DNA detection with a polymeric nanochannel device† Paola Fanzio, * ab Valentina Mussi, a Chiara Manneschi, a Elena Angeli, a Giuseppe Firpo, a Luca Repetto a and Ugo Valbusa a Received 22nd March 2011, Accepted 2nd June 2011 DOI: 10.1039/c1lc20243j We present the development and the electrical characterization of a polymeric nanochannel device. Standard microfabrication coupled to Focused Ion Beam (FIB) nanofabrication is used to fabricate a silicon master, which can be then replicated in a polymeric material by soft lithography. Such an elastomeric nanochannel device is used to study DNA translocation events during electrophoresis experiments. Our results demonstrate that an easy and low cost fabrication technique allows creation of a low noise device for single molecule analysis. Introduction The increasing interest in nanopore technology relates to the great potentiality of this kind of device for label-free single molecule analysis and sensing. 1 The detection mechanism is, in fact, extremely simple. The nanopore is mounted in a fluidic cell separating two electrolyte filled reservoirs; two electrodes allow to apply a voltage across the nanopore and to collect the ionic current. Based on the Coulter counter principle, molecules are detected as transient variations in the current during a translocation event. This modulation is directly caused by the passage of the molecules via steric and electrostatic effects, 2 the detectable signal resulting from the balance of an ionic current reduction effect due to the channel physical obstruction, and an ionic conductance increase due to the net charge carried by the molecule itself. In the 1990s, it was proposed to use nanopores for ultra rapid DNA sequencing. 3 In principle, each single nucleotide alters the ionic current in a characteristic way, so that it could be possible to read the DNA sequence by just analysing the current fluctu- ations during a translocation event. However, to achieve this goal it is necessary to overcome some problematic issues: the detection of the small differences in the current level produced by the translocation of each nucleotide requires low noise record- ings. But, the high speed of the molecules forces us to use a high sampling rate, which increases the noise. Nevertheless, nanopore devices are also used as biosensing tools. 4 Several experiments were performed allowing DNA strand length determination, 5 discrimination between ssDNA and dsDNA, 5–7 detection of complementary polynucleotides by engineered nanopores 8 and detection of single nucleotides. 9 Moreover, the range of analytes which can be detected is really wide: from small molecules to organic polymers, peptides, proteins and enzymes. 4 Different fabrication techniques were proposed and developed to obtain nanopores. The first device, reported by Kasianowicz and co-workers, 5 was based on a-haemolysin, which spontane- ously self assembles in a lipid bilayer forming a biological nanopore. Then, solid state nanopores have been introduced, improving chemical, mechanical and thermal robustness of the final device. 10 Usually, the pore is produced in a thin solid state membrane (SiO 2 , Si 3 N 4 ) by ion beam sculpting, 11 FIB milling or electron beam sputtering. 12 Electron beams and ion beams can also be used to reduce the final dimension of the pore by fluid- izing the surface adatoms, 13 but these remain expensive fabrica- tion techniques. Moreover, surface chemical modification can be exploited to improve the nanopore detection capabilities, by removing undesired properties, reducing the effective dimen- sion 14 and giving selectivity to the device to identify specific biomolecules or analyze specific interactions. 4 This emerging research field will certainly have a great impact on bioanalysis and on the study of chemical interactions at the nanoscale. Track-etching is, instead, the most used production technique for polymeric nanopores. 15 It has been mainly applied to prepare pores in polymer films such as poly(ethylene terephthalate) (PET), polycarbonate (PC) and polyimide (PI), as well as mica. In this case, a dielectric film is first irradiated with energetic heavy ions. Subsequently, damaged zones created during irra- diation are chemically etched to obtain pores with the desired nanoscale dimensions. The geometry of track-etched nanopores depends on the specific etching approach: both cylindrical and conical pores can be obtained. Here we present the development and the electrical charac- terization of a polymeric nanochannel device for single molecule sensing, also showing preliminary results on DNA translocation event recording. A FIB is used to fabricate a nanochannel on a pre-patterned silicon master. Soft lithography is then applied to a Nanomed Labs, Dipartimento di Fisica, Universit  a di Genova, via Dodecaneso 33, 16146 Genova, Italy. E-mail: paola.fanzio@iit.it; Fax: +390105737382; Tel: +390105737382 b Italian Institute of Technology, via Morego 3, 16163 Genova, Italy † Electronic supplementary information (ESI) available. See DOI: 10.1039/c1lc20243j This journal is ª The Royal Society of Chemistry 2011 Lab Chip Dynamic Article Links C < Lab on a Chip Cite this: DOI: 10.1039/c1lc20243j www.rsc.org/loc PAPER Downloaded by UNIVERSITA DI GENOVA - CCSBA on 13 July 2011 Published on 12 July 2011 on http://pubs.rsc.org | doi:10.1039/C1LC20243J View Online