Enzymatic method for continuous monitoring of DNA polymerase activity

Collaborative exercise: analysis of age estimation using a QIAGEN protocol and the PyroMark Q48 platform

Human age estimation from trace samples may give important leads early in a police investigation by contributing to the description of the perpetrator. Several molecular biomarkers are available for the estimation of chronological age, and currently, DNA methylation patterns are the most promising. In this study, a QIAGEN age protocol for age estimation was tested by five forensic genetic laboratories. The assay comprised bisulfite treatment of the extracted DNA, amplification of five CpG loci (in the genes of ELOVL2, C1orf132, TRIM59, KLF14, and FHL2), and sequencing of the amplicons using the PyroMark Q48 platform. Blood samples from 49 individuals with ages ranging from 18 to 64 years as well as negative and methylation controls were analyzed. An existing age estimation model was applied to display a mean absolute deviation of 3.62 years within the reference data set.

Key points

Age determination as an intelligence tool during investigations can be a powerful tool in forensic genetics.In this study, five laboratories ran 49 samples and obtained a mean absolute deviation of 3.62 years.Five markers were analyzed on a PyroMark Q48 platform.

Dual-Emissive Carbon Dots: Exploring Their Fluorescence Properties for Sensitive Turn-Off-On Recognition of Ferric and Pyrophosphate Ions and Its Application in Fluorometric Detection of the Loop-Mediated Isothermal Amplification Reaction

In this study, dual-emissive carbon dots (CDs) were prepared using p-phenylenediamine (pPDA) and phytic acid (PA) precursors via a one-pot-hydrothermal method. The photophysical, morphological, and structural characterization of CDs was carried out using absorption, fluorescence, Fourier transform infrared (FT-IR) spectroscopy, nuclear magnetic resonance (NMR), and high-resolution transmission electron microscopy (HR-TEM) analysis. The as-prepared CDs displayed dual-fluorescence peaks at 525 and 620 nm upon excitation at 450 nm. The CDs showed good photostability and exhibited solvent-dependent fluorescence properties. The solvatochromic behavior of CDs was utilized to detect water content in organic solvents. Furthermore, the dual-emissive property of CDs was utilized for the sequential detection of ferric (Fe³⁺) and pyrophosphate ions (PPi) by a fluorescence turn-off-on mechanism. The proposed assay showed appreciable fluorescence response toward Fe³⁺ and PPi with high selectivity and good tolerance for common interfering ions. The potential practical application of the CD probe was ascertained by carrying out the fluorometric detection of PPi to affirm the loop-mediated isothermal amplification (LAMP) reaction specific for Mycobacterium tuberculosis (negative and positive clinical samples).

Aryl- and Superaryl-Extended Calix[4]pyrroles: From Syntheses to Potential Applications

The incorporation of aryl substituents at the meso-positions of calix[4]pyrrole (C4P) scaffolds produces aryl-extended (AE) and super-aryl-extended (SAE) calix[4]pyrroles. The cone conformation of the all-α isomers of "multi-wall" AE-C4Ps and SAE-C4Ps displays deep aromatic clefts or cavities. In particular, "four-wall" receptors feature an aromatic polar cavity closed at one end with four convergent pyrrole rings and fully open at the opposite end. This makes AE- and SAE-C4P scaffolds effective receptors for the molecular recognition of negatively charged ions and neutral guest molecules with donor-acceptor and hydrogen bonding motifs. In addition, adequately functionalized all-α isomers of multi wall AE- and SAE-C4P scaffolds self-assemble into uni-molecular and supra-molecular aggregates displaying capsular and cage-like structures. The self-assembly process requires the presence of template ions or molecules that lock the C4P cone conformation and complementing the inner polar functions and volumes of their cavities. We envisioned performing an in-depth revision of AE- and SAE-C4P scaffolds owing to their importance in different domains such as supramolecular chemistry, biology, material sciences and pharmaceutical chemistry. Herewith, besides the synthetic details on the elaboration of their structures, we also draw attention to their diverse applications. The organization of this review is mainly based on the number of "walls" present in the AE-C4P derivatives and their structural modifications. The sections are further divided based on the C4P functions and applications. The authors are convinced that this review will be of interest to researchers working in the general area of supramolecular chemistry as well as those involved in the study of the binding properties and applications of C4P derivatives.

A sensor array based on DNA-wrapped bimetallic zeolitic imidazolate frameworks for detection of ATP hydrolysis products

Most current biosensors were designed for the detection of individual analytes, or a group of chemically similar analytes. We reason that sensors designed to track both reactants and products might be useful for following chemical reactions. Adenosine triphosphate (ATP) is a key biomolecule that participates in various biochemical reactions, and its hydrolysis plays a fundamental role in life. ATP can be converted to adenosine diphosphate (ADP) and inorganic phosphate (Pi) via the dephosphorylation process. ATP can also be hydrolyzed to adenosine monophosphate (AMP) and pyrophosphate (PPi) through depyrophosphorylation, depending on where the bond is cleaved. The detection of ATP-related hydrolysates would enable a better understanding of the different reaction pathways with a high level of robustness and confidence. Herein, we prepared a fluorescent sensor array based on a series of bimetallic zeolite imidazole frameworks M/ZIF-8 (M = Ni, Mn, Cu) and ZIF-67 to discriminate ATP hydrolysis and detect ATP hydrolysis related analytes. A fluorescently-labeled DNA oligonucleotide was used for signaling. Interestingly, Cu/ZIF-8 exhibited an ultrahigh selectivity for recognizing pyrophosphate with a detection limit of 2.5 μM. Moreover, the practicality of this sensor array was demonstrated in fetal bovine serum, clearly discriminating ATP hydrolysis products.

Indicator displacement assays: from concept to recent developments

Overcoming the synthetic burden related to covalently connected receptors with appropriate indicators for sensing various analytes via an indicator spacer receptor (ISR) approach, the indicator displacement assay (IDA) seems to be a very sophisticated and versatile supramolecular sensing paradigm, and it has taken the phenomenon of molecular recognition to the next level in the realm of host-guest chemistry. Due to the unavailability of a comprehensive report on what has been done in the last decade in relation to IDAs, we decided to set down this account illustrating diverse indicator displacement assays (IDAs) in detail from the concept stage to recent developments relating to the detection of cationic, anionic, and neutral analytes. The authors conclude this account with future perspectives and highlight the limitations and challenges relating to IDAs which need to be overcome in order to realize the full potential of this popular sensing phenomenon. While we were finalizing our account for publication, a tutorial review by the research groups of Anslyn, Sessler, and Sun was published, which focuses mainly on diverse aspects of the chemistry related to IDAs. As can be seen, our review, besides discussing various basic IDA concepts, has a vast collection of information published in the past decade and hence, hopefully, will be very informative for the supramolecular community. We believe that this work will offer new insights for the construction of novel sensors operating through the IDA approach.

A Highly Selective Turn-On Fluorescent Probe for the Detection of Zinc

A novel turn-on fluorescence probe L has been designed that exhibits high selectivity and sensitivity with a detection limit of 9.53 × 10⁻⁸ mol/L for the quantification of Zn²⁺. ¹H-NMR spectroscopy and single crystal X-ray diffraction analysis revealed the unsymmetrical nature of the structure of the Schiff base probe L. An emission titration experiment in the presence of different molar fractions of Zn²⁺ was used to perform a Job’s plot analysis. The results showed that the stoichiometric ratio of the complex formed by L and Zn²⁺ was 1:1. Moreover, the molecular structure of the mononuclear Cu complex reveals one ligand L coordinates with one Cu atom in the asymmetric unit. On adding CuCl₂ to the ZnCl₂/L system, a Cu-Zn complex was formed and a strong quenching behavior was observed, which inferred that the Cu²⁺ displaced Zn²⁺ to coordinate with the imine nitrogen atoms and hydroxyl oxygen atoms of probe L.

Influence of Triazole Substituents of Bis-Heteroleptic Ru(II) Probes toward Selective Sensing of Dihydrogen Phosphate

A series of seven new bis-heteroleptic Ru(II) probes (1[PF₆]₂-7[PF₆]₂) along with two previously reported probes (8[PF₆]₂ and 9[PF₆]₂) containing a similar anion binding triazole unit (hydrogen bond donor) functionalized with various substituents are employed in a detailed comparative investigation for the development of superior selective probes for H₂PO₄^-. Various solution- and solid-state studies, such as ¹H-DOSY NMR, dynamic light scattering (DLS), single-crystal X-ray crystallography, and transmission electron microscopy (TEM), have established that the selective sensing of H₂PO₄^- by this series of probes is primarily due to supramolecular aggregation driven enhancement of ³MLCT emission. Intestingly, 1[PF₆]₂ and 7[PF₆]₂, having an electron-deficient (π-acidic) aromatic pentafluorophenyl substituent are found to be superior probes for H₂PO₄^- in comparison to the other aryl- and polyaromatic-substituted analogues (2[PF₆]₂-6[PF₆]₂, 8[PF₆]₂, and 9[PF₆]₂), in terms of a higher enhancement of the ³MLCT emission band, a greater binding constant, and a lower detection limit. The superiority of 1[PF₆]₂ and 7[PF₆]₂ could be due to better supramolecular aggregation properties in the cases of pentafluorophenyl analogues via both hydrogen bonding and anion-fluorine/anion-π noncovalent interactions.

The application of DNA polymerases and Cas9 as representative of DNA-modifying enzymes group in DNA sensor design (review)

Rapid detection of nucleic acids (DNA or RNA) by inexpensive, selective, accurate, and highly sensitive methods is very important for biosensors. DNA-sensors based on DNA-modifying enzymes for fast determination and monitoring of pathogenic (Zika, Dengue, SARS-Cov-2 (inducer of COVID-19), human papillomavirus, HIV, etc.) viruses and diagnosis of virus-induced diseases is a key factor of this overview. Recently, DNA-modifying enzymes (Taq DNA polymerase, Phi29 DNA polymerase) have been widely used for the diagnosis of virus or pathogenic disease by gold standard (PCR, qPCR, RT-qPCR) methods, therefore, alternative methods have been reviewed. The main mechanisms of DNA metabolism (replication cycle, amplification) and the genomeediting tool CRISPR-Cas9 are purposefully discussed in order to address strategic possibility to design DNA-sensors based on immobilized DNA-enzymes. However, the immobilization of biologically active proteins on a gold carrier technique with the ability to detect viral or bacterial nucleic acids is individual for each DNA-modifying enzyme group, due to a different number of active sites, C and N terminal locations and arrangement, therefore, individual protocols based on the 'masking' of active sites should be elaborated for each enzyme.

A new half-condensed Schiff base platform: structures and sensing of Zn2+ and H2PO4- ions in an aqueous medium

A newly designed and synthesized half-condensed organic moiety 2-hydroxy-5-methyl-3-[(2-phenylamino-phenylimino)-methyl]-benzaldehyde (HL') and a Zn₂L₄ complex sequentially detect Zn²⁺ and H₂PO₄^- ions as low as 1.13 nM and1.23 μM, respectively. HL' and a dinuclear Zn(ii) complex of in situ generated L^- in a solution formulated as Zn₂L₄ under investigation were characterized by physicochemical and spectroscopic studies along with detailed structural analyses by single-crystal X-ray crystallography. The selectivity and sensitivity of HL' towards Zn²⁺ ions and of the Zn₂L₄ complex towards H₂PO₄^- ions are based on CHEF and via displacement pathways, respectively. Dual sensing of Zn²⁺ ions and H₂PO₄^-ions in an aqueous medium via "Green-Blue-Green" emission with the reversible transformation of in situ formed HL' to HL was established by detailed electronic absorption and emission spectroscopic studies. This non-cytotoxic probe (HL', i.e. produced HL in solution) and Zn₂L₄ complexes are able to monitor the subcellular distribution changes of Zn²⁺ and H₂PO₄^- ions, respectively, by fluorescence microscopy using the human semen sample.

Long walk to genomics: History and current approaches to genome sequencing and assembly

Genomes represent the starting point of genetic studies. Since the discovery of DNA structure, scientists have devoted great efforts to determine their sequence in an exact way. In this review we provide a comprehensive historical background of the improvements in DNA sequencing technologies that have accompanied the major milestones in genome sequencing and assembly, ranging from early sequencing methods to Next-Generation Sequencing platforms. We then focus on the advantages and challenges of the current technologies and approaches, collectively known as Third Generation Sequencing. As these technical advancements have been accompanied by progress in analytical methods, we also review the bioinformatic tools currently employed in de novo genome assembly, as well as some applications of Third Generation Sequencing technologies and high-quality reference genomes.

Fluorenone based fluorescent probe for selective "turn-on" detection of pyrophosphate and alanine

To sense biologically important entities with different size and dimensions, a fluorenone based fluorescent receptor was designed and synthesized. Probe 1 displayed a distinct fluorescence enhancement emission at 565nm for pyrophosphate and 530nm for alanine in polar solvent. The fluorescence titration experiments confirm 1:1 stoichiometric ratio with high-binding constant and very low limit of detection (LoD) values. Receptor 1 showed a highly selective and sensitive recognition to HP₂O₇^3- and to alanine over other competitive anions and amino acids. In addition, the fluorescence lifetime measurement and reversible binding study results support the practical importance of 1.

Tetraphenylethylene-Based AIE-Active Probes for Sensing Applications

This Review provides a comprehensive analysis of recent development in the field of aggregation-induced emission (AIE)-active tetraphenylethylene (TPE) luminophores and their applications in biomolecular science. It begins with a discussion of the diverse range of structural motifs that have found particular applications in sensing, and demonstrates that TPE structures and their derivatives have been used for a diverse range of analytes such as such as H⁺, anions, cations, heavy metals, organic volatiles, and toxic gases. Advances are discussed in depth where TPE is utilized as a mechanoluminescent material in bioinspired receptor units with specificity for analytes for such as glucose or RNA. The rapid advances in sensor research make this summary of recent developments in AIE-active TPE luminophores timely, in order to disseminate the advantages of these materials for sensing of analytes in solution, as well as the importance of solid and aggregated states in controlling sensing behavior.

Analysis of Ribonucleotide 5'-Triphosphate Analogs as Potential Inhibitors of Zika Virus RNA-Dependent RNA Polymerase by Using Nonradioactive Polymerase Assays

Zika virus (ZIKV) is an emerging human pathogen that is spreading rapidly through the Americas and has been linked to the development of microcephaly and to a dramatically increased number of Guillain-Barré syndrome cases. Currently, no vaccine or therapeutic options for the prevention or treatment of ZIKV infections exist. In the study described in this report, we expressed, purified, and characterized full-length nonstructural protein 5 (NS5) and the NS5 polymerase domain (NS5pol) of ZIKV RNA-dependent RNA polymerase. Using purified NS5, we developed an in vitro nonradioactive primer extension assay employing a fluorescently labeled primer-template pair. Both purified NS5 and NS5pol can carry out in vitro RNA-dependent RNA synthesis in this assay. Our results show that Mn²⁺ is required for enzymatic activity, while Mg²⁺ is not. We found that ZIKV NS5 can utilize single-stranded DNA but not double-stranded DNA as a template or a primer to synthesize RNA. The assay was used to compare the efficiency of incorporation of analog 5'-triphosphates by the ZIKV polymerase and to calculate their discrimination versus that of natural ribonucleotide triphosphates (rNTPs). The 50% inhibitory concentrations for analog rNTPs were determined in an alternative nonradioactive coupled-enzyme assay. We determined that, in general, 2'-C-methyl- and 2'-C-ethynyl-substituted analog 5'-triphosphates were efficiently incorporated by the ZIKV polymerase and were also efficient chain terminators. Derivatives of these molecules may serve as potential antiviral compounds to be developed to combat ZIKV infection. This report provides the first characterization of ZIKV polymerase and demonstrates the utility of in vitro polymerase assays in the identification of potential ZIKV inhibitors.

A turn-on green channel Zn2+ sensor and the resulting zinc(ii) complex as a red channel HPO42− ion sensor: a new approach

A turn-on green channel Zn²⁺ sensor and the resulting zinc(ii) complex as a red channel HPO₄²⁻ ion sensor: a new approach.

Pyrophosphate Sensor Based on Principal Component Analysis of Conjugated Polyelectrolyte Fluorescence

The pyrophosphate anion (PPi) plays an important role in biochemical processes. Therefore, a simple but reliable analytical technique is essential for selective detection of PPi in biochemical systems. Here, we present a principal component analysis (PCA) method for analytical determination of PPi concentration using a fluorescent conjugated polyelectrolyte (CPE) combined with a polyamine modifier. The CPE has anionic side chains and dissolves molecularly in water, as indicated by its structured fluorescence emission spectrum. However, addition of tris(3-aminoethyl)amine (tetraamine or N4) quenches the CPE fluorescence emission. Tetraamine, which is a polycation at neutral pH, binds multiple anionic CPE chains, leading to aggregate formation, resulting in aggregation-induced fluorescence quenching. Addition of PPi to the polymer-amine aggregate reverses the process, resulting in fluorescence recovery. The relatively higher concentration of PPi compared to that of the polymer allows it to effectively compete to bind the amine, thus releasing molecularly dissolved polymer chains. Fluorescence correlation spectroscopy of the P1/N4 complex and of P1/N4/PPi confirms the change in size of the CPE aggregates that occurs upon reversible aggregation. Application of PCA to the fluorescence emission data set of standard samples yields two principal components, which are used to create a predictive model for PPi analysis. The PCA method is able to directly determine the concentration of PPi with approximately 95% accuracy within the concentration range from 100 μM to 3 mM, without the need for a reference state as is typically needed for ratiometric fluorescence assays.

Benzothiazole based multi-analyte sensor for selective sensing of Zn2+and Cd2+and subsequent sensing of inorganic phosphates (Pi) in mixed aqueous medium

A multi-analyte sensor selectively senses Zn²⁺and Cd²⁺ions and subsequently responds to phosphates in mixed aqueous medium.

The sequence of sequencers: The history of sequencing DNA

Determining the order of nucleic acid residues in biological samples is an integral component of a wide variety of research applications. Over the last fifty years large numbers of researchers have applied themselves to the production of techniques and technologies to facilitate this feat, sequencing DNA and RNA molecules. This time-scale has witnessed tremendous changes, moving from sequencing short oligonucleotides to millions of bases, from struggling towards the deduction of the coding sequence of a single gene to rapid and widely available whole genome sequencing. This article traverses those years, iterating through the different generations of sequencing technology, highlighting some of the key discoveries, researchers, and sequences along the way.

A Cyanuric Acid Platform Based Tripodal Bis-heteroleptic Ru(II) Complex of Click Generated Ligand for Selective Sensing of Phosphates via C-H···Anion Interaction

A new bis-heteroleptic trinuclear Ru(II) complex (1[PF6]6) has been synthesized from electron deficient cyanuric acid platform based copper-catalyzed azide-alkyne cycloaddition, i.e., CuAAC click generated ligand, 1,3,5-tris [(2-aminoethyl-1H-1,2,3-triazol-4-yl)-pyridine]-1,3,5-triazinane-2,4,6-trione (L1). Complex 1[PF6]6 displays weak luminescence (ϕf = 0.002) at room temperature with a short lifetime of ∼5 ns in acetonitrile. It shows selective sensing of hydrogen pyrophosphate (HP2O7(3-)) through 20-fold enhanced emission intensity (ϕf = 0.039) with a 15 nm red shift in emission maxima even in the presence of a large excess of various competitive anions like F(-), Cl(-), AcO(-), BzO(-), NO3(-), HCO3(-), HSO4(-), HO(-), and H2PO4(-) in acetonitrile. Selective change in the decay profile as well as in the lifetime of 1[PF6]6 in the presence of HP2O7(3-) (108 ns) further supports its selectivity toward HP2O7(3-). UV-vis and photoluminescence titration profiles and corresponding Job's plot analyses suggest 1:3 host-guest stoichiometric binding between 1[PF6]6 and HP2O7(3-). High emission enhancement of 1[PF6]6 in the presence of HP2O7(3-) has resulted in the detection limit of the anion being as low as 0.02 μM. However, 1[PF6]6 shows selectivity toward higher analogues of phosphates (e.g., ATP, ADP, and AMP) over HP2O7(3-)/H2PO4(-) in 10% Tris HCl buffer (10 mM)/acetonitrile medium. Downfield shifting of the triazole C-H in a (1)H NMR titration study confirms that the binding of HP2O7(3-)/H2PO4(-) is occurring via C-H···anion interaction. The single crystal X-ray structure of complex 1 having NO3(-) counteranion, 1[NO3]6 shows binding of NO3(-) with complex 1 via C-H···NO3(-) interactions.

Cd(II)-terpyridine-based complex as a ratiometric fluorescent probe for pyrophosphate detection in solution and as an imaging agent in living cells

The terpyridine anthracene ligand was synthesized and characterized. is a ratiometric fluorescent probe for Cd(2+) with a recognition mechanism based on intramolecular charge transfer (ICT). An complex was isolated, and its structure was established using single-crystal XRD. The complex was able to serve as a novel reversible chemosensing ensemble to allow ratiometric response to pyrophosphate (PPi) in aqueous media. Moreover, the fluorescence imaging in living cells from these two emission channels suggested that was a ratiometric probe for Cd(2+), and the in situ generated complex was also a ratiometric ensemble for PPi detection in living cells.

Software-Based Pyrogram® Evaluation

Pyrosequencing(®) is a widely used technology to detect gene mutations in a molecular research or diagnostics laboratory. Compared to Sanger sequencing, it is inherently more quantitative with a superior limit of detection, although it has a shorter read length and has difficulty with homopolymeric sequences.Results of Pyrosequencing experiments are typically presented as traces with sequential peaks, called Pyrograms(®). For the majority of clinical diagnostic cases, Pyrograms are straightforward to read. However, there are occasionally complex results that are uninterpretable or difficult to interpret. In this chapter, we demonstrate a computer software, named Pyromaker that has been developed to help with the analysis of Pyrograms. Pyromaker is a freely and publically available software program to assist in the recognition of patterns of mutations, interpretation of difficult or ambiguous testing results and design of an optimal strategy to detect potential mutations by generating simulated Pyrograms. In addition to help diagnostic activities, Pyromaker can also be used as a virtual and user-friendly educational tool to teach newcomers the fundamental mechanism of Pyrosequencing, and correct interpretation of actual Pyrosequencing data.

Emerging technologies for the clinical microbiology laboratory

In this review we examine the literature related to emerging technologies that will help to reshape the clinical microbiology laboratory. These topics include nucleic acid amplification tests such as isothermal and point-of-care molecular diagnostics, multiplexed panels for syndromic diagnosis, digital PCR, next-generation sequencing, and automation of molecular tests. We also review matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) and electrospray ionization (ESI) mass spectrometry methods and their role in identification of microorganisms. Lastly, we review the shift to liquid-based microbiology and the integration of partial and full laboratory automation that are beginning to impact the clinical microbiology laboratory.

The History of Pyrosequencing(®)

One late afternoon in the beginning of January 1986, bicycling from the lab over the hill to the small village of Fulbourn, the idea for an alternative DNA sequencing technique came to my mind. The basic concept was to follow the activity of DNA polymerase during nucleotide incorporation into a DNA strand by analyzing the pyrophosphate released during the process. Today, the technique is used in multidisciplinary fields in academic, clinical, and industrial settings all over the word. This technique can be used for both single-base sequencing and whole-genome sequencing, depending on the format used.In this chapter, I give my personal account of the development of Pyrosequencing(®)-beginning on a winter day in 1986, when I first envisioned the method-until today, nearly 30 years later.

Nanomolar Zn(ii) sensing and subsequent PPi detection in physiological medium and live cells with a benzothiazole functionalized chemosensor

Nanomolar zinc detection and subsequent pyrophosphate sensing in physiological media using a benzothiazole modified conjugated ligand and their application in paper strip and live cell imaging is demonstrated.

A case of oxoanion recognition based on combined cationic and neutral C–H hydrogen bond interactions

A bidentate bis-(benzimidazolium) receptor containing pyrene as fluorescent signaling units recognizes sulphate and hydrogenpyrophosphate in a competitive water–DMSO medium through combinations of cationic and neutral C–H hydrogen bonding.

Pyridinum-based flexible tripodal cleft: a case of fluorescence sensing of ATP and dihydrogenphosphate under different conditions and cell imaging

Pyridinium-based chemosensor 1 built on tris(aminomethyl)amine (tren) has been designed, synthesized and established as a chemosensor for ATP over ADP, AMP and a series of other anions in aqueous CH₃CN at pH 6.5.

PyroMark® Instruments, Chemistry, and Software for Pyrosequencing® Analysis

Since the early 2000s, Pyrosequencing(®) technology has been adapted for various instrument platforms to enable users to examine the role of epigenetic DNA methylation in gene expression regulation, genetic markers for specific phenotypes in livestock, drug resistance development in pathogens, and polymorphisms in forensic samples of mitochondrial DNA.The instruments, software, and chemistry have been modified to facilitate different sample throughputs and sample amounts. Just recently, major changes have been implemented to enable increased read length and more precise Pyrosequencing results. These improvements were made possible through a number of changes to various system components. In addition, assay development has been streamlined through the availability of optimized PCR and Pyrosequencing reagents, automated assay design tools, and a number of predesigned Pyrosequencing assays.In future, instruments with smaller footprints and the ability to automate crucial steps of the Pyrosequencing protocol will be available and will provide even more convenient and standardized Pyrosequencing analysis with flexible throughput.

A high-throughput screening method to reengineer DNA polymerases for random mutagenesis

A screening system for directed evolution of DNA polymerases employing a fluorescent Scorpion probe as a reporter has been developed. The screening system has been validated in a directed evolution experiment of a distributive polymerase from the Y-polymerase family (Dpo4 from Sulfolobus solfataricus) which was improved in elongation efficiency of consecutive mismatches. The engineering campaign yielded improved Dpo4 polymerase variants one of which was successfully benchmarked in a sequence saturation mutagenesis experiment especially with regard to the desirable consecutive transversion mutations ([2.5-fold increase in frequency relative to a reference library prepared with Dpo4 WT). The Scorpion probe screening system enables to reengineer polymerases with low processivity and fidelity, and no secondary activities (i.e. exonuclease activity or strand displacement activity) to match demands in diversity generation for directed protein evolution.

Recent advances in molecular diagnostics of hepatitis B virus

Hepatitis B virus (HBV) is one of the important global health problems today. Infection with HBV can lead to a variety of clinical manifestations including severe hepatic complications like liver cirrhosis and hepatocellular carcinoma. Presently, routine HBV screening and diagnosis is primarily based on the immuno-detection of HBV surface antigen (HBsAg). However, identification of HBV DNA positive cases, who do not have detectable HBsAg has greatly encouraged the use of nucleic acid amplification based assays, that are highly sensitive, specific and are to some extent tolerant to sequence variation. In the last few years, the field of HBV molecular diagnostics has evolved rapidly with advancements in the molecular biology tools, such as polymerase chain reaction (PCR) and real-time PCR. Recently, apart of PCR based amplification methods, a number of isothermal amplification assays, such as loop mediated isothermal amplification, transcription mediated amplification, ligase chain reaction, and rolling circle amplification have been utilized for HBV diagnosis. These assays also offer options for real time detection and integration into biosensing devices. In this manuscript, we review the molecular technologies that are presently available for HBV diagnostics, with special emphasis on isothermal amplification based technologies. We have also included the recent trends in the development of biosensors and use of next generation sequencing technologies for HBV.

A benzimidazolium-based new flexible cleft built on the piperazine unit: a case of selective fluorometric sensing of ATP

A benzimidazole-based compound 1 which is highly selective and sensitive towards ATP over ADP and AMP in CH₃CN/H₂O (1 : 1, v/v, using 10 mM HEPES buffer, pH 6.4) has been designed and synthesized. Compound 1 can detect the presence of ATP in Human cervical cancer cells (HeLa).

Highly sensitive and selective detection of the pyrophosphate anion biomarker under physiological conditions

Self-assembled monolayers on gold of a multidentate adsorbate bearing a bis(carbazolyl)urea unit are prepared and used as a surface resonance plasmon sensor for the detection of hydrogen pyrophosphate anions under physiological conditions.

Pyrosequencing: powerful and quantitative sequencing technology

Pyrosequencing is a sequencing-by-synthesis method for DNA analysis that has emerged as a platform not only for de novo sequencing applications, but also for quantitative analysis of genomic methylation, single-nucleotide polymorphisms, and allele quantification. In this unit, we describe a complete workflow from sample to result that is suitable for each of these applications. As cytosine conversion is a key element of successful methylation analysis using pyrosequencing, a support protocol for bisulfite treatment is also included.

Bis(carbazolyl)ureas as selective receptors for the recognition of hydrogenpyrophosphate in aqueous media

Recognition properties of the novel bis(carbazole) tris-ureidic-based receptors 1 and 2 toward different anions have been studied by (1)H NMR and absorption and emission spectroscopy, as well as by DFT calculations. Receptor 1, in which the two urea-functionalized arms are decorated with p-nitrophenyl rings, behaves as a highly selective chromogenic molecular probe for hydrogenpyrophosphate anion in a competitive medium (acetonitrile/water, 70/30). Receptor 2, bearing two urea arms decorated with photoactive pyrenyl rings, acts as a highly selective fluorescent molecular probe for hydrogenpyrophosphate anion in either acetonitrile or an aqueous mixture (acetonitrile/water, 85/15). Receptor 2 exhibits a dual monomer-excimer emission spectrum and undergoes a remarked ratiometry in acetonitrile in the presence of hydrogenpyrophosphate: the excimer band disappears, whereas the monomer band is slightly increased. However, in the aqueous mixture, a strong increase of the excimer emission band was observed, while the monomer emission bands remained almost unaffected. The resulting binding modes and spectroscopic features are explained by suitable structures of model complexes for both receptors. In such complexes, a peripheral cooperative effect was found, alleviating the excess of negative charge in the guest toward the outer surface of the host, as well as the required enlargement on its internal cavity.

Role of metal ion in specific recognition of pyrophosphate ion under physiological conditions and hydrolysis of the phosphoester linkage by alkaline phosphatase

Complexes synthesized from Zn(II), Cu(II), and Cd(II), using a dipicolyl amine derivative (L), showed unique specificity toward pyrophosphate ion (PPi or P4O7(4-)) among all other common anionic analytes, including different biologically significant phosphate ion (PO4(3-), H2PO4(2-)) or phosphate-ion-based nucleotides, such as AMP, ADP, ATP, and CTP. However, the relative affinities of PPi toward these three metal complexes were found to vary and follow the order K(a)(L.Zn-PPi) > are given in units of (a)(L.Cu-PPi) ≥ K(a)(L.Cd-PPi). Luminescence responses of the receptor L were substantial on binding to Zn(2+) and Cd(2+), while relatively a much smaller luminescence response was observed in the presence of Cu(2+). Luminescence responses of L.M-PPi (M is Zn(2+), Cd(2+), and Cu(2+)) were further modified on binding to the PPi ion. This could be utilized for quantitative detection of PPi in physiological condition as well as for developing a real time "turn-on" (for L.Zn and L.Cu) and "turn-off" (for L.Cd) fluorescence assay for evaluating the enzymatic activity of alkaline phosphatase (ALP). Experimental results revealed how the subtle differences in the binding affinities between PPi and M in L.M (M is Zn(2+), Cd(2+), and Cu(2+)), could influence the cleavage of the phosphoester linkage in PPi by ALP. The DFT calculations further revealed that the hydrolytic cleavage of the metal ion coordinated phosphoester bond is kinetically faster than that for free PPi and thus, rationalized the observed difference in the cleavage of the phosphoester bond by an important mammalian enzyme such as ALP in the presence of different metal complexes.

Fundamentals of pyrosequencing

CONTEXT

DNA sequencing is critical to identifying many human genetic disorders caused by DNA mutations, including cancer. Pyrosequencing is less complex, involves fewer steps, and has a superior limit of detection compared with Sanger sequencing. The fundamental basis of pyrosequencing is that pyrophosphate is released when a deoxyribonucleotide triphosphate is added to the end of a nascent strand of DNA. Because deoxyribonucleotide triphosphates are sequentially added to the reaction and because the pyrophosphate concentration is continuously monitored, the DNA sequence can be determined.

OBJECTIVE

To demonstrate the fundamental principles of pyrosequencing.

DATA SOURCES

Salient features of pyrosequencing are demonstrated using the free software program Pyromaker ( http://pyromaker.pathology.jhmi.edu ), through which users can input DNA sequences and other pyrosequencing parameters to generate the expected pyrosequencing results.

CONCLUSIONS

We demonstrate how mutant and wild-type DNA sequences result in different pyrograms. Using pyrograms of established mutations in tumors, we explain how to analyze the pyrogram peaks generated by different dispensation sequences. Further, we demonstrate some limitations of pyrosequencing, including how some complex mutations can be indistinguishable from single base mutations. Pyrosequencing is the basis of the Roche 454 next-generation sequencer and many of the same principles also apply to the Ion Torrent hydrogen ion-based next-generation sequencers.

Ortho-phenylenediamine-based open and macrocyclic receptors in selective sensing of H2PO4(-), ATP and ADP under different conditions

Ortho-phenylenediamine-based open and macrocyclic receptors have been designed and synthesized. The open receptor 1 and the macrocyclic receptor 2 fluorimetrically distinguish H(2)PO(4)(-) from the other anions examined in CH(3)CN with appreciable binding constant values. As practical applications, they are also sensible to nucleotides in aq. CH(3)CN (1 : 1, v/v). The receptor 1 shows significant emission change upon complexation of ATP and ADP. ADP is selectively distinguished by a ratiometric change in emission. In contrast, the macrocyclic receptor 2, under similar conditions, shows good binding with ATP over the others.

Microsatellites grant more stable flanking genes

Background

Microsatellites, or simple sequence repeats (SSRs), are DNA sequences that include tandem copies of specific sequences no longer than six bases. SSRs are ubiquitous in all genomes and highly mutable.

Presentation of the hypothesis

Results from previous studies suggest that flanking regions of SSR are exhibit high stability in a wide range of organisms. We hypothesized that the SSRs ability to discard weak DNA polymerases could be responsible for this unusual stability. . When the weak polymerases are being decayed over SSRs, the flanking sequences would have higher opportunity to be replicated by more stable DNA polymerases. We present evidence of the molecular basis of our hypothesis.

Testing the hypothesis

The hypothesis could be tested by examining the activity of DNA polymerase during and after a number of PCRs. The PCR reactions should be run with the same SSR locus possessing differences in the SSR length. The hypothesis could also be tested by comparing the mutational rate of a transferred gene between two transformations. The first one has a naked T-DNA (transferred DNA), while the second one has the same T-DNA flanked with two SSRs.

Implications of the hypothesis

In any transformation experiment, flanking the T-DNA fragment with SSR sequences would result in more stably transferred genes. This process would decrease the unpredictable risks that may occur because of the mutational pressure on this foreign segment.