A functional chimeric DNA primase: the Cys4 zinc-binding domain of bacteriophage T3 primase fused to the helicase of bacteriophage T7

Two colinear bacteriophage T7 gene 4 proteins provide helicase and primase functions in vivo. T7 primase differs from T7 helicase by an additional 63 residues at the amino terminus. This terminal domain contains a zinc-binding motif which mediates an interaction with the basic primase recognition sequence 3'-CTG-5'. We have generated a chimeric primase in which the 81 amino-terminal residues are derived from the primase of phage T3 and the 484 carboxyl-terminal residues are those of phage T7 helicase. The amino-terminal domain of T3 primase is 50% homologous with that of T7 primase. The resulting T3/T7 chimeric protein is a functional primase in vivo. While the primase activity of the purified protein is about one-third that of T7 primase, the recognition sites used and the oligoribonucleotides synthesized from these sites are identical. We conclude that the residues responsible for the interaction with the sequence 3'-CTG-5' are conserved between the chimeric and T7 proteins.

Controlled RAFT polymerization and zinc binding performance of catechol-inspired homopolymers

Incorporation of catechols into polymers has long been of interest due to their ability to chelate heavy metals and their use in the design of adhesives, metal-polymer nanocomposites, antifouling coatings, and so on. This paper reports, for the first time, the reversible addition-fragmentation chain transfer (RAFT) polymerization of a protected catechol-inspired monomer, 3,4-dimethoxystyrene (DMS), using commercially available trithiocarbonate, 2-(dodecylthiocarbonothioylthio)-2-methylpropionic acid (DDMAT), as a chain transfer agent. Our identified RAFT system produces well-defined polymers across a range of molecular weights (5-50 kg/mol) with low molar mass dispersities (Mw/Mn < 1.3). Subsequent facile demethylation of poly(3,4-dimethoxystyrene) (PDMS) yields poly(3,4-dihydroxystyrene) (PDHS), a catechol-bearing polymer, in quantitative yields. Semiquantitative zinc binding capacity analysis of both polymers using SEM/EDXA has demonstrated that both PDMS and PDHS have considerable surface binding (65% and 87%, respectively), although the films deposited from PDMS are of a better quality and processability due to solubility and lower processing temperatures. © 2014 American Chemical Society.

The Cys4 zinc finger of bacteriophage T7 primase in sequence-specific single-stranded DNA recognition

Bacteriophage T7 DNA primase recognizes 5'-GTC-3' in single-stranded DNA. The primase contains a single Cys4 zinc-binding motif that is essential for recognition. Biochemical and mutagenic analyses suggest that the Cys4 motif contacts cytosine of 5'-GTC-3' and may also contribute to thymine recognition. Residues His33 and Asp31 are critical for these interactions. Biochemical analysis also reveals that T7 primase selectively binds CTP in the absence of DNA. We propose that bound CTP selects the remaining base G, of 5'-GTC-3', by base pairing. Our deduced mechanism for recognition of ssDNA by Cys4 motifs bears little resemblance to the recognition of trinucleotides of double-stranded DNA by Cys2His2 zinc fingers.

Design, synthesis and RAFT polymerisation of a quinoline-based monomer for use in metal-binding composite microfibres

Metal-binding polymer fibres have attracted major attention for diverse applications in membranes for metal sequestration from waste waters, non-woven wound dressings, matrices for photocatalysis, and many more. This paper reports the design and synthesis of an 8-hydroxyquinoline-based zinc-binding styrenic monomer, QuiBoc. Its subsequent polymerisation by reversible addition–fragmentation chain transfer (RAFT) yielded well-defined polymers, PQuiBoc, of controllable molar masses (6 and 12 kg mol−1) with low dispersities (Đ, Mw/Mn < 1.3). Protected (PQuiBoc) and deprotected (PQuiOH) derivatives of the polymer exhibited a high zinc-binding capacity, as determined by semi-quantitative SEM/EDXA analyses, allowing the electrospinning of microfibres from a PQuiBoc/polystyrene (PS) blend without the need for removal of the protecting group. Simple “dip-coating” of the fibrous mats into ZnO suspensions showed that PQuiBoc/PS microfibres with only 20% PQuiBoc content had almost three-fold higher loadings of ZnO (29%) in comparison to neat PS microfibres (11%).

Synthesis and characterisation of interfacial layers in organic solar cells

The quest for renewable energy sources has led to growing attention in the research of organic photovoltaics (OPVs), as a promising alternative to fossil fuels, since these devices have low manufacturing costs and attractive end-user qualities, such as ease of installation and maintenance. Wide application of OPVs is majorly limited by the devices lifetime. With the development of new encapsulation materials, some degradation factors, such as water and oxygen ingress, can almost be excluded, whereas the thermal degradation of the devices remains a major issue. Two aspects have to be addressed to solve the problem of thermal instability: bulk effects in the photoactive layer and interfacial effects at the photoactive layer/charge-transporting layers. In this work, the interface between photoactive layer and electron-transporting zinc oxide (ZnO) in devices with inverted architecture was engineered by introducing polymeric interlayers, based on zinc-binding ligands, such as 3,4-dihydroxybenzene and 8-hydroxyquinoline. Also, a cross-linkable layer of poly(3,4-dimethoxystyrene) and its fullerene derivative were studied. At first, controlled reversible addition-fragmentation chain transfer (RAFT) polymerisation was employed to achieve well-defined polymers in a range of molar masses, all bearing a chain-end functionality for further modifications. Resulting polymers have been fully characterised, including their thermal and optical properties, and introduced as interlayers to study their effect on the initial device performance and thermal stability. Poly(3,4-dihydroxystyrene) and its fullerene derivative were found unsuitable for application in devices as they increased the work function of ZnO and created a barrier for electron extraction. On the other hand, their parental polymer, poly(3,4-dimethoxystyrene), and its fullerene derivative, upon cross-linking, resulted in enhanced efficiency and stability of devices, if compared to control. Polymers based on 8-hydroxyquinoline ligand had a negative effect on the initial stability of the devices, but increased the lifetime of the cells under accelerated thermal stress. Comprehensive studies of the key mechanisms, determining efficiency, such as charge generation and extraction, were performed by using time-resolved electrical and spectroscopic techniques, in order to understand in detail the effect of the interlayers on the device performance. Obtained results allow deeper insight into mechanisms of degradation that limit the lifetime of devices and prompt the design of better materials for the interface stabilisation.

The development of a model system and high throughput assay for the study of interactions between zinc finger proteins and DNA

It has been recognised for some time that a full code of amino acid-based recognition of DNA sequences would be useful. Several approaches, which utilise small DNA binding motifs called zinc fingers, are presently employed. None of the current approaches successfully combine a combinatorial approach to the elucidation of a code with a single stage high throughput screening assay. The work outlined here describes the development of a model system for the study of DNA protein interactions and the development of a high throughput assay for detection of such interactions. A zinc finger protein was designed which will bind with high affinity and specificity to a known DNA sequence. For future work it is possible to mutate the region of the zinc finger responsible for the specificity of binding, in order to observe the effect on the DNA / protein interactions. The zinc finger protein was initially synthesised as a His tagged product. It was not possible however to develop a high throughput assay using the His tagged zinc finger protein. The gene encoding the zinc finger protein was altered and the protein synthesised as a Glutathione S-Transferase (GST) fusion product. A successful assay was developed using the GST protein and Scintillation Proximity Assay technology (Amersham Pharmacia Biotech). The scintillation proximity assay is a dynamic assay that allows the DNA protein interactions to be studied in "real time". This assay not only provides a high throughput method of screening zinc finger proteins for potential ligands but also allows the effect of addition of reagents or competitor ligands to be monitored.

Role of β-adrenergic receptors in the anti-obesity and anti-diabetic effects of zinc-α2-glycoprotien (ZAG)

Objectives: The goal of the current study is to determine whether the ß-adrenoreceptor (ß-AR) plays a role in the anti-obesity and anti-diabetic effects of zinc-a2-glycoprotein (ZAG). Material and methods: This has been investigated in CHO-K1 cells transfected with the human ß1-, ß2-, ß3-AR and in ob/ob mice. Cyclic AMP assays were carried out along with binding studies. Ob/ob mice were treated with ZAG and glucose transportation and insulin were examined in the presence or absence of propranolol. Results: ZAG bound to the ß3-AR with higher affinity (Kd 46±1nM) than the ß2-AR (Kd 71±3nM) while there was no binding to the ß1-AR, and this correlated with the increases in cyclic AMP in CHO-K1 cells transfected with the various ß-AR and treated with ZAG. Treatment of ob/ob mice with ZAG increased protein expression of ß3-AR in gastrocnemius muscle, and in white and brown adipose tissues, but had no effect on expression of ß1- and ß2-AR. A reduction of body weight was seen and urinary glucose excretion, increase in body temperature, reduction in maximal plasma glucose and insulin levels in the oral glucose tolerance test, and stimulation of glucose transport into skeletal muscle and adipose tissue, were completely attenuated by the non-specific ß-AR antagonist propranolol. Conclusion: The results suggest that the effects of ZAG on body weight and insulin sensitivity in ob/ob mice are manifested through a ß-3AR, or possibly a ß2-AR.

Discovering properties of new DNA-binding activity of proteins

Protein-DNA interactions are an essential feature in the genetic activities of life, and the ability to predict and manipulate such interactions has applications in a wide range of fields. This Thesis presents the methods of modelling the properties of protein-DNA interactions. In particular, it investigates the methods of visualising and predicting the specificity of DNA-binding Cys2His2 zinc finger interaction. The Cys2His2 zinc finger proteins interact via their individual fingers to base pair subsites on the target DNA. Four key residue positions on the a- helix of the zinc fingers make non-covalent interactions with the DNA with sequence specificity. Mutating these key residues generates combinatorial possibilities that could potentially bind to any DNA segment of interest. Many attempts have been made to predict the binding interaction using structural and chemical information, but with only limited success. The most important contribution of the thesis is that the developed model allows for the binding properties of a given protein-DNA binding to be visualised in relation to other protein-DNA combinations without having to explicitly physically model the specific protein molecule and specific DNA sequence. To prove this, various databases were generated, including a synthetic database which includes all possible combinations of the DNA-binding Cys2His2 zinc finger interactions. NeuroScale, a topographic visualisation technique, is exploited to represent the geometric structures of the protein-DNA interactions by measuring dissimilarity between the data points. In order to verify the effect of visualisation on understanding the binding properties of the DNA-binding Cys2His2 zinc finger interaction, various prediction models are constructed by using both the high dimensional original data and the represented data in low dimensional feature space. Finally, novel data sets are studied through the selected visualisation models based on the experimental DNA-zinc finger protein database. The result of the NeuroScale projection shows that different dissimilarity representations give distinctive structural groupings, but clustering in biologically-interesting ways. This method can be used to forecast the physiochemical properties of the novel proteins which may be beneficial for therapeutic purposes involving genome targeting in general.