General Gel-sol Method to Synthesize Various Highly Fluorescent Nanoclusters and Assay of Nuclease with the Near Infrared-emitting Gold Nanoclusters.

A general egg white gel-sol strategy for fabrication of highly fluorescent Au, Ag, Cu, and Pt nanoclusters (NCs) and the first example of using Au NCs for assay of nuclease activity and inhibition were described. The Au NCs enabled bright red fluorescence, and the other Ag, Cu, and Pt NCs have highly blue emission. The red-emitting Au NCs were further applied in assay of S1 nuclease activity and inhibition. Free hemin efficiently quenches the emission of Au NCs by photoinduced electron transfer due to the formation of Au NCs-hemin conjugates. However, G-quadruplex/hemin exerts negligible effect on its fluorescence due to no Au NCs-hemin conjugate formed. There are stronger electrostatic repulsion effects between both negatively charged G-quadruplex and Au NCs. Therefore, a novel G-quadruplex/hemin-based Au NCs fluorescent sensor for S1 nuclease was designed. A known G-rich oligonucleotide (ODN) serves as not only substrate for S1 nuclease but also for the construction of G-quadruplex/hemin. The G-rich ODN is hydrolyzed into fragments by S1 nuclease resulting in no G-quadruplex/hemin formation. Therefore, the free hemin quenches Au NCs fluorescence remarkably and the assay of S1 nuclease activity and inhibition has accomplished. Both the fluorescent NCs syntheses and the detection of S1 nuclease are facile and efficient.

Identification of osteosarcoma by microRNA-coupled nuclease digestion on interdigitated electrode sensor.

Osteosarcoma is a type of tumor originating from the bone cells, most often from long bones. Children and adolescents are mainly affected by osteosarcoma. Identifying the condition with osteosarcoma is mandatory to provide proper treatment to the affected patients. This research work has introduced an identification of an osteosarcoma biomarker "miRNA-21" on the interdigitated electrochemical sensor by nuclease digestion. The target RNA sequence of miRNA-21 was hybridized to the capture DNA and placed on the sensing electrode surface with the aid of the biotin-streptavidin interaction. The unhybridized immobilized single-standard capture DNA was digested by S1-nuclease. The current response of the digestion level was considered as the duplex formation between the target and capture DNA. Using this technique, the detection limit of the target was reached to 1 fM and a similar response of current was noted with the target RNA-spiked human serum, indicating the selective identification of target RNA. Further, single mismatched, triple mismatched, and random miRNA sequences (miRNA-195) failed to interact with the immobilized capture DNA, representing the specific identification of target RNA. This nuclease digestion technique with miRNA-21 identification helps in detecting osteosarcoma and related issues.

Molecular architecture of G-quadruplex structures generated on duplex Rif1-binding sequences.

G-quadruplexes (G4s) are four-stranded DNA structures comprising stacks of four guanines, are prevalent in genomes, and have diverse biological functions in various chromosomal structures. A conserved protein, Rap1-interacting factor 1 (Rif1) from fission yeast (Schizosaccharomyces pombe), binds to Rif1-binding sequence (Rif1BS) and regulates DNA replication timing. Rif1BS is characterized by the presence of multiple G-tracts, often on both strands, and their unusual spacing. Although previous studies have suggested generation of G4-like structures on duplex Rif1BS, its precise molecular architecture remains unknown. Using gel-shift DNA binding assays and DNA footprinting with various nuclease probes, we show here that both of the Rif1BS strands adopt specific higher-order structures upon heat denaturation. We observed that the structure generated on the G-strand is consistent with a G4 having unusually long loop segments and that the structure on the complementary C-strand does not have an intercalated motif (i-motif). Instead, we found that the formation of the C-strand structure depends on the G4 formation on the G-strand. Thus, the higher-order structure generated at Rif1BS involved both DNA strands, and in some cases, G4s may form on both of these strands. The presence of multiple G-tracts permitted the formation of alternative structures when some G-tracts were mutated or disrupted by deazaguanine replacement, indicating the robust nature of DNA higher-order structures generated at Rif1BS. Our results provide general insights into DNA structures generated at G4-forming sequences on duplex DNA.

Label-Free Fluorescence Assay of S1 Nuclease and Hydroxyl Radicals Based on Water-Soluble Conjugated Polymers and WS2 Nanosheets.

We developed a new method for detecting S1 nuclease and hydroxyl radicals based on the use of water-soluble conjugated poly[9,9-bis(6,6-(N,N,N-trimethylammonium)-fluorene)-2,7-ylenevinylene-co-alt-2,5-dicyano-1,4-phenylene)] (PFVCN) and tungsten disulfide (WS2) nanosheets. Cationic PFVCN is used as a signal reporter, and single-layer WS2 is used as a quencher with a negatively charged surface. The ssDNA forms complexes with PFVCN due to much stronger electrostatic interactions between cationic PFVCN and anionic ssDNA, whereas PFVCN emits yellow fluorescence. When ssDNA is hydrolyzed by S1 nuclease or hydroxyl radicals into small fragments, the interactions between the fragmented DNA and PFVCN become weaker, resulting in PFVCN being adsorbed on the surface of WS2 and the fluorescence being quenched through fluorescence resonance energy transfer. The new method based on PFVCN and WS2 can sense S1 nuclease with a low detection limit of 5 × 10(-6) U/mL. Additionally, this method is cost-effective by using affordable WS2 as an energy acceptor without the need for dye-labeled ssDNA. Furthermore, the method provides a new platform for the nuclease assay and reactive oxygen species, and provides promising applications for drug screening.

Label-free fluorometric detection of S1 nuclease activity by using polycytosine oligonucleotide-templated silver nanoclusters.

S1 nuclease has an important function in DNA transcription, replication, recombination, and repair. A label-free fluorescent method for the detection of S1 nuclease activity has been developed using polycytosine oligonucleotide-templated silver nanoclusters (dC12-Ag NCs). In this assay, dC12 can function as both the template for the stabilization of Ag NCs and the substrate of the S1 nuclease. Fluorescent Ag NCs could be effectively formed using dC12 as the template without S1 nuclease. In the presence of S1 nuclease, dC12 is degraded to mono- or oligonucleotide fragments, thereby resulting in a reduction in fluorescence. S1 nuclease with an activity as low as 5×10(-8)Uµl(-1) (signal/noise=3) can be determined with a linear range of 5×10(-7) to 1×10(-3)Uµl(-1). The promising application of the proposed method in S1 nuclease inhibitor screening has been demonstrated using pyrophosphate as the model inhibitor. Furthermore, the S1 nuclease concentrations in RPMI 1640 cell medium were validated. The developed method for S1 nuclease is sensitive and facile because its operation does not require any complicated DNA labeling or laborious fluorescent dye synthesis.

In vivo detection of DNA secondary structures using permanganate/S1 footprinting with direct adapter ligation and sequencing (PDAL-Seq).

DNA secondary structures are essential elements of the genomic landscape, playing a critical role in regulating various cellular processes. These structures refer to G-quadruplexes, cruciforms, Z-DNA or H-DNA structures, amongst others (collectively called 'non-B DNA'), which DNA molecules can adopt beyond the B conformation. DNA secondary structures have significant biological roles, and their landscape is dynamic and can rearrange due to various factors, including changes in cellular conditions, temperature, and DNA-binding proteins. Understanding this dynamic nature is crucial for unraveling their functions in cellular processes. Detecting DNA secondary structures remains a challenge. Conventional methods, such as gel electrophoresis and chemical probing, have limitations in terms of sensitivity and specificity. Emerging techniques, including next-generation sequencing and single-molecule approaches, offer promise but face challenges since these techniques are mostly limited to only one type of secondary structure. Here we describe an updated version of a technique permanganate/S1 nuclease footprinting, which uses potassium permanganate to trap single-stranded DNA regions as found in many non-B structures, in combination with S1 nuclease digest and adapter ligation to detect genome-wide non-B formation. To overcome technical hurdles, we combined this method with direct adapter ligation and sequencing (PDAL-Seq). Furthermore, we established a user-friendly pipeline available on Galaxy to standardize PDAL-Seq data analysis. This optimized method allows the analysis of many types of DNA secondary structures that form in a living cell and will advance our knowledge of their roles in health and disease.

Atomic resolution studies of S1 nuclease complexes reveal details of RNA interaction with the enzyme despite multiple lattice-translocation defects.

S1 nuclease from Aspergillus oryzae is a single-strand-specific nuclease from the S1/P1 family that is utilized in biochemistry and biotechnology. S1 nuclease is active on both RNA and DNA but with differing catalytic efficiencies. This study clarifies its catalytic properties using a thorough comparison of differences in the binding of RNA and DNA in the active site of S1 nuclease based on X-ray structures, including two newly solved complexes of S1 nuclease with the products of RNA cleavage at atomic resolution. Conclusions derived from this comparison are valid for the whole S1/P1 nuclease family. For proper model building and refinement, multiple lattice-translocation defects present in the measured diffraction data needed to be solved. Two different approaches were tested and compared. Correction of the measured intensities proved to be superior to the use of the dislocation model of asymmetric units with partial occupancy of individual chains. As the crystals suffered from multiple lattice translocations, equations for their correction were derived de novo. The presented approach to the correction of multiple lattice-translocation defects may help to solve similar problems in the field of protein X-ray crystallography.

Plasmid DNA Isolation and Visualization: Isolation and Characterization of Plasmids from Clinical Samples.

Plasmids are important in carrying antibiotic resistance and other genes between bacterial cells, and a number of methods can be employed to characterize plasmids from clinical isolates. Single colonies typically obtained as part of hospital workflow can undergo S1 nuclease treatment to linearize plasmids followed by pulsed-field gel electrophoresis to enable determination of the number and sizes of plasmids present. Hybridization of S1/PFGE gels can be used to associate replicon types and passenger genes, such as those conferring antibiotic resistance, with a particular plasmid band. Individual plasmids, obtained by conjugation or transformation, can be compared by gel electrophoresis following restriction digestion of plasmid DNA prepared by alkaline lysis methods, including using specialized kits.

Isolation and Visualization of Plasmids from Gram-Positive Bacteria of Interest in Public Health.

This chapter describes the methods to extract and characterize plasmids of Gram-positive bacterial species of interest in public health (biomedicine, veterinary, and food safety) as Staphylococcus, Streptococcus, Enterococcus, Listeria, and Clostridium and lactic acid bacteria. References for detailed plasmid classification are given in order to provide a comprehensive landscape in the interpretation of their plasmidomes.

Fluorescence strategy for sensitive detection of adenosine triphosphate in terms of evaluating meat freshness.

A novel simple, sensitive and reliable sensor based on S1 nuclease, FAM-labeled ssDNA (DNA-F) and graphene oxide (GO) was developed for detecting adenosine triphosphate (ATP) and evaluating the freshness of meat (beef) samples. With S1 nuclease as the cleaver of DNA-F and ATP as the inhibitor of S1 nuclease, the fluorescence of DNA-F could be obviously quenched by GO, which exhibits the fluorescence of system gradually decrease as the increasing ATP concentration. Under the optimal conditions, a linear correlation between the fluorescence and the ATP concentration from 20 µM to 3500 µM is obtained with a detection limit of 3.2 µM. Furthermore, the proposed ATP detection method was applied to the ATP detection in microorganisms in meat samples, which acquired the satisfying results, respectively.

Assessing Oligonucleotide Binding to Double-Stranded DNA.

Sequence-specific targeting of double-stranded DNA (dsDNA) using synthetic oligonucleotides (ONs) has been under investigation in different therapeutic approaches. Several methods can be used to evaluate ONs effect and binding capacity to their target sequence. Here we describe some of the methods, which have been frequently used for assessing ONs binding to dsDNA.

Artificial Restriction DNA Cutter Using Nuclease S1 for Site-Selective Scission of Genomic DNA.

By combining a pair of pseudo-complementary peptide nucleic acids (pcPNAs) with S1 nuclease, a novel tool to cut DNA at a predetermined site can be obtained. Complementary pcPNAs invade the DNA duplex and base pair to each strand of a target site, creating single-stranded regions that are cleaved by S1 nuclease. The scission site can be freely modulated by the design of pcPNAs. This method can be used to cleave a single site in the human genome. This protocol presents experimental details for site-selective scission using this versatile new tool. © 2019 by John Wiley & Sons, Inc.

MnO2 Nanosheet-based Fluorescence Sensing Platform for Sensitive Detection of Endonuclease.

A novel fluorescence sensing platform for ultrasensitive detection of S1 nuclease activity has been constructed based on MnO2 nanosheets and FAM labeled single-stranded DNA (FAM-ssDNA). In this system, MnO2 nanosheets were found to have different adsorbent ability toward ssDNA and mono- or oligonucleotide fragments. FAM-ssDNA could adsorb on MnO2 nanosheets and resulted in significant fluorescence quenching through fluorescence resonance energy transfer (FRET), while mono- or oligonucleotide fragments could not adsorb on MnO2 nanosheets and still retained strong fluorescence emission. With the addition of S1 nuclease, FAM-ssDNA was cleaved into mono- or oligonucleotide fragments, which were not able to adsorb on MnO2 nanosheets and the fluorescence signal was never quenched. The different fluorescence intensity allowed for examination of S1 nuclease activity. The developed method can detect S1 nuclease activity in the range of 0 - 20 U mL-1 with a detection limit of 0.05 U mL-1. Benefits of the system include less time-consuming processes and more simple design compared to other endonuclease assays. Satisfactory performance for S1 nuclease in complex samples has been successfully demonstrated with the system. The developed assay could potentially provide a new platform in bioimaging and clinical diagnosis.

Prevalence and Molecular Characteristics of Extended-Spectrum ß-Lactamase Genes in Escherichia coli Isolated from Diarrheic Patients in China.

Background: The emergence and spread of antimicrobial resistance has become a major global public health concern. A component element of this is the spread of the plasmid-encoded extended-spectrum b-lactamase (ESBL) genes, conferring resistance to third-generation cephalosporins. The purpose of this study was to investigate the molecular characteristics of ESBL-encoding genes identified in Escherichia coli cultured from diarrheic patients in China from 2013 to 2014. Materials and Methods: A total of 51 E. coli were confirmed as ESBL producers by double-disk synergy testing of 912 E. coli isolates studied. Polymerase chain reaction (PCR) and DNA sequencing were performed to identify the corresponding ESBL genes. Susceptibility testing was tested by the disk diffusion method. Plasmids were typed by PCR-based replicon typing and their sizes were determined by S1-nuclease pulsed-field gel electrophoresis. Multi-locus sequence typing (MLST) and phylogrouping were also performed. Broth mating assays were carried out for all isolates to determine whether the ESBL marker could be transferred by conjugation. Results: Of the 51 ESBL-positive isolates identified, blaCTX-M, blaTEM, blaOXA, and blaSHV were detected in 51, 26, 3, 1 of these isolates, respectively. Sequencing revealed that 7 blaCTX-M subtypes were detected, with blaCTX-M-14 being the most common, followed by blaCTX-M-79 and blaCTX-M-28. Of the 26 TEM-positive isolates identified, all of these were blaTEM-1 genotypes. All isolates contained one to three large plasmids and 10 replicon types were detected. Of these, IncFrep (n = 50), IncK/B (n = 31), IncFIB (n = 26), IncB/O (n = 14), and IncI1-Ir (n = 8) replicon types were the predominating incompatibility groups. Twenty-six isolates demonstrated the ability to transfer their cefotaxime resistance marker at high transfer rates. MLST typing identified 31 sequence types and phylogenetic grouping showed that 12 of the 51 donor strains belonged to phylogroup B2. Conclusion: This study highlights the diversity of the ESBL producing E. coli and also the diversity of ESBL genes and plasmids carrying these genes in China, which poses a threat to public health.

DNA Fiber Analysis: Mind the Gap!

Understanding the mechanisms of replication stress response following genotoxic stress induction is rapidly emerging as a central theme in cell survival and human disease. The DNA fiber assay is one of the most powerful tools to study alterations in replication fork dynamics genome-wide at single-molecule resolution. This approach relies on the ability of many organisms to incorporate thymidine analogs into replicating DNA and is widely used to study how genotoxic agents perturb DNA replication. Here, we review different approaches available to prepare DNA fibers and discuss important limitations of each approach. We also review how DNA fiber analysis can be used to shed light upon several replication parameters including fork progression, restart, termination, and new origin firing. Next, we discuss a modified DNA fiber protocol to monitor the presence of single-stranded DNA (ssDNA) gaps on ongoing replication forks. ssDNA gaps are very common intermediates of several replication stress response mechanisms, but they cannot be detected by standard DNA fiber approaches due to the resolution limits of this technique. We discuss a novel strategy that relies on the use of an ssDNA-specific endonuclease to nick the ssDNA gaps and generate shorter DNA fibers that can be used as readout for the presence of ssDNA gaps. Finally, we describe a follow-up DNA fiber approach that can be used to study how ssDNA gaps are repaired postreplicatively.

Fabrication of DNA/RNA Hybrids Through Sequence-Specific Scission of Both Strands by pcPNA-S1 Nuclease Combination.

By combining two strands of pseudo-complementary peptide nucleic acid (pcPNA) with S1 nuclease, a tool for site-selective and dual-strand scission of DNA/RNA hybrids has been developed. Both of the DNA and the RNA strands in the hybrids are hydrolyzed at desired sites to provide unique sticky ends. The scission fragments are directly ligated with other DNA/RNA hybrids by using T4 DNA ligase, resulting in the formation of desired recombinant DNA/RNA hybrids.

Construction of Metal-Ion-Free G-quadruplex-Hemin DNAzyme and Its Application in S1 Nuclease Detection.

In this work, a new kind of peroxidase-mimicking DNAzyme (G-quadruplex-hemin DNAzyme, G4-hemin) was constructed by using hemin-modified G-rich DNA (hemin-G-DNA). Experimental results demonstrated that the G-rich DNA can form a G-quadruplex structure by the inducement of terminally modified hemin, rendering the assembly of hemin and G-quadruplex structure spontaneously and efficiently. As a result, G-hemin revealed higher peroxidase activity than traditional G-quadruplex/hemin DNAzyme (G4/hemin). Besides, different from G4/hemin, G4-hemin was constructed in one step without the participation of metal ions and adscititious hemin. Accordingly, the construction procedure was significantly simplified and the background signal from dissociative hemin was remarkably reduced. In a proof-of-concept trial, according to the colorimetric signals of G4-hemin, a novel biosensor for the detection of S1 nuclease activity was established, which provides a novel perspective for designing peroxidase-mimicking DNAzyme-based biosensors.

Identification of the σ7°-Dependent Promoter Controlling Expression of the ansPAB Operon of the Nitrogen-Fixing Bacterium Rhizobium etli.

The aim of the present work was to examine the putative promoter region of the operon ansPAB and to determine the general elements required for the regulation of transcriptional activity. The transcriptional start site of the ansPAB promoter was determined by using highresolution S1-nuclease mapping. Sequence analysis of this region showed -10 and -35 elements, which were consistent with consensus sequences for R. etli promoters that are recognized by the major form of RNA polymerase containing the σ(70) transcription factor. Mutation studies affecting several regions located upstream of the transcriptional start site confirmed the importance of these elements on transcriptional expression.

The σ(F)-specific anti-sigma factor RsfA is one of the protein kinases that phosphorylates the pleiotropic anti-anti-sigma factor BldG in Streptomyces coelicolor A3(2).

The anti-anti-sigma factor BldG has a role in the morphological differentiation and antibiotic production of Streptomyces coelicolor A3(2). Together with the anti-sigma factor UshX it is involved in the "partner-switching"-like activation of the sigma factor σ(H) that has a dual role in the osmotic stress response and morphological differentiation in S. coelicolor A3(2). Although BldG is phosphorylated in vivo in S. coelicolor, neither of the interacting anti-sigma factors UshX and ApgA is found to phosphorylate it. By using a combination of several approaches, we demonstrated a direct interaction between BldG and the anti-sigma factor RsfA, which has been previously shown to regulate antibiotic production and morphological differentiation in S. coelicolor and to specifically interact with the sporulation-specific sigma factor σ(F). RsfA phosphorylates BldG in vitro, demonstrating that RsfA is a specific kinase for BldG and negatively regulates its activity. However, another interacting anti-anti-sigma factor homolog, SCO0869, was not phosphorylated by RsfA. Transcriptional analyses of rsfA revealed a single promoter, the activity of which was repressed by osmotic stress and decreased during differentiation. These data suggested that BldG has a pleiotropic role in the regulation of at least two sigma factors, σ(H) and σ(F), in S. coelicolor.

A gene determining a new member of the SARP family contributes to transcription of genes for the synthesis of the angucycline polyketide auricin in Streptomyces aureofaciens CCM 3239.

Three regulators, Aur1P, Aur1R and a SARP-family Aur1PR3, have been previously found to control expression of the aur1 cluster for the angucycline antibiotic auricin in Streptomyces aureofaciens CCM 3239. Here, we describe an additional regulatory gene, aur1PR4, encoding a homologue from the SARP-family regulators. Its role in auricin regulation was confirmed by its disruption that dramatically affected auricin production. However, transcription from the aur1Ap promoter, directing expression of 22 auricin biosynthetic genes, was not substantially affected in the Δaur1PR4 mutant. A new promoter, sa13p, directing transcription of four putative auricin tailoring genes, was found to be dependent on aur1PR4. Moreover, analysis of the sa13p promoter region revealed the presence of three heptameric repeat sequences corresponding to putative SARP-binding sites. Expression of aur1PR4 is directed by a single promoter, aur1PR4p, which is induced after entry into stationary phase. Transcription from aur1PR4p was absent in a S. aureofaciens Δaur1P mutant strain, and Aur1P was shown to bind specifically to the aur1PR4p promoter. These results indicate a complex network of regulation of the auricin gene cluster. Both Aur1P and Aur1PR3 are involved in regulation of the core aur1A-U biosynthetic genes, and Aur1PR4 in regulation of putative auricin tailoring genes.