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A versatile method for generating single DNA molecule patterns: Through the combination of directed capillary assembly and (micro/nano) contact printing

  • Aline Cerf (a1), Xavier Dollat (a1), Jérôme Chalmeau (a2), Angélique Coutable (a3) and Christophe Vieu (a4)...

One of the challenges in the development of molecular scale devices is the integration of nano-objects or molecules onto desired locations on a surface. This integration comprises their accurate positioning, their alignment, and the preservation of their functionality. Here, we proved how capillary assembly in combination with soft lithography can be used to perform DNA molecular combing to generate chips of isolated DNA strands for genetic analysis and diagnosis. The assembly of DNA molecules is achieved on a topologically micropatterned polydimethylsiloxane stamp inducing almost simultaneously the trapping and stretching of single molecules. The DNA molecules are then transferred onto aminopropyltriethoxysilane-coated surfaces. In fact, this technique offers the possibility to tightly control the experimental parameters to direct the assembly process. This technique does not induce a selection in size of the objects, therefore it can handle complex solutions of long (tens of kbp) but also shorter (a few thousands of bp) molecules directly in solution to allow the construction of future one-dimensional nanoscale building templates.

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1.Kricka L.J.: Microchips, microarrays, biochips and nanochips: Personal laboratories for the 21st century. Clin. Chim. Acta 307, 219 (2001).
2.Seeman N.C.: DNA in a material world. Nature 421, 427 (2003).
3.Niemeyer C.M.: Progress in “engineering up” nanotechnology devices utilizing DNA as a construction material. Appl. Phys., A: Mater. Sci. Process. 68, 119 (1999).
4.Lund K., Manzo A.J., Dabby N., Michelotti N., Johnson-Buck A., Nangreave J., Taylor S., Pei R., Stojanovic M.N., Walter N.G., Winfree E., and Yan H.: Molecular robots guided by prescriptive landscapes. Nature 465, 206 (2010).
5.Gerhold D., Rushmore T., and Caskey C.T.: DNA chips: Promising toys have become powerful tools. Trends Biochem. Sci. 24, 168 (1999).
6.Cuzin M.: DNA chips: A new tool for genetic analysis and diagnostics. Transfus. Clin. Biol. 8, 291 (2001).
7.Braun E., Eichen Y., Sivan U., and Ben-Yoseph G.: DNA templated self-assembly of a conductive wire connecting two electrodes. Nature 391, 775 (1998).
8.Keren K., Krueger M., Gilad R., Ben-Yoseph G., Sivan U., and Braun E.: Sequence-specific molecular lithography on single DNA molecules. Science 297, 72 (2002).
9.Deng Z.X. and Mao C.D.: DNA-templated fabrication of 1D parallel and 2D crossed metallic nanowire arrays. Nano Lett. 3, 1545 (2003).
10.Monson C.F. and Woolley A.T.: DNA-templated construction of copper nanowires. Nano Lett. 3, 359 (2003).
11.Nguyen K., Monteverde M., Filoramo A., Goux-Capes L., Lyonnais S., Jegou P., Viel P., Goffman M., and Bourgoin J-P.: Synthesis of thin and highly conductive DNA-based palladium nanowires. Adv. Mater. 20, 1099 (2008).
12.Köhler J.M., Csáki A., Reichert J., Möller R., Straube W., and Fritzsche W.: Selective labeling of oligonucleotide monolayers by metallic nanobeads for fast optical readout of DNA-chips. Sens. Actuators B 76, 166 (2001).
13.Bensimon D., Bensimon A., and Heslot F.: Process for aligning, adhering and stretching nucleic acid strands on a support surface by passage through a meniscus. U.S. Patent No. 5 840 862 (1998).
14.Bensimon D., Simon A.J., Croquette V., and Bensimon A.: Stretching DNA with a receding meniscus: Experiments and models. Phys. Rev. Lett. 74, 4754 (1995).
15.Bensimon A., Simon A., Chiffaudel A., Croquette V., Heslot F., and Bensimon D.: Alignment and sensitive detection of DNA by a moving interface. Science 265, 2096 (1994).
16.Lyubchenko Y.L., Gall A.A., Shlyakhtenko L.S., Harrington R.E., Jacobs B.L., Oden S.M., and Lindsay P.I.: Atomic force microscopy imaging of double stranded DNA and RNA. J. Biomol. Struct. Dyn. 10(3), 589 (1992).
17.Vesenka J., Guthold M., Tang C.L., Keller D., Delaine E., and Bustamante C.: Substrate preparation for reliable imaging of DNA molecules with scanning force microscope. Ultramicroscopy 4244(2), 1243 (1992).
18.Bustamante C., Vesenka J., Tang C.L., Rees W., Gothold M., and Keller R.: Circular DNA molecules imaged in air by scanning force microscopy. Biochemistry 31(1), 22 (1992).
19.Thundat T., Allison D.P., Warmack R.J., Brown G.M., Jacobson K.B., Schrick J.J., and Ferrell T.L.: Atomic force microscopy of DNA on mica and chemically modified mica. Scanning Microsc. 6(4), 911 (1992).
20.Kaji N., Tezuka Y., Takamura Y., Ueda M., Nishimoto T., Nakanishi H., Horiike Y., and Baba Y.: Separation of long DNA molecules by quartz nanopillar chips under a direct current electric field. Anal. Chem. 76(1), 15 (2004).
21.Maubach G., Csaki A., Seidel R., Mertig M., Pompe W., Born D., and Fritzsche W.: Controlled positioning of one individual DNA molecule in an electrode setup based on self-assembly and microstructuring. Nanotechnology 14, 546 (2003).
22.Washizu M. and Kurosawa O.: Electrostatic manipulation of DNA in microfabricated structures. IEEE Trans. Ind. Appl. 26(6), 1165 (1990).
23.Wolff A., Leiterer C., Csaki A., and Fritzsche W.: Dielectrophoretic manipulation of DNA in microelectrode gaps for single-molecule constructs. Front. Biosci. 13, 6834 (2008).
24.Petit C.A.P. and Carbeck J.D.: Combing of molecules in microchannels (COMMIC): A method for micropatterning and orienting molecules of DNA on a surface. Nano Lett. 3, 1141 (2003).
25.Opitz J., Braun F., Seidel R., Pompe W., Voit B., and Mertig M.: Site-specific binding and stretching of DNA molecules at UV-light patterned aminoterpolymer films. Nanotechnology 15, 717 (2004).
26.Gad M., Sugiyama S., and Ohtani T.: Method for patterning stretched DNA molecules on mica surfaces by soft lithography. J. Biomol. Struct. Dyn. 2, 387 (2003).
27.Björk P., Holmström S., and Inganäs O.: Soft lithographic printing of patterns of stretched DNA and DNA/electronic polymer wires by surface-energy modification and transfer. Small 89, 1068 (2006).
28.Nakao H., Shiigi H., Yamamoto Y., Tokonami S., Nagaoka T., Sugiyama S., and Ohtani T.: Highly ordered assemblies of Au nanoparticles organized on DNA. Nano Lett. 3, 1391 (2003).
29.Nakao H., Gad M., Sugiyama S., Otobe K., and Ohtani T.: Transfer-printing of highly aligned DNA nanowires. JACS 125, 7162 (2003).
30.Guan J. and Lee L.J.: Generating highly ordered DNA nanostrand arrays. PNAS. 102, 18321 (2005).
31.Malaquin L., Kraus T., Schmid H., Delamarche E., and Wolf H.: Controlled particle placement through convective and capillary assembly. Langmuir 23, 11513 (2007).
32.Xia Y. and Whitesides G.M.: Soft lithography. Angew. Chem. Int. Ed. 37, 550 (1998).
33.Kraus T., Malaquin L., Schmid H., Riess W., Spencer N.D., and Wolf H.: Nanoparticle printing with single particle resolution. Nat. Nanotechnol. 2, 570 (2007).
34.Smith D.E., Perkins T.T., and Chu S.: Dynamical scaling of DNA diffusion coefficients. Macromolecules 29, 1372 (1996).
35.Perkins T., Smith D., Larson R., and Chu S.: Stretching of a single tethered polymer in a uniform flow. Science 268, 83 (1995).
36.Tegenfeldt J.O., Prinz C., Cao H., Chou S., Reisner W.W., Riehn R., Wang Y.M., Cox E.C., Sturm J.C., Silberzan P., and Austin R.H.: The dynamics of genomic-length DNA molecules in 100 nm channels. PNAS. 101, 10979 (2004).
37.Armbrust E.V., Berges J.A., Bowler C., Green B.R., Martinez D., Putnam N.H., Zhou S., Allen A.E., Apt K.E., Bechner M., Brzezinski M.A., Chaal B.K., Chiovitti A., Davis A.K., Demarest M.S., Detter J.C., Glavina T., Goodstein G., Hadi M.Z., Hellsten U., Hildebrand M., Jenkins B.D., Jurka J., Kapitonov V.V., Kroger N., Lau W.W.Y., Lane T.W., Larimer F.W., Lippmeier J.C., Lucas S., Medina M., Montsant A., Obornik M., Parker M.S., Palenik B., Pazour G.J., Richardson P.M., Rynearson T.A., Saito M.A., Schwartz D.C., Thamatrakoln K., Valentin K., Vardi A., Wilkerson F.P., and Rokhsar D.S.: The genome of the diatom Thalassiosira Pseudonana: Ecology, evolution, and metabolism. Science 306, 79 (2004).
38.Dimalanta E.T., Lim A., Runnheim R., Lamers C., Churas C., Forrest D.K., de Pablo J.J., Graham M.D., Coppersmith S.N., Goldstein S., and Schwartz D.C.: A microfluidic system for large DNA molecule arrays. Anal. Chem. 76, 5293 (2004).
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Journal of Materials Research
  • ISSN: 0884-2914
  • EISSN: 2044-5326
  • URL: /core/journals/journal-of-materials-research
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