Flexible Substrates For DNA Arrays

Array fabrication technologies date back to the early 1990s when Affymetrix first used ultraviolet light to control the stepwise synthesis of biopolymers from a surface.[1] The most commercially successful result of this technology was high-density arrays of DNA. At the time, DNA arrays were one of the most efficient ways to detect and measure nucleic acids on a genome-wide scale.

The underlying array substrates were optimized with such analytical experiments in mind. Silanized glass quickly emerged as the industry-standard surface because it was affordable, used straightforward chemistry, and can be manufactured with a high level of precision.

The ideal surface chemistry can nonetheless vary widely with the experiment.  Emergent array applications often require hydrolysis resistant bonds between the surface and the DNA or strategies for reducing non-specific analyte binding. These needs have motivated interest in developing alternative solid support chemistry.

The use of flexible array substrates was first explored in 2012.[2] The concept was to coat a plastic film with covalently crosslinked polymer bilayers, which could then be treated to display the hydroxyl groups needed for DNA synthesis. A key advantage of arrays made on plastic films is that they easily can be cut into subsections with a laser, dramatically increasing the throughput of fabrication.[3]

This approach worked quite well for arrays comprised of short (~ 50 nucleotides) sequences, but it was difficult to synthesize longer DNA sequences without degrading the bilayers. Recently published work highlights how DNA can instead be synthesized from the ends of the polymer chains in a polyester film.[4]

The concept is to base-treat the polyester (poly(ethylene terephthalate), or PET, was used in the study) so that a low level of degradation exposes the hydroxyl groups needed to initiate the array synthesis. The substrate is stable throughout the fabrication, enabling the synthesis of longer (nearly 90 nucleotides) DNA sequences. The polyester substrate performs similarly to silanized glass for detecting fluorescently-labeled complementary DNA sequences, with a comparable density of molecules on the surface.

The major field of use for this substrate is likely to be synthetic biology. One of the fastest growing areas of array technologies is gene synthesis. For gene synthesis, the DNA oligonucleotides are typically cleaved or amplified from the array surface into solution, then enzymatically assembled into a full-length gene.[5] While arrays are one of the most affordable sources of oligonucleotides, most array synthesizers are overpowered for this application.

Even relatively dated array synthesizers can generate tens, if not hundreds of thousands of different DNA sequences on the surface, which is far more than can be reliably assembled in a single reaction.  A cuttable surface is especially useful in this context because it offers a straightforward way to separate a large array into multiple sub-assembly reactions. There are also many opportunities to explore new array possibilities, akin to those emerging in the realms of flexible electronics and 3D printing.

References

  1. S. P. Fodor, J. L. Read, M. C. Pirrung, L. Stryer, A. T. Lu, D. Solas, Science 1991, 251, 767.
  2. A. H. Broderick, M. R. Lockett, M. E. Buck, Y. Yuan, L. M. Smith, D. M. Lynn, Chemistry of Materials 2012, 24, 938-945.
  3. M. T. Holden, M. C. D. Carter, C.-H. Wu, J. Wolfer, E. Codner, M. R. Sussman, D. M. Lynn, L. M. Smith, Analytical Chemistry 2015, 87, 11420-11428; K. W. Heinrich, J. Wolfer, D. Hong, M. LeBlanc, M. R. Sussman, Plant Physiology 2012, 159, 548-557.
  4. M. T. Holden, M. C. D. Carter, S. K. Ting, D. M. Lynn, L. M. Smith, ChemBioChem 2017, 18, 1914-1916.
  5. M. Baker, Nat Meth 2011, 8, 457-460; S. Kosuri, G. M. Church, Nature Methods 2014, 11, 499-507.

This study, Parallel DNA Synthesis on Poly(ethylene terephthalate) was recently published in the journal ChemBioChem.

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