Low-Cost Fabrication of Centimeter-Scale Periodic Arrays of Single Plasmid DNA Molecules

Brett Kirkland,a Zhibin Wang,a Peipei Zhang,a Shin-ichiro Takebayashi,b Steven

Lenhert,b,c David M. Gilbert, b and Jingjiao Guan*a,c

†Department of Chemical and Biomedical Engineering, FAMU-FSU College of
Engineering, Florida State University, Tallahassee, Florida, 32310, United States
§Integrative NanoScience Institute, Florida State University, Tallahassee, Florida,
32310, United States
‡Department of Biological Science, Florida State University, Tallahassee, Florida,
32310, United States
Manipulation of single DNA molecules is essential to a number of advanced biomedical assays. Patterning single DNA molecules into a two-dimensional periodic array can facilitate high-throughput and highly parallel data acquisition and analysis. However, a low-cost, high-throughput fabrication method that allows generation of centimeter-scale periodic arrays of single unmodified DNA much longer than 2 kilobase pairs has not been reported. We have developed a low-cost microcontact printing method for fabricating a centimeter-scale periodic array of positively charged nanofeatures called nanopatches.(Figure 1) The nanopatches allowed immobilization of unmodified DNA molecules and largely restricted the occupancy of one 200 nm- wide nanopatch to a single plasmid DNA molecule of 11 kilobase pairs, so that a single- DNA array was produced. The immobilized DNA was amenable to enzymatic and physical manipulation, suggesting that this novel single-DNA array can be used for various biomedical assays such as sequencing of single DNA molecules and fiber assays.

Figure 1. Fabrication and characterization of nanopatches. PAA: sodium salt of polyacrylic acid. APTES: 3-aminopropyltriethoxysilane. (a) Schematic diagram of the process for generating a centimeter-wide array of single plasmid DNA. (b) Atomic force microscopy image of 196 nm-

diameter APTES nanopatches on glass. (c) Plot of nanopatch size versus PAA concentration. (d) Fluorescence micrograph of APTES nanopatches stained with fluorescein isothiocyanate.