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Interactions between a zwitterionic polythiophene derivative and oligonucleotides as resolved by fluorescence resonance energy transfer
Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, The Institute of Technology.
Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, The Institute of Technology.
Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, The Institute of Technology.ORCID iD: 0000-0002-5582-140X
Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, The Institute of Technology.
2005 (English)In: Chemistry of Materials, ISSN 0897-4756, E-ISSN 1520-5002, Vol. 17, no 16, 4204-4211 p.Article in journal (Refereed) Published
Abstract [en]

The interactions between a zwitterionic polythiophene derivative, POWT, and DNA oligonucleotides in solution have been studied by FRET (fluorescence resonance energy transfer). When POWT and ssDNA are bound alone in a complex, the distance between them is at its smallest. The distance increases when adding complementary DNA, but POWT is still mainly bound to the first DNA strand. We find that two POWT chains bind to one DNA strand, and the two POWT chains seem held together in pairs, unable to separate, as they can only bind to and quench half their own amount of labeled DNA. This POWT−POWT complex appears to dissociate at lower concentrations. ssDNA attached to POWT in a complex can also be substituted by other ssDNA in solution; this occurs to 50% when the free DNA is present in 10-fold concentration compared to the ssDNA bound to POWT. Titration studies at different concentrations show positive cooperativity in the binding of POWT and ssDNA into a complex. The hybridization of complementary DNA to the same complex involves no cooperativity. These observations indicate interesting possibilities for the use of POWT as a DNA sensor.

Place, publisher, year, edition, pages
2005. Vol. 17, no 16, 4204-4211 p.
National Category
Natural Sciences
Identifiers
URN: urn:nbn:se:liu:diva-30356DOI: 10.1021/cm050328xLocal ID: 15901OAI: oai:DiVA.org:liu-30356DiVA: diva2:251178
Available from: 2009-10-09 Created: 2009-10-09 Last updated: 2017-12-13
In thesis
1. Hydrogels of conjugated polyelectrolytes for biosensor and biochip applications
Open this publication in new window or tab >>Hydrogels of conjugated polyelectrolytes for biosensor and biochip applications
2005 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

This thesis describes the use of conjugated polyelectrolytes (CPEs) in biosensor devices. The method is based on non-covalent assembly of the biomolecule of interest and the CPE functioning as the reporter, in one case as a transducer, of biomolecular events. Devices of these assemblies on solid supports that can operate in liquid solutions have been the focus. Polythiophenes, both semiconducting and conducting, is the class of materials that has been used in this work. The semiconducting polythiophenes have ionic side chains which makes them water soluble. This ionic side chain is capable of both forming electrostatic and hydrogen bonds, and when paired with the hydrophobic backbone of the polymer a great number of interactions with biomolecules are possible. The highly conducting polythiophene derivative PEDOT -PSS, (PEDOT) doped with ionic and water soluble PSS polyelectrolyte, was used as the conducting material in 3D-electrode. Both the semiconducting and conducting polymers described above forms hydrogels on solid supports if crosslinked with the appropriate ion, biomolecule or polymer. Evaluation of the CPEs, both with and without biomolecules, was performed in liquid, solid and hydrogel state using a number of techniques. This was done to understand how the CPEs behave when exposed to different buffer systems and various biomolecules.

Hydrogels of conjugated polyelectrolytes combined with biomolecules are attractive as biosensors. The advantage with the hydrogel format is the high water content, the porous structure and the large capacity of binding molecules. High water content is important to preserve the biomolecules by providing the correct buffered environment. In this thesis we demonstrated a hydrogel of the highly conducting PEDOT -PSS polymer that was crosslinked on a solid support together with horseradish peroxidase (HRP) enzyme, forming an enzyme-enhanced electrode. Further studies of hydrogels were done using in situ quartz crystal microbalance with dissipation (QCM-D). POWT is a CPE withproperties well suited for biochip applications and readily forms hydrogels when exposed to water-based buffer solutions or biomolecule solutions. Detection ofcomplementary DNA and rejection of non-complementary DNA in a POWT hydrogel was demonstrated. The interaction between POWT and DNAoligonucleotides was also evaluated using fluorescence resonance energy transfer (FRET) in solution. Labeled DNA oligonucleotides with energy accepting or donating fluorophores allowed us to determine distance and binding stoichiometry in the non-covalent POWT-DNA complex.

Patterning and anchoring of biomolecules and non-covalent assembled CPE-biomolecule complexes to a chip surface was studied; in the adsorbed state these complexes are hydrogels. Our novel method is based on the modification of the surface energy of a hydrophilic substrate surface using hydrophobic poly(dimethylsiloxane) (PDMS) elastomer stamp containing a relief pattern. Different conformations in biomolecules could be detected using fluorescence microscopy, where the CPEs acts as reporters and the PDMS modified substrates as discriminator. Also, excellent enzyme activity in patterned CPE/Horseradish peroxidase (HRP) enzyme was shown.

Distances between the individual molecules in solid state devices of conjugated polymers can be small. In luminescence devices, such as light emitting diodes or fluorescence biosensors, there is a chance of interaction between conjugated molecules especially if more than one type of molecule is present. Quenching of the light and fluorescence energy transfer can occur and a simple approach to study this was developed.

Place, publisher, year, edition, pages
Linköping: Linköpings universitet, 2005. 78 p.
Series
Linköping Studies in Science and Technology. Dissertations, ISSN 0345-7524 ; 982
National Category
Natural Sciences
Identifiers
urn:nbn:se:liu:diva-30215 (URN)15710 (Local ID)91-85457-58-2 (ISBN)15710 (Archive number)15710 (OAI)
Public defence
2005-12-09, Hörsal Planck, Campus Valla, Linköping, 10:15 (Swedish)
Opponent
Available from: 2009-10-09 Created: 2009-10-09 Last updated: 2012-12-03

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Åsberg, PeterNilsson, PeterInganäs, Olle

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