Directed organization of DNA filaments in a soft matter template.

We have developed a noninvasive, all-optical, holographic technique for permanently aligning liquid crystalline DNA filaments in a microperiodic template realized in soft-composite (polymeric) materials. By combining optical intensity holography with a selective microfluidic etching process, a channelled microstructure has been realized which enables self-assembly of DNA. The striking chemicophysical properties of the structure immobilize the DNA filaments within the microchannels without the need of any kind of surface chemistry or functionalization. Polarized optical, confocal, and electronic microscopies have been used for characterizing the DNA geometry inside the microchannels in terms of birefringence, fluorescence, and nanoscale organization properties. In particular, observation of a far-field diffraction pattern confirms a periodic organization of the DNA filaments inside the polymeric template.

[1]  S. Mouritsen,et al.  Use of psoralens for covalent immobilization of biomolecules in solid phase assays. , 1994, Bioconjugate chemistry.

[2]  P. Hagerman.  Flexibility of DNA. , 1988, Annual review of biophysics and biophysical chemistry.

[3]  Noel A. Clark,et al.  End-to-End Stacking and Liquid Crystal Condensation of 6– to 20–Base Pair DNA Duplexes , 2007, Science.

[4]  K. Downing,et al.  Cryoelectron microscopy of λ phage DNA condensates in vitreous ice: The fine structure of DNA toroids , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[5]  Myung Chul Choi,et al.  Ordered patterns of liquid crystal toroidal defects by microchannel confinement. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[6]  A. Boisen,et al.  Immobilisation of DNA to polymerised SU-8 photoresist. , 2006, Biosensors & bioelectronics.

[7]  R. Franklin,et al.  Molecular Configuration in Sodium Thymonucleate , 1953, Nature.

[8]  C. Dekker,et al.  Dynamics of RecA filaments on single-stranded DNA , 2009, Nucleic acids research.

[9]  M. T. Martínez,et al.  Label-free DNA biosensors based on functionalized carbon nanotube field effect transistors. , 2009, Nano letters.

[10]  R. Rill.  Liquid crystalline phases in concentrated aqueous solutions of Na+ DNA. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[11]  R. Larson,et al.  Protein-assisted stretching and immobilization of DNA molecules in a microchannel. , 2006, Nano letters.

[12]  Toshio Nakamura,et al.  Voltammetric study of interaction of Co(phen)33+ with DNA at gold nanoparticle self-assembly electrode , 2004 .

[13]  M. Miyazaki,et al.  Direct observation of long-strand DNA conformational changing in microchannel flow and microfluidic hybridization assay. , 2004, Analytical biochemistry.

[14]  Y. Chang,et al.  Carbon nanotube DNA sensor and sensing mechanism. , 2006, Nano letters.

[15]  Eric S. Lander,et al.  Journey to the Center of Biology , 2000, Science.

[16]  L. Onsager.  THE EFFECTS OF SHAPE ON THE INTERACTION OF COLLOIDAL PARTICLES , 1949 .

[17]  E. Sambriski,et al.  Sequence effects in the melting and renaturation of short DNA oligonucleotides: structure and mechanistic pathways , 2009, Journal of physics. Condensed matter : an Institute of Physics journal.

[18]  D. Psaltis,et al.  Microfluidic assays for DNA manipulation based on a block copolymer immobilization strategy. , 2010, Biomacromolecules.

[19]  Kai Xu,et al.  Recent Development of Nano-Materials Used in DNA Biosensors , 2009, Sensors.

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

[21]  C. Bustamante,et al.  Overstretching B-DNA: The Elastic Response of Individual Double-Stranded and Single-Stranded DNA Molecules , 1996, Science.

[22]  Giuseppe Strangi,et al.  Universal soft matter template for photonic applications , 2011 .

[23]  C. Bustamante,et al.  Masking generates contiguous segments of metal-coated and bare DNA for scanning tunneling microscope imaging. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[24]  M. Washizu,et al.  Electrostatic manipulation of DNA in microfabricated structures , 1989, Conference Record of the IEEE Industry Applications Society Annual Meeting,.

[25]  T. G. Drummond,et al.  Electrochemical DNA sensors , 2003, Nature Biotechnology.

[26]  Eric C Greene,et al.  Organized arrays of individual DNA molecules tethered to supported lipid bilayers. , 2006, Langmuir : the ACS journal of surfaces and colloids.

[27]  Susan R. Mikkelsen,et al.  Covalent immobilization of DNA onto glassy carbon electrodes , 1992 .

[28]  R. Caputo,et al.  Characterization of the diffraction efficiency of new holographic gratings with a nematic film-polymer-slice sequence structure , 2004 .

[29]  John A. Tainer,et al.  X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution , 2007, Quarterly Reviews of Biophysics.

[30]  H. Yowanto,et al.  Electronic detection of nucleic acids: a versatile platform for molecular diagnostics. , 2001, The Journal of molecular diagnostics : JMD.

[31]  R. Caputo,et al.  Development of a new kind of switchable holographic grating made of liquid-crystal films separated by slices of polymeric material. , 2004, Optics letters.

[32]  K. Yoshikawa,et al.  Probing biopolymer conformation by metallization with noble metals , 2006 .