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Biological Sensing and DNA Templated Electronics Using Conjugated Polymers
Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics . Linköping University, The Institute of Technology.
2007 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

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.

Place, publisher, year, edition, pages
Institutionen för fysik, kemi och biologi , 2007.
Series
Linköping Studies in Science and Technology. Dissertations, ISSN 0345-7524 ; 1154
Keyword [en]
conjugated polymer, conjugated polyelectrolyte, DNA, sensor, nanowire
National Category
Industrial Biotechnology
Identifiers
URN: urn:nbn:se:liu:diva-10180ISBN: 978-91-85895-17-5 (print)OAI: oai:DiVA.org:liu-10180DiVA: diva2:16933
Public defence
2007-12-14, Planck, Fysikhuset, Campus Valla, Linköpings Universitet, Linköping, 10:15 (English)
Opponent
Supervisors
Available from: 2007-12-07 Created: 2007-12-07 Last updated: 2009-04-23
List of papers
1. Dynamics of complex formation between biological and luminescent conjugated polyelectrolytes - a surface plasmon resonance study
Open this publication in new window or tab >>Dynamics of complex formation between biological and luminescent conjugated polyelectrolytes - a surface plasmon resonance study
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2005 (English)In: Biosensors and Bioelectronics, ISSN 0956-5663, Vol. 20, no 9, 1764-1771 p.Article in journal (Refereed) Published
Abstract [en]

A water-soluble polythiophene, POWT, with zwitterionic peptide like side chains possess good characteristics for biosensor applications. The zwitterionic side chains of the polymer can couple to biomolecules via electrostatic and hydrogen bonding. This creates possibilities to imprint biomolecules to spin-coated polymer films with maintained functionality, and use the resulting matrix as a biosensor. Polymer-biomolecular interaction studies done with surface plasmon resonance (SPR) reveal a well performing sensor matrix with high affinity for DNA hybridizations as well as for protein detection. The responses are distinct and very specific. A directional dependence of antibodies binding to POWT layer has also been observed. The polymer films have also been characterized by optical methods. Emission and absorption measurements in different buffer systems confirm that the polymer matrix can undergo structural and conformational changes on surfaces. The dielectric function in the interval 300–800 nm of POWT is reported, based on variable angle spectroscopic ellipsometry. This modeling reveals that a considerable amount of water is included in the material. The polymer layer possesses the characteristics needed for biochip applications and micro array techniques.

Keyword
DNA; Protein; SPR; Sensor; Conjugated polymer; Ellipsometry
National Category
Engineering and Technology
Identifiers
urn:nbn:se:liu:diva-12725 (URN)10.1016/j.bios.2004.07.001 (DOI)
Available from: 2007-12-07 Created: 2007-12-07 Last updated: 2014-04-08
2. Hydrogels from a water-soluble Zwitterionic polythiophene: dynamics under pH change and biomolecular interactions observed using quartz crystal microbalance with dissipation monitoring
Open this publication in new window or tab >>Hydrogels from a water-soluble Zwitterionic polythiophene: dynamics under pH change and biomolecular interactions observed using quartz crystal microbalance with dissipation monitoring
2005 (English)In: Langmuir, ISSN 0743-7463, E-ISSN 1520-5827, Vol. 21, no 16, 7292-7298 p.Article in journal (Refereed) Published
Abstract [en]

The water-soluble zwitterionic polythiophene, poly(3-((S)-5-amino-5- carboxyl-3-oxapentyl)-2,5-thiophene) hydrochloride (POWT), is a conjugated polyelectrolyte (CPE) with properties well suited for biochip applications. CPEs readily form hydrogels when exposed to water-based buffer solutions or biomolecule solutions. In this work, we used in situ quartz crystal microbalance with dissipation (QCM-D) monitoring to collect information on the interaction between POWT films exposed to buffers with different pH and POWT/DNA chains. Our data show that POWT swells significantly when exposed to low-pH buffers, such as pH 4 acetate, this is seen as an increase in thickness and decrease in viscosity obtained via a Voight-based modeling of combined f and D QCM-D measurements. The magnitude of thickness and viscosity change upon changing from a pH 10 carbonate buffer to pH 4 acetate is 100% increase in thickness and 50% decrease in viscosity. The response of the hydrogel under pH change is well correlated with fluorescence data from POWT films on glass. The state of the hydrogel is important during interaction with biomolecules; illustrated by the observation that a swollen CPE hydrogel adsorbs a higher amount of DNA than a compacted one. In agreement with previous results, the QCM-D data confirmed that the POWT/DNA hydrogel sense complementary DNA specifically and with negligible binding of noncomplementary DNA. These results are important for efficient constructions of biochips in water environments using this class of materials.

National Category
Engineering and Technology
Identifiers
urn:nbn:se:liu:diva-12726 (URN)10.1021/la050479e (DOI)
Available from: 2007-12-07 Created: 2007-12-07 Last updated: 2012-12-03
3. Conjugated polythiophene probes target lysosome-related acidic vacuoles in cultured primary cells
Open this publication in new window or tab >>Conjugated polythiophene probes target lysosome-related acidic vacuoles in cultured primary cells
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2007 (English)In: Molecular and Cellular Probes, ISSN 0890-8508, Vol. 21, no 5-6, 329-337 p.Article in journal (Refereed) Published
Abstract [en]

Conformation-sensitive optical probes for studying biological processes and structures are of great interest. The present work shows for the first time that conjugated polyelectrolyte (CPE) probes can be used for specific targeting of chromatin, nuclear and cytoplasmatic vesicles, and cytoskeletal components in a complex system of cultured cells. One of the probes could also be used for vital staining of live cells. When bound to different entities, the polythiophene derivative probes emitted light with different colors due to the unique spectral properties of these conformation sensitive probes. The physical pre-requisites for binding could also be exploited for characterization of the target. Unexpectedly, lysosome-related acidic vacuoles were targeted in cultured primary cells by both anionic, cationic, and zwitter-ionic polythiophene derivatives. Pre-treatment with Bafilomycin A1, a specific inhibitor of vacuolar-type H+-ATPase, caused redistribution of the staining. The targeting of lysosome-related acidic vesicles could not be demonstrated in transformed cells (melanoma, neuroblastoma, and prostate cancer cell lines), indicating a difference in the localization, structure, accessibility, or quantity of the target in cultured normal cells as compared with the malignant cell lines. The chemical nature of the conjugated polyelectrolyte complex in the cytoplasmatic vacuoles remains elusive.

Keyword
Conjugated polyelectrolyte; Polythiophene; Fibroblast; Lysosome; Cancer
National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:liu:diva-12727 (URN)10.1016/j.mcp.2007.04.005 (DOI)
Available from: 2007-12-07 Created: 2007-12-07 Last updated: 2014-04-08
4. Soft lithographic printing of patterns of stretched DNA and DNA/electronic polymer wires by surface-energy modification and transfer
Open this publication in new window or tab >>Soft lithographic printing of patterns of stretched DNA and DNA/electronic polymer wires by surface-energy modification and transfer
2006 (English)In: Small, ISSN 1613-6810, Vol. 2, no 8-9, 1068-1074 p.Article in journal (Refereed) Published
Abstract [en]

Aligned and stretched λ DNA is directed to specific locations on solid substrates. Surface-energy modification of glass substrates by using patterned polydimethylsiloxane (PDMS) stamps is used to direct DNA onto the surface-energy-modified micrometer-scale pattern through molecular combing. As an alternative, patterned and nonpatterned PDMS stamps modified with polymethylmethacrylate (PMMA) are utilized to direct the stretched DNA to the desired location and the results are compared. The DNA is elongated through molecular combing on the stamp and transfer printed onto the surfaces. PMMA-modified stamps show a more defined length of the stretched DNA, as compared to bare PDMS stamps. A combination of these two methods is also demonstrated. As an application example, transfer printing of DNA decorated with a semiconducting conjugated polyelectrolyte is shown. The resulting patterned localization of stretched DNA can be utilized for functional nanodevice structures, as well as for biological applications.

Keyword
conjugation, DNA, lithography, patterning, polymers
National Category
Engineering and Technology
Identifiers
urn:nbn:se:liu:diva-12728 (URN)10.1002/smll.200600126 (DOI)
Available from: 2007-12-07 Created: 2007-12-07
5. Single molecular imaging and spectroscopy of conjugated polyelectrolytes decorated on stretched aligned DNA
Open this publication in new window or tab >>Single molecular imaging and spectroscopy of conjugated polyelectrolytes decorated on stretched aligned DNA
2005 (English)In: Nano Letters, ISSN 1530-6984, Vol. 5, no 10, 1948-1953 p.Article in journal (Refereed) Published
Abstract [en]

DNA is the prototype template for building nanoelectronic devices by self-assembly. The electronic functions are made possible by coordinating electronic polymer chains to DNA. This paper demonstrates two methods for fabrication of aligned and ordered DNA nanowires complexed with conjugated polyelectrolytes (CPEs). The complex can be formed either in solution prior to stretching or after stretching of the bare DNA on a surface. Molecular combing was used to stretch the complexes on surface energy patterned surfaces, and PMMA for the bare DNA. Single molecular spectroscopy, in fluorescence, and microscopy, in atomic force microscopy, give evidence for coordination of the short CPE chains to the aligned DNA.

National Category
Engineering and Technology
Identifiers
urn:nbn:se:liu:diva-12729 (URN)10.1021/nl051328z (DOI)
Available from: 2007-12-07 Created: 2007-12-07 Last updated: 2009-02-13
6. Structural studies of a well defined conjugated polyelectrolyte and its interaction with DNA
Open this publication in new window or tab >>Structural studies of a well defined conjugated polyelectrolyte and its interaction with DNA
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Manuscript (Other academic)
Identifiers
urn:nbn:se:liu:diva-12730 (URN)
Available from: 2007-12-07 Created: 2007-12-07 Last updated: 2010-01-13

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