New and Old Technologies for Generation of Microarrays

A special issue of Microarrays (ISSN 2076-3905).

Deadline for manuscript submissions: closed (31 March 2015) | Viewed by 73073

Special Issue Editor


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Guest Editor
Albert-Ludwigs-University Freiburg, Center for Biological Systems Analysis (ZBSA), Habsburgerstrasse 49, D-79104 Freiburg, Germany
Interests: microarrays; label-free detection and binding kinetic determination; mobile applications; copying NGS chips into microarrays

Special Issue Information

Dear Colleagues,

Microarrays have been the first method of choice for highly parallel DNA and RNA analysis as well as in molecular interaction studies. Even though Next Generation Sequencing (NGS) is believed to soon be able to count each RNA copy in a single cell; microarrays are still irreplaceable, especially in the field of proteins, antibodies and small molecules. Nevertheless the increasing demand in throughput, molecular purity, robustness and effective production leads to improvement of the old techniques of microarray generation and to innovative ideas of ‘making’ microarrays in completely new ways. Therefore ‘the simple act’ of Microarray Generation is the focus of this Special Issue “Microarray Generation—Old Paths and New Ways”. It will highlight the old and successful paths such as light-synthesis, spot-synthesis and outline future improvements to the reader, but also offer a glimpse into what is emerging at the moment and what is yet to come, i.e., what new possibilities may become available in the not too distant future. You are invited to present new ways of microarray generation, but also to provide proof that the old ‘paths’ still bear potential for vast improvements.

With best regards,

Dr. Günter Roth
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microarrays is an international peer-reviewed open access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 350 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.


Keywords

  • microarray generation
  • DNA synthesis
  • RNA synthesis
  • protein synthesis
  • DAPA
  • NAPPA
  • PISA
  • microarray copying
  • light synthesis
  • spot synthesis
  • microarray printing

Published Papers (7 papers)

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Review

631 KiB  
Review
Microintaglio Printing for Soft Lithography-Based in Situ Microarrays
by Manish Biyani and Takanori Ichiki
Microarrays 2015, 4(3), 311-323; https://doi.org/10.3390/microarrays4030311 - 14 Jul 2015
Cited by 2 | Viewed by 8689
Abstract
Advances in lithographic approaches to fabricating bio-microarrays have been extensively explored over the last two decades. However, the need for pattern flexibility, a high density, a high resolution, affordability and on-demand fabrication is promoting the development of unconventional routes for microarray fabrication. This [...] Read more.
Advances in lithographic approaches to fabricating bio-microarrays have been extensively explored over the last two decades. However, the need for pattern flexibility, a high density, a high resolution, affordability and on-demand fabrication is promoting the development of unconventional routes for microarray fabrication. This review highlights the development and uses of a new molecular lithography approach, called “microintaglio printing technology”, for large-scale bio-microarray fabrication using a microreactor array (µRA)-based chip consisting of uniformly-arranged, femtoliter-size µRA molds. In this method, a single-molecule-amplified DNA microarray pattern is self-assembled onto a µRA mold and subsequently converted into a messenger RNA or protein microarray pattern by simultaneously producing and transferring (immobilizing) a messenger RNA or a protein from a µRA mold to a glass surface. Microintaglio printing allows the self-assembly and patterning of in situ-synthesized biomolecules into high-density (kilo-giga-density), ordered arrays on a chip surface with µm-order precision. This holistic aim, which is difficult to achieve using conventional printing and microarray approaches, is expected to revolutionize and reshape proteomics. This review is not written comprehensively, but rather substantively, highlighting the versatility of microintaglio printing for developing a prerequisite platform for microarray technology for the postgenomic era. Full article
(This article belongs to the Special Issue New and Old Technologies for Generation of Microarrays)
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752 KiB  
Review
Label and Label-Free Detection Techniques for Protein Microarrays
by Amir Syahir, Kenji Usui, Kin-ya Tomizaki, Kotaro Kajikawa and Hisakazu Mihara
Microarrays 2015, 4(2), 228-244; https://doi.org/10.3390/microarrays4020228 - 24 Apr 2015
Cited by 129 | Viewed by 15283
Abstract
Protein microarray technology has gone through numerous innovative developments in recent decades. In this review, we focus on the development of protein detection methods embedded in the technology. Early microarrays utilized useful chromophores and versatile biochemical techniques dominated by high-throughput illumination. Recently, the [...] Read more.
Protein microarray technology has gone through numerous innovative developments in recent decades. In this review, we focus on the development of protein detection methods embedded in the technology. Early microarrays utilized useful chromophores and versatile biochemical techniques dominated by high-throughput illumination. Recently, the realization of label-free techniques has been greatly advanced by the combination of knowledge in material sciences, computational design and nanofabrication. These rapidly advancing techniques aim to provide data without the intervention of label molecules. Here, we present a brief overview of this remarkable innovation from the perspectives of label and label-free techniques in transducing nano‑biological events. Full article
(This article belongs to the Special Issue New and Old Technologies for Generation of Microarrays)
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1061 KiB  
Review
NAPPA as a Real New Method for Protein Microarray Generation
by Paula Díez, María González-González, Lucía Lourido, Rosa M. Dégano, Nieves Ibarrola, Juan Casado-Vela, Joshua LaBaer and Manuel Fuentes
Microarrays 2015, 4(2), 214-227; https://doi.org/10.3390/microarrays4020214 - 24 Apr 2015
Cited by 17 | Viewed by 7501
Abstract
Nucleic Acid Programmable Protein Arrays (NAPPA) have emerged as a powerful and innovative technology for the screening of biomarkers and the study of protein-protein interactions, among others possible applications. The principal advantages are the high specificity and sensitivity that this platform offers. Moreover, [...] Read more.
Nucleic Acid Programmable Protein Arrays (NAPPA) have emerged as a powerful and innovative technology for the screening of biomarkers and the study of protein-protein interactions, among others possible applications. The principal advantages are the high specificity and sensitivity that this platform offers. Moreover, compared to conventional protein microarrays, NAPPA technology avoids the necessity of protein purification, which is expensive and time-consuming, by substituting expression in situ with an in vitro transcription/translation kit. In summary, NAPPA arrays have been broadly employed in different studies improving knowledge about diseases and responses to treatments. Here, we review the principal advances and applications performed using this platform during the last years. Full article
(This article belongs to the Special Issue New and Old Technologies for Generation of Microarrays)
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725 KiB  
Review
Up-to-Date Applications of Microarrays and Their Way to Commercialization
by Sarah Schumacher, Sandra Muekusch and Harald Seitz
Microarrays 2015, 4(2), 196-213; https://doi.org/10.3390/microarrays4020196 - 23 Apr 2015
Cited by 8 | Viewed by 9161
Abstract
This review addresses up-to-date applications of Protein Microarrays. Protein Microarrays play a significant role in basic research as well as in clinical applications and are applicable in a lot of fields, e.g., DNA, proteins and small molecules. Additionally they are on the way [...] Read more.
This review addresses up-to-date applications of Protein Microarrays. Protein Microarrays play a significant role in basic research as well as in clinical applications and are applicable in a lot of fields, e.g., DNA, proteins and small molecules. Additionally they are on the way to enter clinics in routine diagnostics. Protein Microarrays can be powerful tools to improve healthcare. An overview of basic characteristics to mediate essential knowledge of this technique is given. To reach this goal, some challenges still have to be addressed. A few applications of Protein Microarrays in a medical context are shown. Finally, an outlook, where the potential of Protein Microarrays is depicted and speculations how the future of Protein Microarrays will look like are made. Full article
(This article belongs to the Special Issue New and Old Technologies for Generation of Microarrays)
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544 KiB  
Review
Aptamer Microarrays—Current Status and Future Prospects
by Martin Witt, Johanna-Gabriela Walter and Frank Stahl
Microarrays 2015, 4(2), 115-132; https://doi.org/10.3390/microarrays4020115 - 24 Mar 2015
Cited by 40 | Viewed by 8476
Abstract
Microarray technologies are state of the art in biological research, which requires fast genome, proteome and transcriptome analysis technologies. Often antibodies are applied in protein microarrays as proteomic tools. Since the generation of antibodies against toxic targets or small molecules including organic compounds [...] Read more.
Microarray technologies are state of the art in biological research, which requires fast genome, proteome and transcriptome analysis technologies. Often antibodies are applied in protein microarrays as proteomic tools. Since the generation of antibodies against toxic targets or small molecules including organic compounds remains challenging the use of antibodies may be limited in this context. In contrast to this, aptamer microarrays provide alternative techniques to circumvent these limitations. In this article we review the latest developments in aptamer microarray technology. We discuss similarities and differences between DNA and aptamer microarrays and shed light on the post synthesis immobilization of aptamers including corresponding effects on the microarray performance. Finally, we highlight current limitations and future prospects of aptamer microarray technology. Full article
(This article belongs to the Special Issue New and Old Technologies for Generation of Microarrays)
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862 KiB  
Review
Reverse Phase Protein Arrays—Quantitative Assessment of Multiple Biomarkers in Biopsies for Clinical Use
by Stefanie Boellner and Karl-Friedrich Becker
Microarrays 2015, 4(2), 98-114; https://doi.org/10.3390/microarrays4020098 - 24 Mar 2015
Cited by 44 | Viewed by 9110
Abstract
Reverse Phase Protein Arrays (RPPA) represent a very promising sensitive and precise high-throughput technology for the quantitative measurement of hundreds of signaling proteins in biological and clinical samples. This array format allows quantification of one protein or phosphoprotein in multiple samples under the [...] Read more.
Reverse Phase Protein Arrays (RPPA) represent a very promising sensitive and precise high-throughput technology for the quantitative measurement of hundreds of signaling proteins in biological and clinical samples. This array format allows quantification of one protein or phosphoprotein in multiple samples under the same experimental conditions at the same time. Moreover, it is suited for signal transduction profiling of small numbers of cultured cells or cells isolated from human biopsies, including formalin fixed and paraffin embedded (FFPE) tissues. Owing to the much easier sample preparation, as compared to mass spectrometry based technologies, and the extraordinary sensitivity for the detection of low-abundance signaling proteins over a large linear range, RPPA have the potential for characterization of deregulated interconnecting protein pathways and networks in limited amounts of sample material in clinical routine settings. Current aspects of RPPA technology, including dilution curves, spotting, controls, signal detection, antibody validation, and calculation of protein levels are addressed. Full article
(This article belongs to the Special Issue New and Old Technologies for Generation of Microarrays)
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1324 KiB  
Review
Particle-Based Microarrays of Oligonucleotides and Oligopeptides
by Alexander Nesterov-Mueller, Frieder Maerkle, Lothar Hahn, Tobias Foertsch, Sebastian Schillo, Valentina Bykovskaya, Martyna Sedlmayr, Laura K. Weber, Barbara Ridder, Miriam Soehindrijo, Bastian Muenster, Jakob Striffler, F. Ralf Bischoff, Frank Breitling and Felix F. Loeffler
Microarrays 2014, 3(4), 245-262; https://doi.org/10.3390/microarrays3040245 - 28 Oct 2014
Cited by 10 | Viewed by 14193
Abstract
In this review, we describe different methods of microarray fabrication based on the use of micro-particles/-beads and point out future tendencies in the development of particle-based arrays. First, we consider oligonucleotide bead arrays, where each bead is a carrier of one specific sequence [...] Read more.
In this review, we describe different methods of microarray fabrication based on the use of micro-particles/-beads and point out future tendencies in the development of particle-based arrays. First, we consider oligonucleotide bead arrays, where each bead is a carrier of one specific sequence of oligonucleotides. This bead-based array approach, appearing in the late 1990s, enabled high-throughput oligonucleotide analysis and had a large impact on genome research. Furthermore, we consider particle-based peptide array fabrication using combinatorial chemistry. In this approach, particles can directly participate in both the synthesis and the transfer of synthesized combinatorial molecules to a substrate. Subsequently, we describe in more detail the synthesis of peptide arrays with amino acid polymer particles, which imbed the amino acids inside their polymer matrix. By heating these particles, the polymer matrix is transformed into a highly viscous gel, and thereby, imbedded monomers are allowed to participate in the coupling reaction. Finally, we focus on combinatorial laser fusing of particles for the synthesis of high-density peptide arrays. This method combines the advantages of particles and combinatorial lithographic approaches. Full article
(This article belongs to the Special Issue New and Old Technologies for Generation of Microarrays)
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