas A&M University, College Station, Texas 77843
| | - Leonid Kaledin
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255, Argonide Corporation, 291 Power Court, Sanford, Florida 32771-1943, and Materials Characterization Facility, Texas A&M University, College Station, Texas 77843
| | - Yordanos Bisrat
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255, Argonide Corporation, 291 Power Court, Sanford, Florida 32771-1943, and Materials Characterization Facility, Texas A&M University, College Station, Texas 77843
| | - Emile A. Schweikert
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255, Argonide Corporation, 291 Power Court, Sanford, Florida 32771-1943, and Materials Characterization Facility, Texas A&M University, College Station, Texas 77843
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50
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Bano F, Fruk L, Sanavio B, Glettenberg M, Casalis L, Niemeyer CM, Scoles G. Toward multiprotein nanoarrays using nanografting and DNA directed immobilization of proteins. NANO LETTERS 2009; 9:2614-2618. [PMID: 19583282 DOI: 10.1021/nl9008869] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Atomic force microscopy nanografting was utilized to prepare DNA nanopatches of different sizes (200 x 200 to 1000 x 1000 nm(2)) onto which DNA-protein conjugates can be anchored through DNA-directed immobilization. Height measurements were used to assess the binding of the proteins as well as their subsequent interaction with other components, such as antibodies. The results indicate that nanografted patch arrays are well suited for application in biosensing and could enable the fabrication of multifeature protein nanoarrays.
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Affiliation(s)
- Fouzia Bano
- ELETTRA, Sincrotrone Trieste, Trieste, 34012, Italy
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