Stretching DNA in polymer nanochannels fabricated by thermal imprint in PMMA

We present results regarding the fast and inexpensive fabrication of polymer biochips for investigating the statics and dynamics of DNA confined in nanochannels. The biochips have been fabricated by means of nanoimprint lithography (NIL) in low molecular weight polymethyl methacrylate (PMMA) using a 4 inch diameter two-level hybrid stamp. The fluidic structures were sealed using thermal polymer fusion bonding. The stamp has nanometer- and micrometer-sized protrusions defined in a thermally grown SiO(2) layer and the sol-gel process derived duromeric hybrid polymer Ormocomp, respectively. The stamp is compatible with molecular vapor deposition (MVD), used for applying a durable chlorosilane based antistiction coating, and allows for imprint up to a temperature of 270 °C. The extension of YOYO-1 stained T4 GT7 bacteriophage DNA inside the PMMA nanochannels has been experimentally investigated using epi-fluorescence microscopy. The measured average extension length amounts to 20% of the full contour length with a standard deviation of 4%. These results are in good agreement with results obtained by stretching DNA in conventional fused silica nanochannels.

[1]  L. Jay Guo,et al.  Recent progress in nanoimprint technology and its applications , 2004 .

[2]  Anders Kristensen,et al.  Combined electron beam and UV lithography in SU-8 , 2007 .

[3]  A combined-nanoimprint-and-photolithography patterning technique , 2004 .

[4]  Holger Becker,et al.  Fabrication of plastic microchips by hot embossing. , 2002, Lab on a chip.

[5]  Christian H. Reccius,et al.  Conformational analysis of single DNA molecules undergoing entropically induced motion in nanochannels. , 2006, Biophysical journal.

[6]  Herbert Wolter,et al.  Synthesis, properties and applications of inorganic–organic copolymers (ORMOCER®s) , 1999 .

[7]  R. Larson,et al.  Stretching of a single tethered polymer in a uniform flow. , 1995, Science.

[8]  A. Larsson,et al.  Influence of optical probing with YOYO on the electrophoretic behavior of the DNA molecule , 1996, Electrophoresis.

[9]  N. Cozzarelli,et al.  Modeling of long‐range electrostatic interactions in DNA , 1995, Biopolymers.

[10]  Oliver Geschke,et al.  CO(2)-laser micromachining and back-end processing for rapid production of PMMA-based microfluidic systems. , 2002, Lab on a chip.

[11]  B. Bilenberg,et al.  High resolution 100kV electron beam lithography in SU-8 , 2006 .

[12]  G. Whitesides,et al.  New approaches to nanofabrication: molding, printing, and other techniques. , 2005, Chemical reviews.

[13]  Morten Bo Lindholm Mikkelsen,et al.  Double thermal oxidation scheme for the fabrication of SiO2 nanochannels , 2007 .

[14]  C. Chou,et al.  Fabrication of Size-Controllable Nanofluidic Channels by Nanoimprinting and Its Application for DNA Stretching , 2004 .

[15]  Alexander S. Mukasyan,et al.  Current Opinion in Solid State and , 2009 .

[16]  Pascal Silberzan,et al.  From the Cover: The dynamics of genomic-length DNA molecules in 100-nm channels. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[17]  Michelle D. Wang,et al.  Estimating the persistence length of a worm-like chain molecule from force-extension measurements. , 1999, Biophysical journal.

[18]  Alexander N. Glazer,et al.  Stable dye–DNA intercalation complexes as reagents for high-sensitivity fluorescence detection , 1992, Nature.

[19]  Anders Kristensen,et al.  Nanoimprint lithography in the cyclic olefin copolymer, Topas®, a highly ultraviolet-transparent and chemically resistant thermoplast , 2004 .

[20]  Nam-Trung Nguyen,et al.  Fabrication of planar nanofluidic channels in a thermoplastic by hot-embossing and thermal bonding. , 2007, Lab on a chip.

[21]  J. Joanny,et al.  Dynamics of Semiflexible Polymers in Solution , 1980 .

[22]  B. Bilenberg,et al.  Comparison of high resolution negative electron beam resists , 2006 .

[23]  R. Sinden.  DNA Structure and Function , 1994 .

[24]  S. Smith,et al.  Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads. , 1992, Science.

[25]  R. Gutmann,et al.  Adhesive wafer bonding , 2006 .

[26]  Anders Kristensen,et al.  Topas based lab-on-a-chip microsystems fabricated by thermal nanoimprint lithography , 2005 .

[27]  Anders Kristensen,et al.  PMMA to SU-8 bonding for polymer based lab-on-a-chip systems with integrated optics , 2004 .

[28]  Erwin Frey,et al.  Statics and dynamics of single DNA molecules confined in nanochannels. , 2005, Physical review letters.

[29]  S. Chou,et al.  Roller nanoimprint lithography , 1998 .

[30]  Frantisek Svec,et al.  Injection molded microfluidic chips featuring integrated interconnects. , 2006, Lab on a chip.

[31]  T. Duke,et al.  Electrohydrodynamic Stretching of DNA in Confined Environments , 1998 .

[32]  P. Gennes.  Scaling Concepts in Polymer Physics , 1979 .

[33]  H. Flyvbjerg,et al.  Nanoconfinement-enhanced conformational response of single DNA molecules to changes in ionic environment. , 2007, Physical review letters.

[34]  L. J. Guo,et al.  Nanoimprint Lithography: Methods and Material Requirements , 2007 .

[35]  Jongyoon Han,et al.  Double-Stranded DNA Diffusion in Slitlike Nanochannels , 2006 .

[36]  Robert Riehn,et al.  Restriction mapping in nanofluidic devices. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[37]  Aigars Piruska,et al.  The autofluorescence of plastic materials and chips measured under laser irradiation. , 2005, Lab on a chip.

[38]  Jianping Fu,et al.  Molecular sieving in periodic free-energy landscapes created by patterned nanofilter arrays. , 2006, Physical review letters.