Photolithographic Synthesis of High-Density DNA and RNA Arrays on Flexible, Transparent, and Easily Subdivided Plastic Substrates

Abstract

The photolithographic fabrication of high-density DNA and RNA arrays on flexible and transparent plastic substrates is reported. The substrates are thin sheets of poly(ethylene terephthalate) (PET) coated with crosslinked polymer multilayers that present hydroxyl groups suitable for conventional phosphoramidite-based nucleic acid synthesis. We demonstrate that by modifying MAS procedures to accommodate the physical and chemical properties of these materials, it is possible to synthesize plastic-backed oligonucleotide arrays with feature sizes as small as 14 × 14 μm and feature densities in excess of 125 000/cm2, similar to specifications attainable using rigid substrates such as glass or glassy carbon. These plastic-backed arrays are tolerant to a wide range of hybridization temperatures, and improved synthetic procedures are described that enable the fabrication of arrays with sequences up to 50 nucleotides in length. These arrays hybridize with S/N ratios comparable to those fabricated on otherwise identical arrays prepared on glass or glassy carbon. This platform supports the enzymatic synthesis of RNA arrays and proof-of-concept experiments are presented showing that the arrays can be readily sub-divided into smaller arrays (or ‘millichips’) using common laboratory-scale laser cutting tools. These results expand the utility of oligonucleotide arrays fabricated on plastic substrates and open the door to new potential applications for these important bioanalytical tools.

Flexible Substrate-Based Devices for Point-of-Care Diagnostics

“…Examples of polymers include polydimethylsiloxane (PDMS), poly(methyl methacrylate) (PMMA), polypropylene (PP), polyimide (PI), hydrogel, and polystyrene (PS), which are transparent and can be used in optical detection platforms such as photonic crystal-based sensing [11], surface plasmon resonance (SPR) [12] or photonic nanosensing [13]. Other polymers, such as polyethylene terephthalate (PET), are generally stable at temperatures up to 180°C and have high heat conductivity [14], which is ideal for temperature-controlled biological reactions. Polymers such as polycarbonate (PC), PET, cyclic olefin copolymer (COC), and poly(methyl methacrylate) (PMMA) are electrochemically inert and can be used for developing electrochemical-based diagnostic devices [15].…”

Layer-by-Layer Assembly of Amine-Reactive Multilayers Using an Azlactone-Functionalized Polymer and Small-Molecule Diamine Linkers

“…14,19 This combination of features renders PEI/PVDMA multilayers useful as platforms for the design of new types of functional and customizable nano/biointerfaces that are stable in harsh and chemically complex environments (e.g., in high ionic strength media, at extremes of pH, and in the presence of high concentrations of surface-active species). 11,14,17,19 …”

Covalently Crosslinked and Physically Stable Polymer Coatings with Chemically Labile and Dynamic Surface Features Fabricated by Treatment of Azlactone-Containing Multilayers with Alcohol-, Thiol-, and Hydrazine-Based Nucleophiles

“…24 Solution-phase functionalization of PVDMA was performed using PVDMA synthesized in the absence of cyclic azlactone-functionalized oligomers. 22 Branched poly(ethyleneimine) (PEI; MW ~25,000), ethylenediamine (99%), n-decylamine (95%), ndecanol (99%), decanethiol (96%), pyrenebutanol (99%), pyrene (98%), 1,8-diazabicycloundec- 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 General Considerations. 1 H NMR spectroscopy was performed using a Bruker Avance-500 (500 MHz) spectrometer using a relaxation delay of 10 seconds.…”