Biophysics and Biopolymers

Bionanotechnology is a branch of nanotechnology which uses biological starting materials, utilises biological design or fabrication principles, or is applied in medicine or biotechnology.

Bionanotechnology has become an exiting field of research and an area of technology development, especially since the length scale nanotecnology can access more and more coincides with the length scale of basic biological structures and fundamental biological components.

Research topics

Biological polymers: Mesoscale structure formation and interactions

Interactions and adoption of higher order organisation of biological macromolecules are of fundamental importance in maintaining biological function and technological exploitation.

Biological polymers: Mesoscale structure formation and interactions

Interactions and adoption of higher order organisation of biological macromolecules are of fundamental importance in maintaining biological function and technological exploitation.

Bioresponsive gelIn our research group, the activities within this area include the study of mesoscale structure formation and interactions of non-crystalline biological macromolecules.

The topics addressed include polyelectrolyte complexation, biopolymer multilayers, gelation kinetics and structure of polysaccharide gels, as well as responsive gels as biospecific signal transducers. Further research topics include immunologically active (1,3)-β-D-glucans and their interactions with polynucleotides, physics of enzymatic mode of action, toll-like receptors and their primary activation step and the target search strategy of DNA repair enzymes.

Monte Carlo simulations of coarse-grained models are used to study the complexation of oppositely charged polyelectriolytes and polyplex formation, the adsorption of macromolecules onto model lipid membranes, and nanoparticle-polyacid interactions.

In addition to classical ensemble averaging techniques, application of single-molecule techniques is a distinctive facet of our approach to tackle core issues within these topics. The tools implemented locally for this research include atomic force microscopy, total internal reflection fluorescence microscopy, dynamic force spectroscopy, high resolution interferometry and rheology. These tools are complemented by additional techniques made available to through collaborations with laboratories either locally, or within national and international collaborations.

References

  1. High resolution interferometry as a tool for characterization of swelling of weakly charged hydrogels subjected to amphiphile and cyclodextrin exposure. Gao, M., Gawel K., and Stokke, B.T. J Coll Interface Sci (2012) in press.
  2. Impregnation of weakly charged anionic microhydrogels with cationic polyelectrolytes and their swelling properties monitored by a high resolution interferometric technique. Transformation from a polyelectrolyte to polyampholyte hydrogel. Gawel K., Gao, M., and Stokke, B.T. Eur Polym J 48 (2012) 1949-1959.
  3. Logic swelling response of DNA-polymer hybrid hydrogel . Gawel K. and Stokke, B.T. Soft Matter 7 (2011) 4615-4618.
  4. Toehold of dsDNA exchange affects the hydrogel swelling kinetics of a polymer-dsDNA hybrid hydrogel. Gao, M., Gawel K., and Stokke, B.T. Soft Matter 7 (2011) 1741-1746.
  5. Responsive hydrogels for label-free signal transduction within biosensors. Gawel K., Barriet D., Sletmoen M., and Stokke, B.T. Sensors 10 (2010) 4381-4409
  6. Interferometric characterization of swelling of covalently crosslinked alginate gel and changes associated with polymer impregnation. Tierney S., Sletmoen, M., Skjåk-Bræk, G. and Stokke, B.T. Carbohydrate Polymers 80 (2010) 828-832.
  7. Development of an oligonucleotide functionalized hydrogel integrated on a high resolution interferometric readout platform as a label free macromolecule sensing device. Tierney, S., and Stokke, B.T. Biomacromolecules 10 (2009) 1619-1626.
  8. Determination of glucose levels using functionalized hydrogel - optical fiber biosensor: Towards continuous monitoring of blood glucose in vivo. Tierney, S., Falch, B.M.H., Hjelme, D.R., and Stokke, B.T. Analytical Chemistry 81 (2009) 3630-3636.
  9. Glucose sensors based on a responsive gel incorporated as a Fabry-Perot cavity on a fiber-optic readout platform. Tierney, S., Volden, S. and Stokke, B.T. Biosensors and Bioelectronics 24 (2009) 2034-2039.
  10. Determination of swelling of responsive gels with nanometer resolution. Fiber-optic based platform for hydrogels as signal transducers. Tierney, S., Hjelme, D.R. and Stokke, B.T. Analytical Chemistry 80 (2008) 5086-5093.

Single-molecular pair interactions

Single-molecular interaction studies were initially undertaken to elucidate pairwise interactions of selected sets of biololgical macromolecules.

Single-molecular pair interactions

Single-molecular interaction studies were initially undertaken to elucidate pairwise interactions of selected sets of biololgical macromolecules.

One example is related to determination of the mode of action of the mannuronan C-5 epimerase when catalyzing the conversion of the mannuronic acid to its C-5 epimer, guluronic acid, at the polymer level. Such single-molecule interactions are currently adopted for characterization of other molecular pairs, e.g., selected part of immunlogical signalling cascades (toll-like receptor 9 (TLR9)), mucin - lectin interactions, DNA-repair enzymes and selected high molecular weight polysaccharides forming physical gels.

References

  1. Single molecular pair interactions between hydrophobically modified hydroethyl cellulose and amylose determined by dynamic force spectroscopy. Takemasa, M., Sletmoen, M., and Stokke, B.T. Langmuir 25 (2009) 10174-10182.
  2. Single-molecule pair unbinding studies of the soybean agglutinin and the α-GalNAc (Tn-antigen) form of porcine submaxillary mucin. Sletmoen, M., Dam, T.K., Gerken, T A., Stokke, B.T., and Brewer, C. F. Biopolymers 91 (2009) 719-728.
  3. Macromolecular motion at the nanoscale of enzymes working on polysaccharides. Sletmoen, M., Bræk G.S., and Stokke, B.T. Lecture Notes in Physics 711 (2007) 161-180.
  4. Mapping enzymatic functionalities of mannuroan C-5-epimerases and their modular units by dynamic force spectroscopy. Sletmoen, M., Skjåk-Bræk, G. and Stokke, B.T. Carbohydr. Res. 340 (2005) 2782-2795.
  5. Single-molecular pair unbinding studies of mannuronan C-5 epimerase AlgE4 and its polymer substrate. Sletmoen, M., Skjåk-Bræk, G. and Stokke, B.T. Biomacromolecules 5 (2004) 1288-1295.

Polyelectrolyte complexes

Electrostatic interactions are important driving forces for numerous biological processes, e.g. organisation of DNA to packed chromosones, or interactions between enzymes and charged ligands.

Polyelectrolyte complexes

Electrostatic interactions are important driving forces for numerous biological processes, e.g. organisation of DNA to packed chromosones, or interactions between enzymes and charged ligands.

This is currently receiving interest, as polycation-induced condensation of DNA is a possible first step in preparing a therapeutic gene delivery vector. The research is two-fold, investigating the use of chitosan (and modified chitosans) for compaction of DNA for gene delivery, and in general investigating the influence of macromolecular properties and preparation conditions on the structure formation of condensing semiflexible biopolymers.

References

  1. PEGylated chitosan complexes DNA while improving polyplex colloidal stability and gene transfection efficiency. Maurstad, G., Stokke, B.T., Vårum, K.M., and Strand, S.P. Carbohydr. Polym. 94 (2013) 436-443.
  2. Isothermal titration calorimetry study of the polyelectrolyte complexation of xanthan and chitosan samples of different degree of polymerization. Maurstad G., Kitamura, S., and Stokke, B.T. Biopolymers 97 (2012) 1-10.
  3. Polyelectrolyte complex formation using alginate and chitosan. Sæther, H.V., Holme, H., Maurstad, G., Smidsrød, O., and Stokke, B.T. Carbohydrate Polymers 74 (2008) 813-821.
  4. The influence of charge density of chitosan in compacting polyanions DNA and xanthan. Maurstad, G., Danielsen, S., Stokke, B.T. Biomacromolecules 8 (2007) 1124-1130.
  5. Toroids of stiff polyelectrolytes. Maurstad, G., and Stokke, B.T. Curr. Opinion in Colloid and Interface Science 10 (2005) 16-21.
  6. Polycation induced DNA condensation and polyplex stability in the presence of competing polyanions. Danielsen, S., Maurstad, G. and Stokke, B.T. Biopolymers 77 (2005) 86-97.
  7. A new approach to chitosan-mediated gene delivery based on easily dissociated chitosan polyplexes of highly defined chitosan oligomers. Köping-Höggård, M., Vårum, K.M., Issa, M., Danielsen, S., Christensen, B E., Stokke, B T., and Artursson, P. Gene Therapy 11 (2004) 1441-1452.
  8. Structural analysis of chitosan mediated DNA condensation by AFM: Influence of chitosan molecular parameters. Danielsen, S., Vårum, K M. and Stokke, B.T. Biomacromolecules 5 (2004) 928-936.
  9. Analysis of compacted semiflexible polyanions visualized by AFM: Influence of chain stiffness on morphologies of polyelectrolyte complexes. Maurstad, G., Danielsen, S. and Stokke, B.T. J. Phys. Chem. B. 107 (2003) 8172 - 8180.

Structure and properties of (1,3)-β-D-glucans

(1,3)-β-D-glucans form a group of biologically active biopolymers that exist in different structural organisations depending on the environmental conditions.

Structure and properties of (1,3)-β-D-glucans

– and interactions with polynucleotides

(1,3)-β-D-glucans form a group of biologically active biopolymers that exist in different structural organisations depending on the environmental conditions.

The biological effects of (1,3)-β-D-glucans is a core issue stimulating large research efforts of the molecular properties and their consequences for action as biological response modifiers.

Our laboratory was in 1991 the first to report that (1,3)-β-D-glucans are able to form a topological cyclic macromolecule. We have performed studies to elucidate both the stability, structure and biological activity of (1,3)-β-D-glucans exposed to different pre-treatments. The fascination for these molecules increased further following the finding of their ability to form complexes of defined geometry with a number of structures.

References

Structure and stability of polynucleotide-(1,3)-β-D-glucan complexes. Sletmoen, M., Næss, S. N., and Stokke, B.T. Carbohydrate Polymers 76 (2009) 389-399

Swelling, mechanical properties and effect of annealing of scleroglucan gels. Aasprong, E., Smidsrød, O., and Stokke, B.T. Carbohydrate Polymers 60 (2005) 363-378.

Small-angle X-ray scattering and rheological characterization of alginate gels. 3. Alginic acid gels. Draget, K., Stokke, B.T., Yuguchi Y., Urakawa, H. and Kajiwara, K. Biomacromolecules 4 (2003) 1661-1668.

Thu, 14 Apr 2016 11:45:42 +0200

Biopolymer multilayers

Multilayers are formed by the alternate deposition of polyanionic and polycationic polymers, and have potential applications within surface modifications, optical devices and separation membranes.

Biopolymer multilayers

Multilayers are formed by the alternate deposition of polyanionic and polycationic polymers, and have potential applications within surface modifications, optical devices and separation membranes.

Surface topography might influence the biocompatibility, adhesive and optical properties of these systems. We are therefore looking at how molecular properties of biopolymers and preparation conditions are influencing the surface topography of biopolymer multilayers. Part of the work includes developing routines for user-independent, quantitative extraction of parameters for analysis of the surface topography.

Reference

Quantitative analysis of atomic force microscopy topographs of biopolymer multilayers: Surface structure and polymer assembly modes. Marken, E. Maurstad, G. and Stokke, B.T. Thin Solid Films 516 (2008) 7770-7776.

Thu, 14 Apr 2016 11:43:38 +0200

Structure of polysaccharide gels

Gels can be formed from a range of biopolymers, based on various types of physical or chemical crosslinks. Alginates form gels in aqueous Ca2+-containing solutions by lateral association of chain segments.

Structure of polysaccharide gels

Gels can be formed from a range of biopolymers, based on various types of physical or chemical crosslinks. Alginates form gels in aqueous Ca2+-containing solutions by lateral association of chain segments.

Lately, the effect of adding free guluronic acid blocks on the gelation kinetics, swelling response and gel strength has been studied. Using rheology, scattering techniques and ultramicroscopy the fractal dimension and junction zone multiplicity of the gels are investigated. The same experimental procedures are used to study gels made from other biopolymers, i.e. (1,3)-β-D-glucans, chitosan and xanthan.

References

Small-angle X-ray scattering study of local structure and collapse transition of (1,3)-β-D-glucan-chitosan gels. Sletmoen, M., Stokke, B.T. and Geissler, E. J. Chem. Phys. 125 (2006) 054908-1-6.

Swelling, mechanical properties and effect of annealing of scleroglucan gels. Aasprong, E., Smidsrød, O., and Stokke, B.T. Carbohydrate Polymers 60 (2005) 363-378.

Small-angle X-ray scattering and rheological characterization of alginate gels. 3. Alginic acid gels. Draget, K., Stokke, B.T., Yuguchi Y., Urakawa, H. and Kajiwara, K.. Biomacromolecules 4 (2003) 1661-1668.

Fri, 28 Oct 2016 11:48:51 +0200

Toll-like receptors of the immune system

Toll-like receptors (TLR) are responsible for an immediate response of the innate immune system against invading pathogens. TLR recognize evolutionary conserved microbial patterns such as glycolipids and bacterial DNA.

Toll-like receptors of the immune system

– studied by atomic force microscopy and confocal microscopy

Toll-like receptors (TLR) are responsible for an immediate response of the innate immune system against invading pathogens. TLR recognize evolutionary conserved microbial patterns such as glycolipids and bacterial DNA.

While many of the trafficking and signalling processes that play a role in TLR mediated immune response have been characterized, the exact mechanisms of interaction between TLR and various ligands and other interacting partners during activation are not known yet. The goal of this project is to study the molecular details of the first step in the TLR signalling cascade; the activation of the receptors.

References

Higher order structure of short immunostimulatory oligonucleotides studied by atomic force microscopy. Klein D.G.C., Latz E., Espevik T., and Stokke, B.T. Ultramicroscopy 110 (2010) 689-693.

Effects of CpG-DNA on Toll-like receptor 9 studied by AFM. Klein, D.C.G., Latz, E., Espevik, T., and Stokke, B.T. Proceedings of the IX. Linz Winter Workshop 2007 Advances in Single Molecule Research for Biology and Nanoscience (2008). Trauner Verlag (ISBN 978-3-85499-400-8).

Physics of enzymatic mode of action

Polysaccharide modifying enzymes may generate specific sequence patterns in polymers (e.g. epimerisation), or produce oligomers of a certain length as a result of depolymerisation.

Physics of enzymatic mode of action

Polysaccharide modifying enzymes may generate specific sequence patterns in polymers (e.g. epimerisation), or produce oligomers of a certain length as a result of depolymerisation.

We are interested in the kinetics, specificity and mode of action of alginate epimerases and lyases. We also study the sequence specificities of lysozyme depolymerisation of partially N-acetylated chitosans and the mode of action of chitin deacetylases. The systems are studied using NMR, dynamic force spectroscopy and simulations. The alginate epimerase AlgE4 produces an alginate with long stretches of alternating MG sequences. The kinetics of formation of this sequence pattern could not be accounted for by a random attack model. Results obtained from dynamic force spectroscopy indicated a processive mode of action. This enzyme might thus be the first known polysaccharide modifying processive enzyme

Reference

Biochemical analysis of the processive mechanism for epimerisation of alginate by mannuronan C-5 epimerase AlgE4. Campa, C., Holtan, S., Nilsen, N., Bjerkan, T. M., Stokke, B.T. and Skjåk-Bræk, G. Biochem. J. 381 (2004) 155-164.

Principal investigators