BIOLOGICAL SENSING AND DNA TEMPLATED ELECTRONICS USING CONJUGATED POLYMERS

Postgraduate

ABSTRACT

Conjugated polymers have been found useful in a wide range of applications such as solar cells, sensor elements and printed electronics, due to their optical and electronic properties. Functionalization with charged side chains has enabled water solubility, resulting in an enhanced interaction with biomolecules. This thesis focus on the emerging research fields, where these conjugated polyelectrolytes (CPEs) are combined with biomolecules for biological sensing and DNA nanowire assembling. 

CPEs have shown large potential in biomolecular detection where the optical read out is due to the geometrical alternation in the backbone and aggregation state. This thesis focused on transferring the biomolecular detection to a surface of CPEs. The characterization of the CPE layer show that a hydrogel can be formed, and how the layer can undergo geometrical changes upon external stimulus such as pH change. A selective sensor surface can be created by imprinting ssDNA or an antibody in the CPE layer. The discrimination for complementary DNA hybridization and specific antibody interaction can be monitored by surface plasmon resonance or quartz crystal microbalance. We have also taken the step out from the controlled test tube experiments to the complex environment of the cell showing the potential for staining of compartments and structures in live and fixed cell. Depending on the conditions and CPE used, cell nuclei, acidic vesicles and cytoskeleton structure can be visualized. Furthermore, the live staining shows no sign of toxic effect on cultured fibroblasts. 

CPEs can also be a valuable element when assembling electronics in the true nano regime. I have used DNA as building template due to its attractive size features, with a width of around 2 nm and a length scale in the µm regime, and the inbuilt base-paring recognition elements. This thesis shows how DNA can be decorated with CPEs and stretched on surfaces into a model for aligned semiconducting nanowire geometries. Not only making the template structures is of importance, but also how to place them on the correct surface position, i.e. on electrodes. Strategies for positioning DNA nanowires using transfer printing and surface energy patterning methods have therefore been developed in the thesis. The stretched DNA decorated with CPE also offers a way to further study the molecular binding interaction between the two molecules. Single molecular spectroscopy in combination with polarization has given information of the variation of the CPE binding along a DNA chain.

GENERAL INTRODUCTION

Biotechnology has in the last decades emerged as a discipline. One of the driving forces behind the fast development is the accelerating use of biosensors. “Analytical devices, which combine biospecific recognition systems with physical or electrochemical signaling” is one definition for biosensors. Biosensors cover a large area of applications and it is the selectivity and defined kinetics for the biospecific reactions that form the base for biosensors. DNA sensors, or gene chips, is the subject of many research groups attention. Screening and genetic diagnostics for pharmaceutical, medical and forensic purpose, and genetic modifications for the food and plant industry are some of the more common applications for gene chips. Detection of pesticides, cells and tissue properties and are examples of non-DNA applications for biosensors.

 

Many of the products on the market today are expensive and require an advanced handling procedure, which often includes a labeling step. Affymetrix is an example of one company, dominating the high density gene chip market, which supplies highly sophisticated, but also expensive products for DNA detection. A cheap, more flexible and label free system with easy handling would be of great competitive strength. The use of conjugated polymers (CP) is one direction that shows large potential for this in biological sensing. The conjugated backbone of the CP with alternating single and double bonds forms the bases for their electrical and photophysical properties. Geometrical alternation in the backbone visualized as chromic or electrical change, can be used as the sensor functionality. CPs also have the advantage that a collective response can amplify the read out compare to small molecule based sensors. The CPs can be made water soluble by adding charged side chains to the polymers. Theses conjugated polyelectrolytes (CPEs) can form interaction with biomolecules and thereby open new routes for designing biological sensors. In the first part of this thesis (paper I-III) we have studied how the CPEs function as sensor layers to be used for detection of DNA hybridization and antibody interaction. We have also taken the step out from the controlled test tube experiments to the complex environment of the cell to see what information can be extracted from animal cells, live as well as fixed.

Another area of increasing interest is biotemplated electronics. This field is still in its early research phase and the inspiration for biotemplated electronics is most often found in nature. There are so many fantastic and sophisticated assemblies evolved during millions and millions years of organism evolution and some of them can offer building blocks in the true nano size regime. The DNA molecules, carrying the genetic information, are maybe the most obvious template. DNA has an extreme aspect ratio with nm width and several µm in length. The assembling can be controlled by the inbuilt recognition elements for precise localization via base paring of the nucleotide sequence and stretched nanowires, crossings, networks, defined multilayer structures and also to some extent moving DNA machines can be formed. Other templates that have been used are amyloid like fibrils, viruses and bacteriophages, self assembled peptides and actin filaments. System flexibility is generally gained when stability is lost for the biotemplates, why you carefully have to select the best template for the actual situation and requirements.

However, these templates have all one property in common; that none of them have the intrinsic possibility for electronic conduction. They need to be functionalized in order to assemble functional electronic devices. Conjugated polymers, and especially the conjugated polyelectrolytes, are candidates that possess many of the requirements for successful functionalization. CPEs can be both water soluble and biocompatible and at the same time have semiconducting properties. The second part of this thesis shows how we can use the knowledge from the CPE biosensor area.