Polymer Pen Lithography-Fabricated DNA Arrays for Highly Sensitive and Selective Detection of Unamplified Ganoderma Boninense DNA.

Ekta Rani,Muhammad Ahmad,Royston Goodacre,Shahrul Alang Ahmad,Lu Wong,Siti Mohshim

doi:10.3390/polym11030561

Abstract

There is an increasing demand for lithography methods to enable the fabrication of diagnostic devices for the biomedical and agri-food sectors. In this regard, scanning probe lithography methods have emerged as a possible approach for this purpose, as they are not only convenient, robust and accessible, but also enable the deposition of “soft” materials such as complex organic molecules and biomolecules. In this report, the use of polymer pen lithography for the fabrication of DNA oligonucleotide arrays is described, together with the application of the arrays for the sensitive and selective detection of Ganoderma boninense, a fungal pathogen of the oil palm. When used in a sandwich assay format with DNA-conjugated gold nanoparticles, this system is able to generate a visually observable result in the presence of the target DNA. This assay is able to detect as little as 30 ng of Ganoderma-derived DNA without any pre-amplification and without the need for specialist laboratory equipment or training.

Highlights

The demand for the fabrication of micro- and nanoscale features of biomolecules such as proteins and oligonucleotides for their applications in biosensing, diagnostics, and tissue engineering is increasingly widespread [1,2,3]
Two DNA “ink” formulations were tested, which were based on previous reports of DNA printing with either dip pen lithography (DPN) [38] or polymer pen lithography (PPL) [13] (Ink formulation 1 and 2 respectively; see Section 2.3.1)
Hybridisation of complementary target/genomic DNA with DNA arrays and DNA-AuNPs can be observed with the naked eye

Summary

Introduction

The demand for the fabrication of micro- and nanoscale features of biomolecules such as proteins and oligonucleotides for their applications in biosensing, diagnostics, and tissue engineering is increasingly widespread [1,2,3]. The lithography of nanoscale features consisting of “soft”. A common soft lithography approach that has been demonstrated for the patterning of biomolecules is microcontact printing (μCP), Polymers 2019, 11, 561; doi:10.3390/polym11030561 www.mdpi.com/journal/polymers. Polymers 2019, 11, 561 which uses an elastomeric stamp to print the molecules on to the surface [4,5,6]. ΜCP offers an easy and inexpensive route for stamping soft molecules over large (cm2 ) areas, under ambient conditions. There is a lack of design flexibility, since the pattern is fixed by the design of the photolithographically fabricated master

Methods

Results

Conclusion