1
|
Frydrych-Tomczak E, Ratajczak T, Kościński Ł, Ranecka A, Michalak N, Luciński T, Maciejewski H, Jurga S, Lewandowski M, Chmielewski MK. Structure and Oligonucleotide Binding Efficiency of Differently Prepared Click Chemistry-Type DNA Microarray Slides Based on 3-Azidopropyltrimethoxysilane. MATERIALS (BASEL, SWITZERLAND) 2021; 14:2855. [PMID: 34073476 PMCID: PMC8199275 DOI: 10.3390/ma14112855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 11/24/2022]
Abstract
The structural characterization of glass slides surface-modified with 3-azidopropyltrimethoxysilane and used for anchoring nucleic acids, resulting in the so-called DNA microarrays, is presented. Depending on the silanization conditions, the slides were found to show different oligonucleotide binding efficiency, thus, an attempt was made to correlate this efficiency with the structural characteristics of the silane layers. Atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS) and X-ray reflectometry (XRR) measurements provided information on the surface topography, chemical composition and thickness of the silane films, respectively. The surface for which the best oligonucleotides binding efficiency is observed, has been found to consist of a densely-packed silane layer, decorated with a high-number of additional clusters that are believed to host exposed azide groups.
Collapse
Affiliation(s)
- Emilia Frydrych-Tomczak
- Poznań Science and Technology Park, Adam Mickiewicz University Foundation, Rubież 46, 61-612 Poznań, Poland; (E.F.-T.); (H.M.)
| | - Tomasz Ratajczak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland;
| | - Łukasz Kościński
- Institute of Molecular Physics, Polish Academy of Sciences, M. Smoluchowskiego 17, 60-179 Poznań, Poland; (Ł.K.); (A.R.); (N.M.); (T.L.)
| | - Agnieszka Ranecka
- Institute of Molecular Physics, Polish Academy of Sciences, M. Smoluchowskiego 17, 60-179 Poznań, Poland; (Ł.K.); (A.R.); (N.M.); (T.L.)
| | - Natalia Michalak
- Institute of Molecular Physics, Polish Academy of Sciences, M. Smoluchowskiego 17, 60-179 Poznań, Poland; (Ł.K.); (A.R.); (N.M.); (T.L.)
| | - Tadeusz Luciński
- Institute of Molecular Physics, Polish Academy of Sciences, M. Smoluchowskiego 17, 60-179 Poznań, Poland; (Ł.K.); (A.R.); (N.M.); (T.L.)
| | - Hieronim Maciejewski
- Poznań Science and Technology Park, Adam Mickiewicz University Foundation, Rubież 46, 61-612 Poznań, Poland; (E.F.-T.); (H.M.)
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614 Poznań, Poland
| | - Stefan Jurga
- NanoBioMedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej 3, 61-614 Poznań, Poland;
| | - Mikołaj Lewandowski
- Institute of Molecular Physics, Polish Academy of Sciences, M. Smoluchowskiego 17, 60-179 Poznań, Poland; (Ł.K.); (A.R.); (N.M.); (T.L.)
- NanoBioMedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej 3, 61-614 Poznań, Poland;
| | - Marcin K. Chmielewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland;
| |
Collapse
|
2
|
Iwasaki Y, Ota T. Efficient biotinylation of methacryloyl-functionalized nonadherent cells for formation of cell microarrays. Chem Commun (Camb) 2011; 47:10329-31. [DOI: 10.1039/c1cc12948a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
3
|
Ben-Yoav H, Melamed S, Freeman A, Shacham-Diamand Y, Belkin S. Whole-cell biochips for bio-sensing: integration of live cells and inanimate surfaces. Crit Rev Biotechnol 2010; 31:337-53. [PMID: 21190513 DOI: 10.3109/07388551.2010.532767] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Recent advances in the convergence of the biological, chemical, physical, and engineering sciences have opened new avenues of research into the interfacing of diverse biological moieties with inanimate platforms. A main aspect of this field, the integration of live cells with micro-machined platforms for high throughput and bio-sensing applications, is the subject of the present review. These unique hybrid systems are configured in a manner that ensures positioning of the cells in designated patterns, and enables cellular viability maintenance, and monitoring of cellular functionality. Here we review both animate and inanimate surface properties and how they affect cellular attachment, describe relevant modifications of both types of surfaces, list technologies for platform engineering and for cell deposition in the desired configurations, and discuss the influence of various deposition and immobilization methods on the viability and performance of the immobilized cells.
Collapse
Affiliation(s)
- Hadar Ben-Yoav
- Department of Physical Electronics, School of Electrical Engineering, Faculty of Engineering, Tel Aviv University, Tel-Aviv, Israel
| | | | | | | | | |
Collapse
|
4
|
Abstract
Living cells are remarkably complex. To unravel this complexity, living-cell assays have been developed that allow delivery of experimental stimuli and measurement of the resulting cellular responses. High-throughput adaptations of these assays, known as living-cell microarrays, which are based on microtiter plates, high-density spotting, microfabrication, and microfluidics technologies, are being developed for two general applications: (a) to screen large-scale chemical and genomic libraries and (b) to systematically investigate the local cellular microenvironment. These emerging experimental platforms offer exciting opportunities to rapidly identify genetic determinants of disease, to discover modulators of cellular function, and to probe the complex and dynamic relationships between cells and their local environment.
Collapse
Affiliation(s)
- Martin L Yarmush
- Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital, Harvard Medical School, Massachusetts 02139, USA.
| | | |
Collapse
|
5
|
Inoue Y, Fujimoto H, Ogino T, Iwata H. Site-specific gene transfer with high efficiency onto a carbon nanotube-loaded electrode. J R Soc Interface 2008; 5:909-18. [PMID: 18192165 PMCID: PMC2607467 DOI: 10.1098/rsif.2007.1295] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A transfection array, which is specifically developed for use in high-throughput analyses of genome functions by the over-expression or suppression of genes on a chip, is expected to become an important method for post-genome research. High efficiency of gene expression or suppression is indispensable for high-throughput analyses because the adherent cell number on a single spot decreases as the density of spots increases in the transfection array. We have studied an electro-stimulated pore formation on the cell membrane for gene delivery. Fine pores should be formed on the cell membrane to increase the efficiency of gene transfection without cell damage. Herein, we examined the electrode carrying chemically functionalized carbon nanotubes (CNTs) on the surface. The CNTs were loaded on a gold electrode with a self-assembled monolayer membrane by electrostatic interaction. Adsorbed plasmid DNA was transfected with higher efficiency into adherent cells on the CNT-loaded electrode than on an electrode without CNTs. This result may be due to the strong but fine field emission formed from the tips of the CNTs.
Collapse
Affiliation(s)
- Y Inoue
- Institute for Frontier Medical Sciences, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | | | | | | |
Collapse
|
6
|
|
7
|
Pannier AK, Ariazi EA, Bellis AD, Bengali Z, Jordan VC, Shea LD. Bioluminescence imaging for assessment and normalization in transfected cell arrays. Biotechnol Bioeng 2008; 98:486-97. [PMID: 17486653 PMCID: PMC2648395 DOI: 10.1002/bit.21477] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Transfected cell arrays (TCAs) represent a high-throughput technique to correlate gene expression with functional cell responses. Despite advances in TCAs, improvements are needed for the widespread application of this technology. We have developed a TCA that combines a two-plasmid system and dual-bioluminescence imaging to quantitatively normalize for variability in transfection and increase sensitivity. The two-plasmids consist of: (i) normalization plasmid present within each spot, and (ii) functional plasmid that varies between spots, responsible for the functional endpoint of the array. Bioluminescence imaging of dual-luciferase reporters (renilla, firefly luciferase) provides sensitive and quantitative detection of cellular response, with minimal post-transfection processing. The array was applied to quantify estrogen receptor alpha (ERalpha) activity in MCF-7 breast cancer cells. A plasmid containing an ERalpha-regulated promoter directing firefly luciferase expression was mixed with a normalization plasmid, complexed with cationic lipids and deposited into an array. ER induction mimicked results obtained through traditional assays methods, with estrogen inducing luciferase expression 10-fold over the antiestrogen fulvestrant or vehicle. Furthermore, the array captured a dose response to estrogen, demonstrating the sensitivity of bioluminescence quantification. This system provides a tool for basic science research, with potential application for the development of patient specific therapies.
Collapse
Affiliation(s)
- Angela K. Pannier
- Department of Interdepartmental Biological Sciences, Northwestern University, Evanston, Illinois
| | | | - Abigail D. Bellis
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd E156, Evanston, Illinois 60208-3120; telephone: 847-491-7043; fax: 847-491-3728; e-mail:
| | - Zain Bengali
- Department of Interdepartmental Biological Sciences, Northwestern University, Evanston, Illinois
| | | | - Lonnie D. Shea
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd E156, Evanston, Illinois 60208-3120; telephone: 847-491-7043; fax: 847-491-3728; e-mail:
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois 60611
| |
Collapse
|
8
|
Müller-Hartmann H, Faust N, Kazinski M, Kretzschmar T. High-throughput transfection and engineering of primary cells and cultured cell lines – an invaluable tool for research as well as drug development. Expert Opin Drug Discov 2007; 2:1453-65. [DOI: 10.1517/17460441.2.11.1453] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
|
9
|
Santori MI, Gonzalez C, Serrano L, Isalan M. Localized transfection with magnetic beads coated with PCR products and other nucleic acids. Nat Protoc 2007; 1:526-31. [PMID: 17406278 DOI: 10.1038/nprot.2006.74] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The bead transfection method involves binding nucleic acids onto 3-microm-diameter paramagnetic beads, treating the beads with transfection reagent, and using them as scaffolds to direct transfection to individual cells or regions in a population. Typically, PCR products are used because they can be conveniently generated using biotinylated primers and can introduce site-directed mutations, without the need for cloning or plasmid purification. However, the method can be adapted to transfect plasmid DNA or RNA. The magnetic properties of the beads allows magnets to direct the loci of transfection in cell culture; magnetic arrays are built in cell culture chambers to allow multiple parallel transfections on the same microscope coverslip. The PCR reaction and transfection can be carried out in 1 d, and transfection results can be viewed in 24-48 h.
Collapse
Affiliation(s)
- Maria Isabel Santori
- EMBL-CRG Systems Biology Programme, Centre for Genomic Regulation, Passeig Maritim 37-49, E-08003 Barcelona, Spain
| | | | | | | |
Collapse
|
10
|
Yamauchi F, Okada M, Kato K, Jakt LM, Iwata H. Array-based functional screening for genes that regulate vascular endothelial differentiation of Flk1-positive progenitors derived from embryonic stem cells. Biochim Biophys Acta Gen Subj 2007; 1770:1085-97. [PMID: 17532144 DOI: 10.1016/j.bbagen.2007.04.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2006] [Revised: 04/02/2007] [Accepted: 04/06/2007] [Indexed: 10/23/2022]
Abstract
Functional genomics is a central topic of current biological research, where a reverse genetic approach is one of the most promising strategies to discover functions of novel genes. Such an approach requires high-throughput methodologies to assess biological functions for a huge number of genes. We have developed a transfection array that permits parallel introduction of multiple plasmids separately into living cells. The feasibility of this array was examined in an assay system. Eleven genes were over-expressed alone, or in combination in vascular progenitors derived from embryonic stem cells. Endothelial differentiation of the cells was monitored through a stably transformed EGFP reporter construct that is expressed only in endothelial cells. Transcriptional activators that promote endothelial differentiation, such as Ets1 and Sox7, were identified. In addition, the assays also revealed an inhibitory effect on endothelial differentiation by several of the factors. These results demonstrate the feasibility of the transfection array for use in cell-based, high-throughput functional assays.
Collapse
Affiliation(s)
- Fumio Yamauchi
- Institute for Frontier Medical Sciences, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | | | | | | | | |
Collapse
|
11
|
Palmer EL, Miller AD, Freeman TC. Identification and characterisation of human apoptosis inducing proteins using cell-based transfection microarrays and expression analysis. BMC Genomics 2006; 7:145. [PMID: 16768789 PMCID: PMC1525185 DOI: 10.1186/1471-2164-7-145] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2006] [Accepted: 06/12/2006] [Indexed: 11/10/2022] Open
Abstract
Background Cell-based microarrays were first described by Ziauddin and Sabatini in 2001 as a powerful new approach for performing high throughput screens of gene function. An important application of cell-based microarrays is in screening for proteins that modulate gene networks. To this end, cells are grown over the surface of arrays of RNAi or expression reagents. Cells growing in the immediate vicinity of the arrayed reagents are transfected and the arrays can then be scanned for cells showing localised changes in function. Here we describe the construction of a large-scale microarray using expression plasmids containing human genes, its use in screening for genes that induce apoptosis when over-expressed and the characterisation of a number of these genes by following the transcriptional response of cell cultures during their induction of apoptosis. Results High-density cell-based arrays were successfully fabricated using 1,959 un-tagged open reading frames (ORFs) taken from the Mammalian Gene Collection (MGC) in mammalian expression vectors. The arrays were then used to screen for genes inducing apoptosis in Human Embryonic Kidney (HEK293T) cells. Using this approach, 10 genes were clearly identified and confirmed to induce apoptosis. Some of these genes have previously been linked to apoptosis, others not. The mechanism of action of three of the 10 genes were then characterised further by following the transcriptional events associated with apoptosis induction using expression profiling microarrays. This data demonstrates a clear pro-apoptotic transcriptional response in cells undergoing apoptosis and also suggests the use of common apoptotic pathways regardless of the nature of the over-expressed protein triggering cell death. Conclusion This study reports the design and use of the first truly large-scale cell-based microarrays for over-expression studies. Ten genes were confirmed to induce apoptosis, some of which were not previously known to possess this activity. Transcriptome analysis on three of the 10 genes demonstrated their use of similar pathways to invoke apoptosis.
Collapse
Affiliation(s)
- Ella L Palmer
- MRC Rosalind Franklin Centre for Genomics Research (RFCGR), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SB, UK
- MRC Laboratory for Molecular Cell Biology and Cell Biology Unit, University College London, Gower Street, London WC1E 6BT, UK
| | - Andrew D Miller
- Imperial College Genetic Therapies Centre, Department of Chemistry, Flowers Building, Armstrong Road, Imperial College London, London SW7 2AZ, UK
| | - Tom C Freeman
- MRC Rosalind Franklin Centre for Genomics Research (RFCGR), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SB, UK
| |
Collapse
|
12
|
van Beijnum JR, Eijgelaar WJ, Griffioen AW. Towards high-throughput functional target discovery in angiogenesis research. Trends Mol Med 2005; 12:44-52. [PMID: 16325471 DOI: 10.1016/j.molmed.2005.11.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2005] [Revised: 10/27/2005] [Accepted: 11/17/2005] [Indexed: 12/18/2022]
Abstract
Angiogenesis is a hallmark of malignancies and other proliferative diseases, and inhibition of this process is considered to be a promising treatment strategy. Classical gene-expression analyses performed during the past decade have generated vast lists of genes associated with disease but have so far yielded only limited novel therapeutic targets for clinical applications. Recently, the focus has shifted from target identification, based on gene-expression analysis, to identification of genes, based on the function of the encoded protein. Disease-target genes can now be identified in a high-throughput fashion based on functional properties that are directly related to the disease phenotype. This new approach significantly shortens the time span for the development of therapeutic applications from the laboratory bench to the hospital bedside.
Collapse
Affiliation(s)
- Judy R van Beijnum
- Angiogenesis Laboratory, Research Institute for Growth and Development, Department of Pathology, Maastricht University Hospital, PO Box 5800, 6202AZ Maastricht, The Netherlands
| | | | | |
Collapse
|