Study of the interaction between the G-quadruplex-forming thrombin-binding aptamer and the porphyrin 5,10,15,20-tetrakis-(N-methyl-4-pyridyl)-21,23H-porphyrin tetratosylate

Is Silver a Precious Metal for G-Quadruplex Stabilization Mediated by Porphyrins?

Cancer is a leading cause of death, so continuous efforts into cancer therapy are imperative. In tumor cells, telomerase and oncogene activity are key points for uncontrolled cell growth. Targeting these processes with ligands that inhibit telomerase and/or reduce oncogene expression has been identified as a promising cancer therapy. This study evaluated the selectivity and affinity of the silverII complex of 5,10,15,20-tetrakis(N-methyl-4-pyridinium)porphyrin (AgTMPyP) to stabilize DNA sequences capable of forming G4 structures mimicking the telomeric and oncogene regions, using spectroscopic, biochemical methods and in vitro assays. The tetracationic silver complex was compared with the free base, H2TMPyP, and the zincII complex, ZnTMPyP. The results obtained from UV-Vis and fluorescence methods pointed to a great affinity and good selectivity of AgTMPyP to G4 structures, especially for the oncogene MYC. In general, an increase in the ability of the studied ligands for 1O2 generation when interacting with oncogenic and telomeric G4 sequences was found. The results of the PCR stop assays proved that AgTMPyP has the ability to inhibit Taq polymerase. Additionally, in vitro assays demonstrated that the silverII complex exhibits low cytotoxicity against HaCaT- an immortalized, non-tumorigenic, skin keratinocytes cell line-and, although nonexclusive, AgTMPyP shows nuclear co-localization.

Harnessing DNA as a Designable Scaffold for Asymmetric Catalysis: Recent Advances and Future Perspectives

Since the first report of DNAzyme by in vitro selection in 1994, catalytic DNA has investigated extensively, and their application has expanded continually in virtue of rapid advances in molecular biology and biotechnology. Nowadays, DNA is in the second prime time by way of DNA-based hybrid catalysts and DNA metalloenzymes in which helical chirality of DNA serves to asymmetric catalysis. DNA-based hybrid catalysts are attractive system to respond the demand of the times to pursuit green and sustainable society beyond traditional catalytic systems that value reaction efficiency. Herein, we highlight the recent advances and perspective of DNA-based hybrid catalysts with various aspects of DNA as a versatile scaffold for asymmetric synthesis. We hope that scientists in a variety of fields will be encouraged to join and promote remarkable evolution of this interesting research.

Assays to Estimate the Binding Affinity of Aptamers

Aptamers have become coming-of-age molecular recognition elements in both diagnostic and therapeutic applications. Generated by SELEX, the 'quality control' of aptamers, which involves the validation of their binding affinity against their respective targets is pivotal to ascertain their potency prior to use in any downstream assays or applications. Several aptamers have been isolated thus far, however, the usage of inappropriate validation assays renders some of these aptamers dubitable in terms of their binding capabilities. Driven by this need, we provide an up-to-date critical review of the various strategies used to determine the aptamer-target binding affinity with the aim of providing researchers a better comprehension of the different analytical approaches in respect to the molecular properties of aptamers and their intended targets. The techniques reported have been classified as label-based techniques such as fluorescence intensity, fluorescence anisotropy, filter-binding assays, gel shift assays, ELISA; and label-free techniques such as UV-Vis spectroscopy, circular dichroism, isothermal titration calorimetry, native electrospray ionization-mass spectrometry, quartz crystal microbalance, surface plasmon resonance, NECEEM, backscattering interferometry, capillary electrophoresis, HPLC, and nanoparticle aggregation assays. Hybrid strategies combining the characteristics of both categories such as microscale thermophoresis have been also additionally emphasized. The fundamental principles, complexity, benefits, and challenges under each technique are elaborated in detail.

Mathematical approaches in estimating aptamer-target binding affinity

The performance of aptamers as versatile tools in numerous analytical applications is critically dependent on their high target binding specificity and selectivity. However, only the technical or methodological aspects of measuring aptamer-target binding affinities are focused, ignoring the equally important mathematical components that play pivotal roles in affinity measurements. In this study, we aim to provide a comprehensive review regarding the utilization of different mathematical models and equations, along with a detailed description of the computational steps involved in mathematically deriving the binding affinity of aptamers against their specific target molecules. Mathematical models ranging from one-site binding to multiple aptameric binding site-based models are explained in detail. Models applied in several different approaches of affinity measurements such as thermodynamics and kinetic analysis, including cooperativity and competitive-assay based mathematical models have been elaborately discussed. Mathematical models incorporating factors that could potentially affect affinity measurements are also further scrutinized.

The Effect of Temperature on the Interaction of Phenanthroline-based Ligands with G-quadruplex: In Silico Viewpoint

AIM AND OBJECTIVE

The stability of the G-quadruplex structure can increase its activity in telomerase inhibiting cancer cells. In this study, a molecular dynamics simulation method was used to study the effect of three phenanthroline-based ligands on the structure of G-quadruplex at the temperatures of 20, 40, 60 and 80°C.

MATERIALS AND METHODS

RMSD values and frequency of calculated RMSD in the presence and absence of ligands show that ligands cause the relative stability of the G-quadruplex, particularly at low temperatures. The calculation of hydrogen bonds in Guanine-tetrads in three different quadruplex sheets shows that the effect of ligands on the sheets is not the same so that the bottom sheet of G-quadruplex is most affected by the ligands at high temperatures, and the Guaninetetrads in this sheet are far away. Conformation factor was calculated as a measure of ligands binding affinity for each of the G-quadruplex residues.

RESULTS

The results show that the studied ligands interact more with the G-quadruplex than loop areas, although with increasing temperature, the binding area also includes the G-quadruplex sheets. The contribution of each of the residues involved in the G-quadruplex binding area with ligands was also calculated.

CONCLUSION

The calculations performed are consistent with the previous experimental observations that can help to understand the molecular mechanism of the interaction of phenanthroline and its derivatives with quadruplex.

Simultaneous label-free screening of G-quadruplex active ligands from natural medicine via a microfluidic chip electrophoresis-based energy transfer multi-biosensor strategy

Rapid screening of active compounds plays a crucial role in the research and application of complex natural medicines. Herein, a new method of simultaneous label-free multi-drug screening based on a selective aptamer-carboxyfluorescein/graphene oxide energy transfer optical sensor combined with microfluidic chip electrophoretic separation is reported. In this study, seven traditional Chinese medicinal monomers were chosen as targets for the screening of G-quadruplex ligands. The screening results of the G-quadruplex active ligands, including daidzein, berberine hydrochloride, jatrorrhizine hydrochloride, and fangchinoline, and non-active ligands, including geniposide and oxymatrine, were consistent with those reported in literature. Moreover, one new potential G4DNA active drug, jujuboside A, was identified. Molecular simulation of the interaction between G4DNA and drugs was also carried out using HyperChem and AutoDock to verify the results of the experimental screening. It further demonstrated the reliability of our strategy. This novel separation and concentration based multi-sensing strategy provides a simple, rapid, and sensitive tool for simultaneous multi-drug screening, which is very meaningful for drug screening and bio-interaction analysis.

Influence of the SPR Experimental Conditions on the G-Quadruplex DNA Recognition by Porphyrin Derivatives

Surface plasmon resonance (SPR) is a powerful technique to study the interactions of ligands with analytes and therefore a number of biosensor surfaces and injection methods have been developed so far. However, many experimental parameters can affect the interactions and consequently the affinity measurements. In particular, the interactions of positively charged analytes (often used for anionic nucleic acids targets) can be influenced by the sensing surfaces (e.g., negatively charged), leading to significant nonspecific interactions as well as regeneration problems. The aim of the present work is to investigate the effect of different parameters, including ionic strength, SPR biosensor (i.e., nature of the surfaces), and the injection method on the recognition of porphyrin G-quadruplex ligands. We demonstrate that the injection method does not influence the affinity whereas the ionic strength and the nature of the surface impact the recognition properties of the porphyrin for the G-quadruplex DNA. We also found that self-assembled monolayer coating surface presents many advantages in comparison with carboxymethylated dextran surface for SPR studies of G-quadruplex DNA/ligand interactions: (i) the electrostatic interaction with charged analytes is less important, (ii) its structure/composition is less sensitive to the ionic concentration and less prone to unspecific adsorption, (iii) it is easily homemade, and (iv) the cost is approximately 10 times cheaper.

Recent Advances in SELEX Technology and Aptamer Applications in Biomedicine

Aptamers are short DNA/RNA oligonucleotides capable of binding to target molecules with high affinity and specificity. The process of selecting an aptamer is called Systematic Evolution of Ligands by Exponential Enrichment (SELEX). Thanks to the inherit merits, aptamers have been used in a wide range of applications, including disease diagnosis, targeted delivery agents and therapeutic uses. To date, great achievements regarding the selection, modifications and application of aptamers have been made. However, few aptamer-based products have already successfully entered into clinical and industrial use. Besides, it is still a challenge to obtain aptamers with high affinity in a more efficient way. Thus, it is important to comprehensively review the current shortage and achievement of aptamer-related technology. In this review, we first present the limitations and notable advances of aptamer selection. Then, we compare the different methods used in the kinetic characterization of aptamers. We also discuss the impetus and developments of the clinical application of aptamers.

A Selective G-Quadruplex DNA-Stabilizing Ligand Based on a Cyclic Naphthalene Diimide Derivative

A cyclic naphthalene diimide (cyclic NDI, 1), carrying a benzene moiety as linker chain, was synthesized and its interaction with G-quadruplex DNAs of a-core and a-coreTT as a human telomeric DNA, c-kit and c-myc as DNA sequence at promoter region, or thrombin-binding aptamer (TBA) studied based on UV-VIS and circular dichroism (CD) spectroscopic techniques, thermal melting temperature measurement, and FRET-melting assay. The circular dichroism spectra showed that 1 induced the formation of different types of G-quadruplex DNA structure. Compound 1 bound to these G-quadruplexes with affinities in the range of 10⁶–10⁷ M⁻¹ order and a 2:1 stoichiometry. Compound 1 showed 270-fold higher selectivity for a-core than dsDNA with a preferable a-core binding than a-coreTT, c-kit, c-myc and TBA in the presence of K⁺, which is supported by thermal melting studies. The FRET-melting assay also showed that 1 bound preferentially to human telomeric DNA. Compound 1 showed potent inhibition against telomerase activity with an IC₅₀ value of 0.9 μM and preferable binding to G-quadruplexes DNA than our previously published cyclic NDI derivative 3 carrying a benzene moiety as longer linker chain.

Effects of guanine bases at the central loop on stabilization of the quadruplex DNAs and their interactions with Meso-tetrakis(N-methylpyridium-4-yl)porphyrin

The thermal stability of the G-quadruplex formed from the thrombin-binding aptamer, 5'G2T2G2TGTG2T2G2, in which the guanine (G) base at the central loop was replaced with an adenine (A) or inosine (I) base, was examined to determine the role of the central G base in stabilizing the quadruplex. Replacement of the central G base by the I base resulted in a slight decrease in thermal stability. On the other hand, the stability of the G-quadruplex decreased to a significant extent when it was replaced with the A base. The optimized structure of the G-quadruplex, which was obtained by a molecular dynamic simulation, showed that the carbonyl group of the C5 position of the central G base could form hydrogen bonds with the G1 amine group at the C7 position on the upper G-quartet. This formation of a hydrogen bond contributes to the stability of the G-quadruplex. The spectral property of meso-tetrakis(N-methylpyridium-4yl)porphyrin (TMPyP) associated with the G-quadruplex was characterized by a moderate red shift and hypochromism in the absorption spectrum, a positive CD signal, and two emission maxima in the fluorescence emission spectrum, suggesting that TMPyP binds at the exterior of the G-quadruplex. Spectral properties were slightly altered when the G base at the central loop was replaced with A or I, while the fluorescence decay times of TMPyP associated with the G-quadruplex were identical. Observed spectral properties removes the possibility of intercalation binding mode for TMPyP. TMPyP binds at the exterior of the quadruplex. Whether it stacks on the central loop or binds at the side of the quadruplex is unclear at this stage.

Investigation of C-terminal domain of SARS nucleocapsid protein-Duplex DNA interaction using transistors and binding-site models

AlGaN/GaN high electron mobility transistors (HEMTs) were used to sense the binding between double stranded DNA (dsDNA) and the severe acute respiratory syndrome coronavirus (SARS-CoV) nucleocapsid protein (N protein). The sensing signals were the drain current change of the HEMTs induced by the protein-dsDNA binding. Binding-site models using surface coverage ratios were utilized to analyze the signals from the HEMT-based sensors to extract the dissociation constants and predict the number of binding sites. Two dissociation constants, K _D1 = 0.0955 nM, K _D2 = 51.23 nM, were obtained by fitting the experimental results into the two-binding-site model. The result shows that this technique is more competitive than isotope-labeling electrophoretic mobility shift assay (EMSA). We demonstrated that AlGaN/GaN HEMTs were highly potential in constructing a semiconductor-based-sensor binding assay to extract the dissociation constants of nucleotide-protein interaction.

A convenient sandwich assay of thrombin in biological media using nanoparticle-enhanced fluorescence polarization

A new aptamer biosensor was presented for the detection of thrombin in this work, which was based on fluorescence polarization (FP) using silica nanoparticles as enhancement probe. The silica nanoparticles covered by streptavidin were tagged with a thrombin aptamer (5'-biotin-GGTTGGTGTGGTTGG-3'), which was bound to the surface of silica nanoparticle through the specific interaction between streptavidin and biotin. In the presence of thrombin, it induced the aptamer to form quadruplex structure. When the other thrombin aptamer labeled with fluorescein (5'-FAM-AGTCCGTGGTAGGGCAGGTTGGGGTGACT-3') was added to the above system, a sandwich structure can form at the surface of silica nanoparticles. The fluorescence polarization was therefore enhanced and quantification between fluorescence polarization signal and concentration of thrombin was built. The sensor provided a linear range from 0.6 to 100 nM for thrombin with a detection limit of 0.20 nM (3.29 SB/m, according to the recent recommendation of IUPAC) in a homogeneous media. The same linear range was obtained in spiked human serum samples with a slightly higher detection limit (0.26 nM), demonstrating high anti-interference of the sensor in a complex biological sample matrix. And the sensor can be used to monitor spiked concentration of thrombin level in real human plasma with satisfactory results obtained.

AlGaN/GaN high electron mobility transistors for protein-peptide binding affinity study

Antibody-immobilized AlGaN/GaN high electron mobility transistors (HEMTs) were used to detect a short peptide consisting of 20 amino acids. One-binding-site model and two-binding-site model were used for the analysis of the electrical signals, revealing the number of binding sites on an antibody and the dissociation constants between the antibody and the short peptide. In the binding-site models, the surface coverage ratio of the short peptide on the sensor surface is relevant to the electrical signals resulted from the peptide-antibody binding on the HEMTs. Two binding sites on an antibody were observed and two dissociation constants, 4.404×10(-11) M and 1.596×10(-9) M, were extracted from the binding-site model through the analysis of the surface coverage ratio of the short peptide on the sensor surface. We have also shown that the conventional method to extract the dissociation constant from the linear regression of curve-fitting with Langmuir isotherm equation may lead to an incorrect information if the receptor has more than one binding site for the ligand. The limit of detection (LOD) of the sensor observed in the experimental result (~10 pM of the short peptide) is very close to the LOD (around 2.7-3.4 pM) predicted from the value of the smallest dissociation constants. The sensitivity of the sensor is not only dependent on the transistors, but also highly relies on the affinity of the ligand-receptor pair. The results demonstrate that the AlGaN/GaN HEMTs cannot only be used for biosensors, but also for the biological affinity study.

Targeted in vitro photodynamic therapy via aptamer-labeled, porphyrin-loaded virus capsids

Virus capsids have emerged as multifunctional platform systems for development of bio-derived nanomaterials. In this work we investigate the use of aptamer decorated MS2 bacteriophage capsids, loaded with photosensitizer for targeted photodynamic therapy in vitro. MS2 capsids were loaded with approximately 250 cationic porphyrins through a novel assembly packaging mechanism, followed by exterior decoration of the capsid with a cancer-targeting nucleic acid aptamer via chemical conjugation. The ability of these aptamer-virus-porphyrin constructs to specifically target and eradicate MCF-7 human breast cancer cells upon photoactivation was assessed. Photoinduced cytotoxicity was evaluated via live/dead staining and a metabolic activity assay with MCF-10A cells as a control. Results show that MCF-7 cells incubated with targeted, porphyrin-loaded virus capsids exhibited cell death whereas the MCF-10A cells did not. Furthermore, MCF-7 cells incubated with porphyrin-loaded viruses decorated with a non-targeting aptamer exhibited no observable phototoxicity. Combined, the results presented in this work demonstrate our unique virus-based loading strategy offers a viable approach for efficient targeted delivery of photoactive compounds for site-specific photodynamic cancer therapy using bio-derived nanomaterials.

Multifunctional electrochemical aptasensor for aptamer clones screening, virus quantitation in blood and viability assessment

A novel attempt was made to develop a disposable multifunctional sensor for analysis of vaccinia virus (VACV), a promising oncolytic agent that can replicate in and kill tumor cells. Briefly, we developed aptamers specific to VACV that were negatively selected against human serum as well as human and mouse blood to be further utilized for viral analysis directly in serum and blood. In addition, the aptamers were negatively selected against heat-inactivated VACV to enable them to distinguish between viable and nonviable virus particles. The selected aptamers were integrated onto an electrochemical aptasensor to perform multiple functions, including quantification of VACV, viability assessment of the virus, and estimation of the binding affinity between the virus and the developed aptamers. The aptasensor was fabricated by self-assembling a hybrid of a thiolated ssDNA primer and a VACV-specific aptamer onto a gold nanoparticles modified screen-printed carbon electrode (GNPs-SPCE). Square wave voltammetry was employed to quantify VACV in serum and blood within the range of 150-900 PFU, with a detection limit of 60 PFU in 30 μL. According to the electrochemical affinity measurements, three virus specific aptamer clones, V-2, V-5, and V-9 exhibited the highest affinity to VACV. Furthermore, flow cytometry was employed to estimate the dissociation constants of the clones which were found to be 26.3, 40.9, and 24.7 nM, respectively. Finally, the developed aptasensor was able to distinguish between the intact virus and the heat-inactivated virus thanks to the tailored selectivity of the aptamers that was achieved via negative selection.

Electrochemical aptasensors for microbial and viral pathogens

Aptamers are DNA and RNA oligonucleotides that can bind to a variety of nonnucleic acid targets with high affinity and specificity. Pathogen detection is a promising area in aptamer research. One of its major advantages is the ability of the aptamers to target and specifically differentiate microbial and viral strains without previous knowledge of the membrane-associated antigenic determinants or molecular biomarkers present in that particular microorganism. Electrochemical sensors emerged as a promising field in the area of aptamer research and pathogen detection. An electrochemical sensor is a device that combines a recognition element and an electrochemical transduction unit, where aptamers represent the latest addition to the large catalog of recognition elements. This chapter summarizes and evaluates recent developments of electrochemical aptamer-based sensors for microbial and viral pathogen detection, viability assessment of microorganisms, bacterial typing, identification of epitope-specific aptamers, affinity measurement between aptamers and their respective targets, and estimation of the degree of aptamer protection of oncolytic viruses for therapeutic purposes.

4-Aminophenyl boronic acid modified gold platforms for influenza diagnosis

As a potential pandemic threat to human health, there has been an urgent need for rapid, sensitive, simpler and less expensive detection method for the highly pathogenic influenza A virus. For this purpose, Quartz Crystal Microbalance (QCM) and Surface Plasmon Resonance (SPR) sensors have been developed for the recognition of hemagglutinin (HA) which is a major protein of influenza A virus. 4-Aminophenyl boronic acid (4-APBA) has been synthesized and used as a new ligand for binding of sialic acid (SA) via boronic acid-sugar interaction. SA has an important role in binding of HA. QCM and SPR sensor surfaces have been modified with thiol groups and then 4-APBA and SA have been immobilized on sensor surfaces, respectively. Sensor surfaces have been screened with AFM and used for the determination of HA from aqueous solution. The selective recognition of the QCM and SPR sensors toward Concanavalin A has been reported in this work. Also, the binding capacity and detection limits of QCM and SPR sensors have been calculated and detection limits were found to be 4.7 × 10(-2) μM, (0.26 μg ml(-1)) and 1.28 × 10(-1) μM, (0.72 μg ml(-1)) in the 95% confidence interval, respectively.

Porphyrin binding mechanism is altered by protonation at the loops in G-quadruplex DNA formed near the transcriptional activation site of the human c-kit gene

BACKGROUND

G-quadruplex DNA structures are hypothesized to be involved in the regulation of gene expression and telomere homeostasis. The development of small molecules that modulate the stability of G-quadruplex structures has a potential therapeutic interest in cancer treatment and prevention of aging.

METHODS

Molecular absorption and circular dichroism spectra were used to monitor thermal denaturation, acid base titration and mole ratio experiments. The resulting data were analyzed by multivariate data analysis methods. Surface plasmon resonance was also used to probe the kinetics and affinity of the DNA-drug interactions.

RESULTS

We investigated the interaction between a G-quadruplex-forming sequence in the human c-kit proto-oncogene and the water soluble porphyrin TMPyP4. The role of cytosine and adenine residues at the loops of G-quadruplex was studied by substitution of these residues by thymidines.

CONCLUSIONS

Here, we show the existence of two binding modes between TMPyP4 and the considered G-quadruplex. The stronger binding mode (formation constant around 107) involves end-stacking, while the weaker binding mode (formation constant around 106) is probably due to external loop binding. Evidence for the release of TMPyP4 upon protonation of bases at the loops has been observed.

GENERAL SIGNIFICANCE

The results may be used for the design of porphyrin-based anti-cancer molecules with a higher affinity to G-quadruplex structures which may have anticancer properties.

Methods for investigating G-quadruplex DNA/ligand interactions

DNA is considered an important target for drug design and development. Until recently, the focus was on double-stranded (duplex) DNA structures. However, it has now been shown that single stranded DNA can fold into hairpin, triplex, i-motif and G-quadruplex structures. The more interesting G-quadruplex DNA structures comprise four strands of stacked guanine (G)-tetrads formed by the coplanar arrangement of four guanines, held together by Hoogsteen bonds. The DNA sequences with potential to form G-quadruplex structures are found at the chromosomal extremities (i.e. the telomeres) and also at the intra-chromosomal region (i.e. oncogenic promoters) in several important oncogenes. The formation of G-quadruplex structures is considered to have important consequences at the cellular level and such structures have been evoked in the control of expression of certain genes involved in carcinogenesis (c-myc, c-kit, K-ras etc.) as well as in the perturbation of telomeric organization. It has been shown that the formation of quadruplexes inhibits the telomere extension by the telomerase enzyme, which is up-regulated in cancer cells. Therefore, G-quadruplex structures are an important target for drug design and development and there is a huge interest in design and development of small molecules (ligands) to target these structures. A large number of so-called G-quadruplex ligands, displaying varying degrees of affinity and more importantly selectivity (i.e. the ability to interact only with quadruplex-DNA and not duplex-DNA), have been reported. Access to efficient and robust in vitro assays is needed to effectively monitor and quantify the G-quadruplex DNA/ligand interactions. This tutorial review provides an overview of G-quadruplex ligands and biophysical techniques available to monitor such interactions.

Methods for measuring aptamer-protein equilibria: a review

Aptamers are single stranded DNA or RNA molecules that have been selected using in vitro techniques to bind target molecules with high affinity and selectivity, rivaling antibodies in many ways. In order to use aptamers in research and clinical applications, a thorough understanding of aptamer-target binding is necessary. In this article, we review methods for assessing aptamer-protein binding using separation based techniques such as dialysis, ultrafiltration, gel and capillary electrophoresis, and HPLC; as well as mixture based techniques such as fluorescence intensity and anisotropy, UV-vis absorption and circular dichroism, surface plasmon resonance, and isothermal titration calorimetry. For each method the principle, range of application and important features, such as sample consumption, experimental time and complexity, are summarized and compared.

Thrombin-Binding Aptamer Quadruplex Formation: AFM and Voltammetric Characterization

The adsorption and the redox behaviour of thrombin-binding aptamer (TBA) and extended TBA (eTBA) were studied using atomic force microscopy and voltammetry at highly oriented pyrolytic graphite and glassy carbon. The different adsorption patterns and degree of surface coverage were correlated with the sequence base composition, presence/absence of K(+), and voltammetric behaviour of TBA and eTBA. In the presence of K(+), only a few single-stranded sequences present adsorption, while the majority of the molecules forms stable and rigid quadruplexes with no adsorption. Both TBA and eTBA are oxidized and the only anodic peak corresponds to guanine oxidation. Upon addition of K(+) ions, TBA and eTBA fold into a quadruplex, causing the decrease of guanine oxidation peak and occurrence of a new peak at a higher potential due to the oxidation of G-quartets. The higher oxidation potential of G-quartets is due to the greater difficulty of electron transfer from the inside of the quadruplex to the electrode surface than electron transfer from the more flexible single strands.

"One ring to bind them all"-part I: the efficiency of the macrocyclic scaffold for g-quadruplex DNA recognition

Macrocyclic scaffolds are particularly attractive for designing selective G-quadruplex ligands essentially because, on one hand, they show a poor affinity for the “standard” B-DNA conformation and, on the other hand, they fit nicely with the external G-quartets of quadruplexes. Stimulated by the pioneering studies on the cationic porphyrin TMPyP4 and the natural product telomestatin, follow-up studies have developed, rapidly leading to a large diversity of macrocyclic structures with remarkable-quadruplex binding properties and biological activities. In this review we summarize the current state of the art in detailing the three main categories of quadruplex-binding macrocycles described so far (telomestatin-like polyheteroarenes, porphyrins and derivatives, polyammonium cyclophanes), and in addressing both synthetic issues and biological aspects.

Aptamer-based tumor-targeted drug delivery for photodynamic therapy

A specialized G-rich DNA structure, G-quadruplex, has been studied for its special physical characteristics and biological effects. Herein we report a novel strategy of using G-quadruplex as a drug carrier to target cancer cells for photodynamic therapy (PDT). A G-quadruplex forming AS1411 aptamer could be physically conjugated with six molecules of porphyrin derivative, 5,10,15,20-tetrakis(1-methylpyridinium-4-yl)porphyrin (TMPyP4), to fabricate the apt-TMP complex. The TMPyP4 molecules in the complex were identified to bind tightly to the aptamer by intercalation and outside binding. Because the G-quadruplex structure is known to target the overexpressed nucleolin in cancer cells, in this study, the effect of the G-quadruplex structure as a carrier for the delivery of TMPyP4 into cancer cells by nucleolin-mediated internalization was investigated. The results showed that the apt-TMP complex exhibited a higher TMPyP4 accumulation in MCF7 breast cancer cells than in M10 normal epithelium cells. After treated with light for 180 s, the photodamage in MCF7 cells was larger than in M10 cells. These results indicated that the TMPyP4 delivery and uptake were mediated by the specific interaction of the apt-TMP complex with nucleolin on the cellular surface and that the use of the AS1411 aptamer as a drug carrier may be a potential tactic in cancer therapy.

Grading the commercial optical biosensor literature-Class of 2008: 'The Mighty Binders'

Optical biosensor technology continues to be the method of choice for label-free, real-time interaction analysis. But when it comes to improving the quality of the biosensor literature, education should be fundamental. Of the 1413 articles published in 2008, less than 30% would pass the requirements for high-school chemistry. To teach by example, we spotlight 10 papers that illustrate how to implement the technology properly. Then we grade every paper published in 2008 on a scale from A to F and outline what features make a biosensor article fabulous, middling or abysmal. To help improve the quality of published data, we focus on a few experimental, analysis and presentation mistakes that are alarmingly common. With the literature as a guide, we want to ensure that no user is left behind.

Production of surface plasmon resonance based assay kit for hepatitis diagnosis

Hepatitis B surface antibody (HBsAb) imprinted poly(hydroxyethyl methacrylate-N-methacryloyl-L-tyrosine methyl ester) (PHEMAT) film on the surface plasmon resonance (SPR) sensor chip was prepared for diagnosis of HBsAb in human serum. Gold SPR chip surface was modified with allyl mercaptane and, then, HBsAb-imprinted PHEMAT film was formed on the chip surface. Surface characterization of the non-modified, allyl mercaptane modified and HBsAb-imprinted PHEMAT SPR chips were investigated with contact angle, atomic force microscopy (AFM). Kinetic studies were performed using HBsAb positive human serum. In order to determine the kinetic and binding constants, Scatchard, Langmuir, Freundlich and Langmuir-Freundlich models were applied to experimental data. Scatchard curve shows that HBsAb imprinted SPR chip has some surface heterogeneity, SPR chip obeyed the Langmuir adsorption model. The maximum detection limit was 208.2 mIU/mL. K(A) and K(D) values are 0.015 mIU/mL and 66.0 mL/mIU, respectively. Control experiments of the SPR chip were performed using non-immunized, HBsAb negative serum. The control experiment results show that SPR chip does not give any noticeable response to HBsAb negative serum.