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      Controlled deposition and combing of DNA across lithographically defined patterns on silicon

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          Summary

          We have developed a new procedure for efficient combing of DNA on a silicon substrate, which allows reproducible deposition and alignment of DNA molecules across lithographically defined patterns. The technique involves surface modification of Si/SiO 2 substrates with a hydrophobic silane by using gas-phase deposition. Thereafter, DNA molecules are aligned by dragging the droplet on the hydrophobic substrate with a pipette tip. Using this procedure, DNA molecules were stretched to an average value of 122% of their contour length. Furthermore, we demonstrated combing of ca. 900 nm long stretches of genomic DNA across nanofabricated electrodes, which was not possible by using other available combing methods. Similar results were also obtained for DNA–peptide conjugates. We suggest this method as a simple yet reliable technique for depositing and aligning DNA and DNA derivatives across nanofabricated patterns.

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          WSXM: a software for scanning probe microscopy and a tool for nanotechnology.

          In this work we briefly describe the most relevant features of WSXM, a freeware scanning probe microscopy software based on MS-Windows. The article is structured in three different sections: The introduction is a perspective on the importance of software on scanning probe microscopy. The second section is devoted to describe the general structure of the application; in this section the capabilities of WSXM to read third party files are stressed. Finally, a detailed discussion of some relevant procedures of the software is carried out.
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            Dynamic molecular combing: stretching the whole human genome for high-resolution studies.

            DNA in amounts representative of hundreds of eukaryotic genomes was extended on silanized surfaces by dynamic molecular combing. The precise measurement of hybridized DNA probes was achieved directly without requiring normalization. This approach was validated with the high-resolution mapping of cosmid contigs on a yeast artificial chromosome (YAC) within yeast genomic DNA. It was extended to human genomic DNA for precise measurements ranging from 7 to 150 kilobases, of gaps within a contig, and of microdeletions in the tuberous sclerosis 2 gene on patients' DNA. The simplicity, reproducibility, and precision of this approach makes it a powerful tool for a variety of genomic studies.
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              Stretching DNA with a receding meniscus: Experiments and models.

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                Author and article information

                Contributors
                Role: Guest Editor
                Role: Guest Editor
                Journal
                Beilstein J Nanotechnol
                Beilstein J Nanotechnol
                Beilstein Journal of Nanotechnology
                Beilstein-Institut (Trakehner Str. 7-9, 60487 Frankfurt am Main, Germany )
                2190-4286
                2013
                31 January 2013
                : 4
                : 72-76
                Affiliations
                [1 ]Institute of Physics and Nanotechnology, Aalborg University, 9220 Aalborg, Denmark
                Article
                10.3762/bjnano.4.8
                3566866
                23399926
                738d3064-fe27-4d7b-a958-13f2e74eae9a
                Copyright © 2013, Esmail Nazari and Gurevich; licensee Beilstein-Institut.

                This is an Open Access article under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                The license is subject to the Beilstein Journal of Nanotechnology terms and conditions: ( http://www.beilstein-journals.org/bjnano)

                History
                : 20 November 2012
                : 8 January 2013
                Categories
                Letter
                Nanoscience
                Nanotechnology

                afm,dna molecular combing,dna–peptide complexes,molecular electronics,surface modification

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