PNA-PEG Modified Silicon Platforms as Functional Bio-Interfaces for Applications in DNA Microarrays and Biosensors

Abstract

The synthesis and characterization of two types of silicon-based biofunctional interfaces are reported; each interface bonds a dense layer of poly(ethylene glycol) (PEG(n)) and peptide nucleic acid (PNA) probes. Phosphonate self-assembled monolayers were derivatized with PNA using a maleimido-terminated PEG(45). Similarly, siloxane monolayers were functionalized with PNA using a maleimido-terminated PEG(45) spacer and were subsequently modified with a shorter methoxy-terminated PEG(12) ("back-filling"). The long PEG(45) spacer was used to distance the PNA probe from the surface and to minimize undesirable nonspecific adsorption of DNA analyte. The short PEG(12) "back-filler" was used to provide additional passivation of the surface against nonspecific DNA adsorption. X-ray photoelectron spectroscopic (XPS) analysis near the C 1s and N 1s ionization edges was done to characterize chemical groups formed in the near-surface region, which confirmed binding of PEG and PNA to the phosphonate and silane films. XPS also indicated that additional PEG chains were tethered to the surface during the back-filling process. Fluorescence hybridization experiments were carried out with complementary and noncDNA strands; both phosphonate and siloxane biofunctional surfaces were effective for hybridization of cDNA strands and significantly reduced nonspecific adsorption of the analyte. Spatial patterns were prepared by polydimethylsiloxane (PDMS) micromolding on the PNA-functionalized surfaces; selective hybridization of fluorescently labeled DNA was shown at the PNA functionalized regions, and physisorption at the probe-less PEG-functionalized regions was dramatically reduced. These results show that PNA-PEG derivatized phosphonate monolayers hold promise for the smooth integration of device surface chemistry with semiconductor technology for the fabrication of DNA biosensors. In addition, our results confirm that PNA-PEG derivatized self-assembled carboxyalkylsiloxane films are promising substrates for DNA microarray applications.

Restraining non-specific adsorption of protein using Parylene C-caulked polydimethylsiloxane

“…[3][4][5] Meanwhile, in a heterogeneous sensing such as the DNA microarray 6 or the immunoassay 7 biosensor, the NSA of labelled molecules (dyes) may also limit the detection effectiveness. A typical biosensor consists of probe molecules on the surface and a detectable signal will be generated upon the binding between the probes and target molecules.…”

“…NSA of dyes on PDMS surface causes a high background (noise) signal and degrades the sensing performance. 6,7 Efforts have been made to passivate the PDMS surface and restrain the NSA on top. The commonly used surface passivation could be classified into two types.…”

Surface-grafted block copolymer brushes with continuous composition gradients of poly(poly(ethylene glycol)-monomethacrylate) and poly(N-isopropylacrylamide)

“…With the development of new silicon-based biomedical devices such as bio-microelectro-mechanical systems, threedimensional micro-and nano-memory chips, and DNA-and protein-based biochips and biosensors, a great deal of interests have been paid to the functionalization of single-crystal silicon substrate has attracted great interest [1][2][3][4]. Among the methods used so far, the covalent immobilization of polymer brushes has been used frequently and efficiently.…”

A Novel Type of Nucleic Acid-based Biosensors: the Use of PNA Probes, Associated with Surface Science and Electrochemical Detection Techniques

“…Hybridisation has been characterised by XPS among others techniques; the biofunctional interfaces exhibit good resistance against non specific interactions, having potential applications for PNA/DNA microdevices. (Cattani-Scholz et al, 2008;Cattani-Scholz et al, 2009). …”