Template Binding Research Articles

The Roles of Tryptophans in Primer Synthesis by the DNA Primase of Bacteriophage T7

DNA primases catalyze the synthesis of oligoribonucleotides required for the initiation of lagging strand DNA synthesis. Prokaryotic primases consist of a zinc-binding domain (ZBD) necessary for recognition of a specific template sequence and a catalytic RNA polymerase domain. Interactions of both domains with the DNA template and ribonucleotides are required for primer synthesis. Five tryptophan residues are dispersed in the primase of bacteriophage T7: Trp-42 in the ZBD and Trp-69, -97, -147, and -255 in the RNA polymerase domain. Previous studies showed that replacement of Trp-42 with alanine in the ZBD decreases primer synthesis, whereas substitution of non-aromatic residues for Trp-69 impairs both primer synthesis and delivery. However, the roles of tryptophan at position 97, 147, or 255 remain elusive. To investigate the essential roles of these residues, we replaced each tryptophan with the structurally similar tyrosine and examined the effect of this subtle alteration on primer synthesis. The substitution at position 42, 97, or 147 reduced primer synthesis, whereas substitution at position 69 or 255 did not. The functions of the tryptophans were further examined at each step of primer synthesis. Alteration of residue 42 disturbed the conformation of the ZBD and resulted in partial loss of the zinc ion, impairing binding to the ssDNA template. Replacement of Trp-97 with tyrosine reduced the binding affinity to NTP and the catalysis step. The replacement of Trp-147 with tyrosine also impaired the catalytic step. Therefore, Trp-42 is important in maintaining the conformation of the ZBD for template binding; Trp-97 contributes to NTP binding and the catalysis step; and Trp-147 maintains the catalysis step.

Azobenzene-Containing Molecularly Imprinted Polymer Microspheres with Photo- and Thermoresponsive Template Binding Properties in Pure Aqueous Media by Atom Transfer Radical Polymerization

A facile, general, and highly efficient approach to obtain azobenzene (azo)-containing molecularly imprinted polymer (MIP) microspheres with both photo- and thermoresponsive template binding properties in pure aqueous media is described for the first time, which involves the first synthesis of "living" azo-containing MIP microspheres with surface-immobilized alkyl halide groups via atom transfer radical precipitation polymerization (ATRPP) and their subsequent modification via surface-initiated atom transfer radical polymerization (ATRP) of N-isopropylacrylamide (NIPAAm). The successful grafting of poly(NIPAAm) (PNIPAAm) brushes onto the obtained MIP microspheres was confirmed by FT-IR, SEM, water dispersion stability and static contact angle studies, and template binding experiments. The introduction of PNIPAAm brushes onto the azo-containing MIP microspheres significantly improved their surface hydrophilicity and imparted thermoresponsive properties to them, leading to their pure water-compatible and thermoresponsive template binding properties. In addition, the binding affinity of the imprinted sites in the grafted azo-containing MIP microspheres was found to be photoresponsive toward the template in pure water, and this photoregulation process proved to be highly repeatable under photoswitching conditions.

An rRT-PCR Assay to Detect the Matrix Gene of a Broad Range of Avian Paramyxovirus Serotype-1 Strains

The current U.S. Department of Agriculture (USDA)-validated real-time reverse transcription-polymerase chain reaction (rRT-PCR) assay designed to detect the matrix gene of avian paramyxovirus serotype-1 (APMV-1) is the primary screening assay used in the United States. It has previously been shown to be unable to consistently detect all members of class I APMV-1. Diagnostic testing relies on rRT-PCR to quickly detect APMV-1 in wild birds, backyard flocks, live bird markets, commercial poultry, and for export testing. Limitations of the current USDA assay have raised concerns about the potential for some strains of APMV-1 to remain undetected by the primary screening assay. Mismatches in the probe were shown to cause a loss in template binding efficiency, resulting in lack of detection by the assay. Here, we describe the development and analytical validation of a new rRT-PCR assay designed to target a highly conserved region of the matrix gene across a wide range of APMV-1 strains. Limit of detection testing revealed a 3 log10 decrease in sensitivity for one low-virulence strain when compared to the USDA validated assay. Conversely, the assay showed increased sensitivity for a class I isolate and two virulent strains of APMV-1 that were not detected by the USDA-validated assay. The new assay also demonstrated a high degree of specificity by the lack of detection of 43 non-APMV-1 viruses.

Structural basis of human DNA polymerase η-mediated chemoresistance to cisplatin

Cisplatin (cis-diamminedichloroplatinum) and related compounds cause DNA damage and are widely used as anticancer agents. Chemoresistance to cisplatin treatment is due in part to translesion synthesis by human DNA polymerase η (hPol η). Here, we report crystal structures of hPol η complexed with intrastrand cisplatin-1,2-cross-linked DNA, representing four consecutive steps in translesion synthesis. In contrast to the generally enlarged and nondiscriminating active site of Y-family polymerases like Dpo4, Pol η is specialized for efficient bypass of UV-cross-linked pyrimidine dimers. Human Pol η differs from the yeast homolog in its binding of DNA template. To incorporate deoxycytidine opposite cisplatin-cross-linked guanines, hPol η undergoes a specific backbone rearrangement to accommodate the larger base dimer and minimizes the DNA distortion around the lesion. Our structural analyses show why Pol η is inefficient at extending primers after cisplatin lesions, which necessitates a second translesion DNA polymerase to complete bypass in vivo. A hydrophobic pocket near the primer-binding site in human Pol η is identified as a potential drug target for inhibiting translesion synthesis and, thereby, reducing chemoresistance.

Characterization of Swellable Molecularly Imprinted Polymer Particles by Surface Plasmon Resonance Spectroscopy

Surface plasmon resonance (SPR) has been used to investigate template binding at sites in theophylline-imprinted poly-[N-(N-propyl) acrylamide] particles. At concentrations as low as 10(-6) M theophylline, particle swelling is detected as a shift in the angle of minimum reflectance. The binding constant of theophylline estimated from the inflection point of the theophylline calibration curve is approximately 10,000. The imprinted polymer particles do not respond to caffeine or theobromine (which differs from theophylline by a single methyl group) at concentrations as high as 10(-2) M. Full-scale response of the imprinted polymer particles to theophylline (template) occurs in less than 15 minutes, and swelling is reversible. The immobilized imprinted polymer particles can undergo approximately 20 to 25 swelling and shrinking cycles before there is significant loss in functionality. A unique aspect of these imprinted polymer particles is that template binding causes the angle of minimum reflectance to decrease, not increase, in magnitude. Adsorption, which causes an increase in the angle of minimum reflectance, can be readily discriminated from template binding.

Improvement of the homogeneity of protein-imprinted polymer films by orientated immobilization of the template

A method for preparing homogeneous protein-imprinted polymer films with orientated immobilization of template is described. The template methyl parathion hydrolase (MPH) was modified with a peptide linker (Gly-Ser)5–Cys and was immobilized on a cover glass with a fixed orientation via the linker. The activity of the fusion enzyme (MPH-L) was evaluated by determining the product's absorbance at 405nm (A405). Both the free and the immobilized MPH-L showed higher retention of the bioactivity than the wide type enzyme (MPH-W) as revealed by the A405 values for MPH-Lfree/MPH-Wfree (1.159/1.111) and for MPH-Limmobilized/MPH-Wimmobilized (0.348/0.118). The immobilized MPH-L also formed a more homogeneous template stamp compared to the immobilized MPH-W. The molecularly imprinted polymer films prepared with the immobilized MPH-L exhibited high homogeneity with low Std. Deviations of 80 and 200 from the CL intensity mean volumes which were observed for batch-prepared films and an individual film, respectively. MPH-L-imprinted polymer film also had a larger template binding capacity indicated by higher CL intensity mean volume of 3900 INT over 2500 INT for MPH-W-imprinted films. The imprinted film prepared with the orientated immobilization of template showed an imprinting factor of 1.7, while the controls did not show an imprinting effect.

Cooperation between Catalytic and DNA Binding Domains Enhances Thermostability and Supports DNA Synthesis at Higher Temperatures by Thermostable DNA Polymerases

We have previously introduced a general kinetic approach for comparative study of processivity, thermostability, and resistance to inhibitors of DNA polymerases [Pavlov, A. R., et al. (2002) Proc. Natl. Acad. Sci. U.S.A.99, 13510-13515]. The proposed method was successfully applied to characterize hybrid DNA polymerases created by fusing catalytic DNA polymerase domains with various sequence-nonspecific DNA binding domains. Here we use the developed kinetic analysis to assess basic parameters of DNA elongation by DNA polymerases and to further study the interdomain interactions in both previously constructed and new chimeric DNA polymerases. We show that connecting helix-hairpin-helix (HhH) domains to catalytic polymerase domains can increase thermostability, not only of DNA polymerases from extremely thermophilic species but also of the enzyme from a faculatative thermophilic bacterium Bacillus stearothermophilus. We also demonstrate that addition of Topo V HhH domains extends efficient DNA synthesis by chimerical polymerases up to 105 °C by maintaining processivity of DNA synthesis at high temperatures. We found that reversible high-temperature structural transitions in DNA polymerases decrease the rates of binding of these enzymes to the templates. Furthermore, activation energies and pre-exponential factors of the Arrhenius equation suggest that the mechanism of electrostatic enhancement of diffusion-controlled association plays a minor role in binding of templates to DNA polymerases.

Narrowly Dispersed Molecularly Imprinted Polymer Microspheres with Photo- and Thermo-Responsive Template Binding Properties in Pure Aqueous Media by RAFT Polymerization

Narrowly Dispersed Molecularly Imprinted Polymer Microspheres with Photo- and Thermo-Responsive Template Binding Properties in Pure Aqueous Media by RAFT Polymerization

Efficient synthesis of narrowly dispersed molecularly imprinted polymer microspheres with multiple stimuli-responsive template binding properties in aqueous media

A facile, general, and highly efficient approach to obtain narrowly dispersed molecularly imprinted polymer microspheres with multiple stimuli-responsive template binding properties in aqueous media by successive RAFT polymerization is described.

Altered Strand Transfer Activity of a Multiple-Drug-Resistant Human Immunodeficiency Virus Type 1 Reverse Transcriptase Mutant with a Dipeptide Fingers Domain Insertion

Prolonged highly active anti-retroviral therapy with multiple nucleoside reverse transcriptase inhibitors for the treatment of patients infected with human immunodeficiency virus type 1 (HIV-1) can induce the development of an HIV-1 reverse transcriptase (RT) harboring a dipeptide insertion at the RT fingers domain with a background thymidine analog mutation. This mutation renders viral resistance to multiple nucleoside reverse transcriptase inhibitors. We investigated the effect of the dipeptide fingers domain insertion mutation on strand transfer activity using two clinical RT variants isolated during the pre-treatment and post-treatment of an infected patient, termed pre-drug RT without dipeptide insertion and post-drug RT with Ser-Gly insertion, respectively. First, the post-drug RT displayed elevated strand transfer activity compared to the pre-drug RT, with two different RNA templates. Second, the post-drug RT exhibited less RNA template degradation than the pre-drug RT but higher polymerization-dependent RNase H activity. Third, the post-drug RT had a faster association rate (kon) for template binding and a lower equilibrium binding constant Kd for the template, leading to a template binding affinity tighter than that of the pre-drug RT. The koff values for the pre-drug RT and the post-drug RT were similar. Finally, the removal of the dipeptide insertion from the post-drug RT abolished the elevated strand transfer activity and RNase H activity, in addition to the loss of azidothymidine resistance. These biochemical data suggest that the dipeptide insertion elevates strand transfer activity by increasing the interaction of the RT with the RNA donor template, promoting cleavage that generates more invasion sites for the acceptor template during DNA synthesis.

Influence of template/functional monomer/cross‐linking monomer ratio on particle size and binding properties of molecularly imprinted nanoparticles

AbstractA series of molecularly imprinted polymer nanoparticles have been synthesized employing various template/functional monomer/crosslinking monomer ratio and characterized in detail to elucidate the correlation between the synthetic conditions used and the properties (e.g., particle size and template binding properties) of the obtained nanoparticles. In brief, the presence of propranolol (template) in the polymerization mixture turned out to be a critical factor on determination of the size as well as the binding properties of the imprinted nanoparticles. The functional monomer/crosslinking monomer ratio significantly affects the binding capability of the imprinted nanoparticles, but its influence on the size of the nanoparticles was found to be rather limited. The results obtained provide valuable clues for designing molecularly imprinted nanoparticle preparation in future studies, where fine tuning of particle size and binding properties are required to fit practical applications. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2012

Dipyridamole recognition and controlled release by uniformly sized molecularly imprinted nanospheres

We used novel synthetic conditions of precipitation polymerization to obtain uniformly sized molecularly imprinted nanospheres of dipyridamole for application in the design of new drug delivery systems. In addition, the morphology, drug release, and binding properties of molecularly imprinted polymers (MIPs) were studied, and the effects of morphology on other properties were investigated. The MIPs prepared by acetonitrile/chloroform (19:1, v/v) were uniformly sized nanospheres with an average mean diameter of approximately 88 nm at a wetted state, 50 nm at a dry state, and a polydispersity index of 0.062. The imprinted nanospheres showed excellent binding properties and had 62.7% of template binding compared with 17.1% of its blank polymer. The imprinted nanospheres with 67.5 (mg template/of polymer) of binding capacity had better imprinting efficiency than the 50.5% of binding capacity shown by irregularly shaped MIP particles that were prepared by chloroform. The molecular binding abilities of imprinted nanospheres in human serum were evaluated by HPLC analysis (binding about 77% of dipyridamole). Results from release experiments of MIPs showed a very slow, controlled, and satisfactory release of dipyridamole. The loaded drug was released up to 99% in 17 days for nanospheres and 22 days for irregularly shaped particles.

HIV-1 Reverse Transcriptase Dissociates during Strand Transfer

Steps in the replication of human immunodeficiency virus type 1 (HIV-1) occurring in the virus but not in the host are preferred targets of antiretroviral therapy. Strand transfer is unique; the DNA strand being made by viral reverse transcriptase (RT) is moved from one RNA template position to another. Understanding the mechanism requires knowing whether the RT directly mediates the template exchange or dissociates during the exchange, so that it occurs by polymer dynamics. Earlier work in vitro showed that the presence of an RT-trapping polymer would allow synthesis on the original or donor template but completely block transfer and subsequent synthesis on the second or acceptor template. One interpretation is that the RT must dissociate during transfer, but an alternative is that sequestration of non-polymerizing RTs prevents polymerization-independent ribonuclease H (RNase H) cleavages of the donor template necessary for strand exchange. To resolve this ambiguity, we designed a primer–template system that allows strand transfer without RNase H activity. Using an RNase H negative mutant RT, we showed that a polymer trap still prevented strand transfer. This confirms that RT dissociates during strand transfer. The presence of HIV-1 nucleocapsid protein, which promotes strand exchange, had little effect on this outcome. Additional assays showed that both the wild-type RT and a multiple nucleoside RT inhibitor-resistant HIV-1 RT containing an extended fingers domain, which is characterized by its enhanced primer–template binding affinity, were unable to transfer with the trapping polymer. This implies that common sequence variations among RTs are unlikely to alter dissociation feature.

Synthesis of tailor‐made nanoporous polyaniline derived with PVA/alkaline metal system for metal complexation

AbstractNanoporous polyanilines (PANIs) have attracted attention due to well‐defined molecular structures and chemical versatility, which also complicate the mechanisms of interaction between metal ions and PANI. To further understand the complexation with metal ions, tailor‐made nanoporous PANIs were synthesized with self‐stabilized dispersion polymerization (SSDP) using the poly(vinyl alcohol) (PVA) and various alkaline metals for suitable target metal complexation. The effective complexation results for the removal of Cr ions were obtained by the nanoporous PANI derived from a PVA/Li system. The synthesized tailor‐made PANI‐emeraldine base (EB) was easily oxidized by a Cr(VI) oxidant resulting in an pernigraniline form with a rigid polymer template and effective metal ion binding sites, and then the reduced form of Cr(III) can be complexed with the resulting PANI. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2011.

Mechanistic insights into the roles of three linked single-stranded template binding residues of MMLV reverse transcriptase in misincorporation and mispair extension fidelity of DNA synthesis

To obtain some insights into the structure–function relationship of Moloney murine leukemia virus (MMLV) reverse transcriptase (RT), we modeled the catalytic state ternary complexes of this protein using the corresponding RT from human immunodeficiency virus type 1 (HIV-1) and available structures of MMLV RT. We observed that three MMLV RT single-stranded template binding residues, Y64, D114, and R116, act as a linked set through mutual interactions, including hydrogen bonding and ion-pairing. The analogous residues of HIV-1 RT have a somewhat different environment and they lack this linked phenomenon. To understand the functional implication of this linked set of MMLV RT, we performed site-directed mutagenesis at these three positions. Then the mutant enzymes were examined for their biochemical properties and nucleotide selectivity. Mutagenesis of these residues (Y64A, D114A, and R116A) resulted in enzymes with slight to modest changes in polymerase activities. The processivity of DNA synthesis correlated positively with the binding affinity of the MMLV RT variants. Lower fidelity in mutants was indicated by measurements of misincorporation and mispair extension fidelity of wild type (WT) and mutant RTs, in contrast to earlier works that indicate that mutations at the analogous positions in HIV-1 RT result in relatively higher fidelity. These data together with structural analysis suggest that this structural set may therefore be a key factor responsible for the different fidelity of these two RTs.

Structure and function of the primase domain of the replication protein from the archaeal plasmid pRN1

The replication protein of the archaeal plasmid pRN1 is a multifunctional enzyme which appears to carry out several steps at the plasmid replication initiation. We recently determined the structure of the minimal primase domain of the replication protein and found out that the primase domain consists of a catalytic primase/polymerase domain and an accessory helix-bundle domain. Structure-guided mutagenesis allowed us to identify amino acids which are important for template binding, dinucleotide formation and a step before primer extension. On the basis of functional and structural data, we propose a model of the catalytic cycle of primer synthesis by the pRN1 replication protein.

Azobenzene-containing molecularly imprinted polymer microspheres with photoresponsive template binding properties

The first successful preparation of azobenzene (azo)-containing molecularly imprinted polymer (MIP) microspheres with photoresponsive template binding properties is described. A methacrylate azo functional monomer with a pyridine group was used for this purpose, and its good solubility in acetonitrile allowed the implementation of molecular imprinting viaprecipitation polymerization, leading to azo-containing MIP microspheres (number-average diameter = 1.33 μm, polydispersity index = 1.15) with obvious molecular imprinting effects towards the template 2,4-dichlorophenoxyacetic acid (2,4-D), rather fast template rebinding kinetics, and appreciable selectivity over structurally related compounds. The binding association constant Ka and apparent maximum number Nmax for high-affinity sites of the imprinted polymer in the dark environment were determined by Scatchard analysis to be 2.3 × 104 M−1 and 10.0 μmol g−1, respectively. Most importantly, the binding affinity of the imprinted sites in azo-containing MIP microspheres was found to be photoresponsive towards the template, which decreased upon UV light irradiation (as revealed by the resulting lower Ka value for high-affinity sites and reduced specific bindings), whereas it could be recovered during the subsequent thermal (or visible light-induced) back-isomerization. Furthermore, this photoregulation process proved to be highly repeatable under photoswitching conditions.

Zn2+ Inhibits Coronavirus and Arterivirus RNA Polymerase Activity In Vitro and Zinc Ionophores Block the Replication of These Viruses in Cell Culture

Increasing the intracellular Zn2+ concentration with zinc-ionophores like pyrithione (PT) can efficiently impair the replication of a variety of RNA viruses, including poliovirus and influenza virus. For some viruses this effect has been attributed to interference with viral polyprotein processing. In this study we demonstrate that the combination of Zn2+ and PT at low concentrations (2 µM Zn2+ and 2 µM PT) inhibits the replication of SARS-coronavirus (SARS-CoV) and equine arteritis virus (EAV) in cell culture. The RNA synthesis of these two distantly related nidoviruses is catalyzed by an RNA-dependent RNA polymerase (RdRp), which is the core enzyme of their multiprotein replication and transcription complex (RTC). Using an activity assay for RTCs isolated from cells infected with SARS-CoV or EAV—thus eliminating the need for PT to transport Zn2+ across the plasma membrane—we show that Zn2+ efficiently inhibits the RNA-synthesizing activity of the RTCs of both viruses. Enzymatic studies using recombinant RdRps (SARS-CoV nsp12 and EAV nsp9) purified from E. coli subsequently revealed that Zn2+ directly inhibited the in vitro activity of both nidovirus polymerases. More specifically, Zn2+ was found to block the initiation step of EAV RNA synthesis, whereas in the case of the SARS-CoV RdRp elongation was inhibited and template binding reduced. By chelating Zn2+ with MgEDTA, the inhibitory effect of the divalent cation could be reversed, which provides a novel experimental tool for in vitro studies of the molecular details of nidovirus replication and transcription.

Synthesis and evaluation of molecularly imprinted core–shell carbon nanotubes for the determination of triclosan in environmental water samples

Synthetic core–shell molecularly imprinted polymers (MIPs) were prepared for the extraction of trace triclosan in environmental water samples. The synthesis process combined a surface molecular imprinting technique with a sol–gel process based on carbon nanotubes (CNTs) coated with silica. The morphology and structure of the products were characterized by transmission electron microscopy and Fourier transform infrared spectroscopy. The adsorption properties of the polymers were demonstrated by equilibrium rebinding experiments and Scatchard analysis. The prepared imprinted materials exhibited fast kinetics, high capacity and favorable selectivity. The process of synthesis was quite simple and different batches of MIPs and non-imprinted polymers (NIPs) showed good reproducibility in the template binding. The feasibility of determination of triclosan from real samples was testified using spiked river and lake water samples. The recoveries of river water and lake water samples were ranged from 92.1 to 95.3% and 90.7 to 93.6%, respectively, when the environmental water samples were spiked with 0.1, 0.3, and 0.5 μg L −1 of TCS. In addition, the reusability of MIPs and NIPs without any deterioration in capacity was demonstrated for at least 10 repeated cycles.

Preparation and characterisation of core–shell CNTs@MIPs nanocomposites and selective removal of estrone from water samples

This paper reports the preparation of carbon nanotubes (CNTs) functionalized with molecularly imprinted polymers (MIPs) for advanced removal of estrone. CNTs@Est-MIPs nanocomposites with a well-defined core–shell structure were obtained using a semi-covalent imprinting strategy, which employed a thermally reversible covalent bond at the surface of silica-coated CNTs for a large-scale production. The morphology and structure of the products were characterised by transmission electron microscopy and Fourier transform infrared spectroscopy. The adsorption properties were demonstrated by equilibrium rebinding experiments and Scatchard analysis. The results demonstrate that the imprinted nanocomposites possess favourable selectivity, high capacity and fast kinetics for template molecule uptake, yielding an adsorption capacity of 113.5 μmol/g. The synthetic process is quite simple, and the different batches of synthesized CNTs@Est-MIPs nanocomposites showed good reproducibility in template binding. The feasibility of removing estrogenic compounds from environmental water using the CNTs@Est-MIPs nanocomposites was demonstrated using water samples spiked with estrone.