University of Groningen
Bio-organic hybrids of DNA, peptides and surfactants: from liquid crystals to molecular sleds Zhang, Lei
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Publication date: 2017
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Zhang, L. (2017). Bio-organic hybrids of DNA, peptides and surfactants: from liquid crystals to molecular sleds. University of Groningen.
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Summary
Biomacromolecules, including DNA, proteins or even larger architectures like viruses consisting of these building blocks, can be complexed with surfactants to form solvent-free bio-fluids. The driving force to connect both oppositely charged entities is electrostatic interactions. The resulting hybrids comprise extremely high concentrations of structurally and functionally intact biomacromolecules and display novel properties, which are very different from the two individual components. Their applications can be extended into technologies that are incompatible with solvent systems. Examples are catalysis at temperatures beyond the boiling point of water or the fabrication of electronic devices where water is often detrimental for device performance. In this thesis, such electrostatically stabilized solvent systems were further developed. On the one hand a surfactant system was introduced, which contained an extended aromatic π-system. In previous work, simpler surfactant structures were introduced into such solvent systems. The choice of the surfactant significantly changes the physical properties of the resulting polypeptide-based materials. It could be demonstrated that even small shear forces result in a persistent phase change. On the other hand, the aromatic moieties, as part of the surfactant, allow the construction of photo-responsive materials, especially due to incorporation of a switchable azobenzene unit. In this context, light-induced mechanical changes in thin films composed of DNA-based thermotropic liquid crystals were realized.
Another example where electrostatic bonding is very important for evolving dynamic functional systems represents DNA-protein interactions in Nature. A remarkable example is pVIc, a 11-amino-acid peptide, that is capable of diffusing along double stranded DNA. In Nature the one-dimensional diffusion along nucleic acids is important to speed up the cleavage of proteins located on DNA by the sliding protease. This cleavage represents an important step during virus maturation. Inspired by the natural functionality, this concept could be used to speed up a broader class of processes involving common laboratory reactions.
In chapter 1, solvent-free nucleic acid, proteins and virus liquids obtained by complexing these components with surfactants to overcome the intermolecular forces between them were reviewed. Phase transitions temperatures of these bio-fluids can be tuned by changing the alkyl chain length of surfactants. Besides that, they are thermally stable and can be possessed in the absence of any solvents, which offers opportunities for the fabrication of biomaterials-based devices, such as electrochromic and electrochemical circuits.
Inspired by the existing bio-fluids formed through electrostatic complexation, in chapter 2, we described a bio-hydrogel enabled by complexing a series of negatively supercharged polypeptides (SUPs) with cationic surfactant containing an azobenzene unit (AZO). Under application of shear force, an isothermal phase transition occurred from disordered isotropic hydrogel to ordered nematic lyotropic liquid crystal. Due to the π-π interactions between adjacent AZO surfactants in the SUP-AZO complexes, the induced nematic structure can be maintained. Phase transition behavior was further investigated by applying oscillatory shear on SUP-AZO fluids. Results showed that the E144-AZO fluid containing the longest polypeptide backbone exhibited a faster phase transition from isotropic to nematic phase than E72/E36-AZO materials. The molecular weight and charge density of SUPs play an important role in regulating the self-ordering behavior. Moreover, other mechanical stimuli, like fluid flow and finger pressing, were studied. With a water flow rate of 40 ml/s, an orientated liquid crystal structure appeared. The birefringence patterns induced by finger tips were in good agreement with various fingerprint types. Liquid crystal induced birefringence is an excellent read-out signal for potential future individual identification. In chapter 3, we synthesized a novel branched cationic surfactant also containing an azobenzene moiety. The pristine surfactant showed a lamellar LC structure from -5 to 50°C. Upon ultraviolet (UV) light irradiation, the layer spacing of two isomers (trans and cis) changed from 3.82 nm (trans) to 3.43 nm (cis). After complexed with double stranded (ds) and single stranded (ss) DNA and dehydration, a new mesophase of DNA thermotropic liquid crystal (TLC) was achieved. While previously only smectic layers were reported, here, we successfully realized nematic textures. This mesophase is present over the temperature range from -7 to 110°C and only 3~5% water is present in the bulk materials. After dehydration, the double stranded configuration of DNA is obtained in the nematic TLCs as proven by SAXS measurements. DNA-AZO complex showed higher elastic moduli than pristine AZO surfactant and due to the rigidity of DNA, the elastic and viscosity performances of DNA-AZO TLC materials were enhanced significantly compared to the pristine surfactant. Based on the conformational change from trans to cis of the azobenzene moiety under UV irradiation, mechanical photo-responsive behaviors of DNA TLC materials were investigated. It was found that the stiffness of dsDNA-AZO architectures could be successfully manipulated with light as the stimulus.
In addition to the biomacromolecule based LC systems discussed in chapter 2 and 3, the focus in
chapter 4 was shifted to the utilization of the molecular peptide sled, pVIc. Alexander Turkin and
Antoine M. van Oijen provided a proof-of-principle that association between biotin and streptavidin
can be accelerated by using pVIc peptide, which undergoes one-dimensional diffusion along DNA. This reaction is broadly used as versatile conjugation strategy, however, does not really require a rate acceleration. We extended the concept of reducing the three dimensional search of supramolecular reactants to one dimension to a biotechnologically relevant technique, i.e. the polymerase chain reaction (PCR). Therefore, a pair of primers was coupled to the sliding peptide at their 5’ end and were used in accelerating the PCR experiment, especially the primer annealing within this three step process. The melting temperatures of modified primers were identical compared to unmodified ones. In this chapter, two pairs of primers and two lengths of DNA templates were investigated and results showed that the PCR reaction time can be shortened by 15~27% with molecular sled functionalized primers. This enhancement can be attributed to the reduction of search dimensionality that makes primers find and hybridize to their complementary target sequence on DNA template faster and, thus, results in acceleration of the PCR procedure. In chapter 5, we applied this 1D diffusion mechanism to accelerate covalent chemical bond formation and improve the efficiency of DNA photocleavage. For speed up a chemical reaction, a nucleophilic substitution in which a sulfhydryl group on one sled molecule replaces a bromide atom on a second sled molecule was chosen as a model. In the presence of DNA, the initial rate of the reaction can increase up to 17.9-fold by reducing the substrates diffusion dimensionality from three to one compared to the reaction without DNA. Besides, results showed the potential of chiral induction within 1D reaction systems. We further coupled the sled molecule pVIc to a photosensitizer, verteporfin (vp), to photocleave DNA. Under 30 min irradiation, no visible DNA bands were obtained when the concentration of vp-pVIc conjugate increased to 5 μM while there was still 90% DNA left for pure verteporfin. This can be attributed to the 1D diffusion of pVIc along DNA to concentrate the produced reactive oxygen species (ROS) in close proximity to DNA targets. This strategy provides a way to overcome the limitation of the life-span and active radius of ROS. In the future, similar photosensitizer conjugates might improve the treatment modalities of photodynamic therapy.
