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Prokaryote genomes encode diverse programmable DNA endonucleases with significant potential for biotechnology and gene editing. However, these endonucleases differ significantly in their properties, which must be screened and measured. While positive selection screens based on ccdB and barnase have been developed to evaluate such proteins, their high levels of toxicity make them challenging to use. Here, we develop and validate a more robust positive selection screen based on the homing endonuclease I-SceI. Candidate endonucleases target and cure the I-SceI expression plasmid preventing induction of I-SceI-mediated double strand DNA breaks that lead to cell death in

International audience; Meganucleases are rare cutting enzymes that can generate DNA modifications and are part of the plant genome editing toolkit although they lack versatility. Here, we evaluated the use of two meganucleases, I-SceI and a customized meganuclease, in tomato and oilseed rape. Different strategies were explored for the use of these meganucleases. The activity of a customized and a I-SceI meganucleases was first estimated by the use of a reporter construct GFFP with the target sequences and enabled to demonstrate that both meganucleases can generate double-strand break and HDR mediated recombination in a reporter gene. Interestingly, I-SceI seems to have a higher DSB efficiency than the customized meganuclease: up to 62.5% in tomato and 44.8% in oilseed rape. Secondly, the same exogenous landing pad was introduced in both species. Despite being less efficient compared to I-SceI, the customized meganuclease was able to generate the excision of an exogenous transgene (large deletion of up to 3316 bp) present in tomato. In this paper, we also present some pitfalls to be considered before using meganucleases (e.g., potential toxicity) for plant genome editing.

The axolotl (Ambystoma mexicanum ) has been widely used as an animal model for studying development and regeneration. In recent decades, the use of genetic engineering to alter gene expression has advanced our knowledge on the fundamental molecular and cellular mechanisms, pointing us to potential therapeutic targets. We present a detailed, step-by-step protocol for axolotl transgenesis using either I-SceI meganuclease or the mini Tol2 transposon system, by injection of purified DNA into one-cell stage eggs. We add useful tips on the site of injection and the viability of the eggs.

The prevalence of peptic ulcer diseases has decreased over the past decades. The contribution of Helicobacter pylori to these changes has not been clearly delineated. Two cohorts of patients receiving esophagogastroduodenoscopy examination together with urease test were enrolled, 1 from year 2001 (n = 1030), the other from year 2019 (n = 600). The prevalence changes of peptic ulcer diseases as well as the associated clinical factors were analyzed. An independent cohort of gastric biopsy samples (n = 151) positive for H. pylori were retrieved for ureC gene genotype analysis. Comparison between the patients recruited from 2001 and 2019 revealed significant decrease in H. pylori infection (P0.001), duodenal ulcer prevalence (P0.001) and gastric ulcer prevalence (P0.001). Multivariate analysis showed that the decreases of these factors were independent (adjusted P0.001 for all). Intriguingly, in H. pylori positive patients, the prevalence of duodenal ulcer still decreased with year (P0.001), which was not found in gastric ulcer (P = 0.345). Genetic analysis of H. pylori urease gene showed that MboI-restriction fragment length polymorphism-defined genotype 3 UreC was significantly more prevalent in gastric ulcer patients than in others (P = 0.022). Independent decreases of H. pylori infection, gastric ulcer and duodenal ulcer over decades were found. In H. pylori positive patients, duodenal ulcer prevalence decreased overtime while gastric ulcer prevalence remained unchanged. Gastric ulcer/cancer had a higher prevalence of MboI-defined genotype 3 UreC gene.

We demonstrate the remarkable ability of surface-enhanced Raman spectroscopy (SERS) to track the allosteric changes in restriction endonuclease KpnI (R.KpnI) caused by metal ions. R.KpnI binds and promiscuously cleaves DNA upon activation by Mg2+ ions. However, the divalent ion Ca2+ induces high fidelity cleavage, which can be overcome by higher concentrations of Mg2+ ions. In the absence of any 3D crystal structure, for the first time, we have elucidated the structural underpinnings of such a differential effect of divalent ions on the endonuclease activity. A combined SERS and molecular dynamics (MD) approach showed that Ca2+ ion activates an enzymatic switch in the active site, which is responsible for the high fidelity activity of the enzyme. Thus, SERS in combination with MD simulations provides a powerful tool for probing the link between the structure and activity of enzyme molecules that play vital roles in DNA transactions.

Objective To evaluate the influence of certain genetic modifiers on foetal haemoglobin levels in thalassemia major and thalassemia intermedia. Methods The cohort study was conducted from November 2018 to August 2019, at Department of Haematology, University of Health Sciences, Lahore and comprised beta thalassemia intermedia and thalassemia major patients who were referred by various healthcare facilities across Punjab, Pakistan. Foetal haemoglobin was quantified by high performance liquid chromatography. Primary mutation analysis and single nucleotide polymorphisms were done by amplification refractory mutation system-based polymerase chain reaction. Data was analysed using SPSS 20. Results Of the 116 patients, 52(45%) had beta thalassemia intermedia and 64(55%) had thalassemia major. Foetal haemoglobin levels were primarily influenced by alleles of the HBG2 (rs7482144) and BCL11A (rs766432) genes, but single nucleotide polymorphism of HBS1L-MYB (rs9399137) had no significant role (p>0.05). The rs7482144 single nucleotide polymorphism explained 8.3% of the variation in the foetal haemoglobin levels, while 5% of trait variation was explained by rs766432. Conclusions There was found a clear association between foetal haemoglobin level and single nucleotide polymorphisms in HBG2 (rs7482144) and BCL11A (rs766432) genes. This correlation was additive and was seen both in thalassemia major and thalassemia intermedia cohorts.

DNA target search is a key step in cellular transactions that access genomic information. How DNA binding proteins combine 3D diffusion, sliding and hopping into an overall search strategy remains poorly understood. Here we report the use of a single molecule DNA tethering method to characterize the target search kinetics of the type II restriction endonuclease NdeI. The measured search rate depends strongly on DNA length as well as salt concentration. Using roadblocks, we show that there are significant changes in the DNA sliding length over the salt concentrations in our study. To explain our results, we propose a model including cycles of 3D and 1D search in which salt concentration modulates the strategy by varying the length of DNA probed per 1D scan. At low salt NdeI makes a single non-specific encounter with DNA followed by an effective and complete 1D scan. At higher salt, NdeI must execute multiple cycles of target search due to the reduced efficacy of 1D search.

Polymorphisms of vitamin D receptors (VDRs), ApaI, BsmI, FokI, and TaqI might affect susceptibility to tuberculosis (TB). In this systematic review and meta-analysis, all published articles which investigated the effects of these polymorphisms on the risk of TB in the Iranian population were retrieved. PubMed and Scopus were searched with no date or language restrictions. In this meta-analysis, the Comprehensive Meta-Analysis (CMA) version 2.0 and random effects model were applied. The association of polymorphisms with TB risk was assessed by measuring the odds ratio (ORs) at 95% CI. Heterogeneity was investigated based on Cochran Q-test and I2-index statistics. The significance level was set at 0.05. Also, Egger's regression intercept was determined to measure publication bias. A total of six articles on Iranian populations were included. TaqI (5/6 included studies) showed a significant association with the increased risk of TB based on ORs (allele comparison: 1.57 (1.0, 2.3), p-value: 0.02; additive model of tt/TT: 1.57 (0.9, 2.5), p-value: 0.05; recessive model (tt/Tt+TT): 1.99(1.2, 3.2), p-value: 0.00; dominant model (tt+Tt/TT): 1.98 (1.1, 3.5), p-value: 0.01). BsmI showed a significant positive effect on TB risk only in its dominant genotype (bb+bB/BB) (1.44 (1.0, 1.9); p-value: 0.02). FokI and ApaI did not show any significant effects on TB development in Iranian populations. Findings showed the significant effect of TaqI polymorphism in all genetic models and the dominant model of BsmI on the increased risk of TB. However, the effects of TaqI and BsmI should be further investigated in a larger sample size.

A bacterial strain 2H isolated from soil and identified as Thermoactinomyces vulgaris produce a potent Type II restriction endonuclease activity that has been extracted by a PEG/dextran aqueous two-phase system. Optimal temperature for the restriction endonuclease activity was 55-65°C. Specific DNA cleavage was obtained at pH range 7-10 and 10-20mM MgCl2. Restriction cleavage analysis followed by sequencing confirms GG^CC as the recognition sequence. This enzyme, named Tvu2HI, is a thermostable isoschizomer of the mesophilic prototype restriction endonuclease HaeIII. Sequencing of the complete Thermoactinomyces vulgaris 2H genome revealed the presence of two adjacent ORFs coding for the restriction endonuclease Tvu2HI and the corresponding methyltransferase; an ORF coding for a putative Vsr nicking enzyme was found close to those coding for the Tvu2HI restriction-modification system. Phylogenetic analysis based on sequence alignment suggests a common origin of Tvu2HI R-M system with HaeIII-like R-M systems. This is the first investigation dealing with a Type II restriction endonuclease identified in a natural isolate of the genus Thermoactinomyces.

Introduction. Herpes simplex virus type 1 (HSV-1) is a virus that causes serious human disease and establishes a long-term latent infection. The latent form of this virus has shown to be resistant to antiviral drugs. Clustered Regularly Interspace Short Palindromic Repeats (CRISPR), is an important tool in genome engineering and composed of guide RNA (gRNA) and Cas9 nuclease that makes an RNA-protein complex to digest exclusive target sequences implementation of gRNA. Moreover, CRISPR-Cas9 system effectively suppresses HSV-1 infection by knockout of some viral genes. Materials and methods. To survey the efficacy of Cas9 system on HSV-1 genome destruction, we designed several guide RNAs (gRNAs) that all packaged in one vector. Additionally, we performed a one-step restriction using BamHI and Esp3I enzymes. Results. CRISPR/Cas9 system targeted against the gD gene of HSV-1 was transfected into HEK-AD cells that showed a significant reduction of HSV-1 infection by plaque assay and real-time PCR. Conclusion. The pCas-Guide-EF1a-GFP CRISPR vector can create a fast and efficient method for gRNA cloning by restriction enzymes (Esp3I (BsmBI) and BamHI). Therefore, the CRISPR/Cas9 system may be utilized for the screening of genes critical for the HSV-1 infection and developing new strategies for targeted therapy of viral infections caused by HSV-1.

The Saccharomyces cerevisiae HO gene is a model regulatory system with complex transcriptional regulation. Budding yeast divide asymmetrically and HO is expressed only in mother cells where a nucleosome eviction cascade along the promoter during the cell cycle enables activation. HO expression in daughter cells is inhibited by high concentration of Ash1 in daughters. To understand how Ash1 represses transcription, we used a myo4 mutation which boosts Ash1 accumulation in both mothers and daughters and show that Ash1 inhibits promoter recruitment of SWI/SNF and Gcn5. We show Ash1 is also required for the efficient nucleosome repopulation that occurs after eviction, and the strongest effects of Ash1 are seen when Ash1 has been degraded and at promoter locations distant from where Ash1 bound. Additionally, we defined a specific nucleosome/nucleosome-depleted region structure that restricts HO activation to one of two paralogous DNA-binding factors. We also show that nucleosome eviction occurs bidirectionally over a large distance. Significantly, eviction of the more distant nucleosomes is dependent upon the FACT histone chaperone, and FACT is recruited to these regions when eviction is beginning. These last observations, along with ChIP experiments involving the SBF factor, suggest a long-distance loop transiently forms at the HO promoter.

Aims: New methods of DNA recombination that capture the principal advantages of the BioBrick standard (ease of design) and Golden Gate assembly (decreased labor) are demonstrated here. Methods & materials: Both methods employ DNA methyltransferase expression vectors, available from Addgene, that protect selected sites on different plasmids from particular Type II restriction endonucleases. No other reagents are required. Results: The 4R/2M discontinuous DNA assembly is more efficient (produces more desired recombinant plasmids) and as specific (produces few undesired recombination products) as conventional subcloning. The 5RM continuous DNA assembly is approximately as efficient and specific as conventional Golden Gate assembly, even though in vivo methylation of one plasmid is incomplete. Conclusion: Both methylase-assisted methods streamline BioBrick assembly workflows without complicating the design of synthetic parts.

Transgenesis with the meganuclease I-SceI is a safe and efficient method, but the underlying mechanisms remain unclear due to the lack of information on transgene localization. Using I-SceI, we previously developed a transgenic Xenopus tropicalis line expressing enhanced green fluorescent protein driven by the neural crest-specific snai2 promoter/enhancer, which is a powerful tool for studying neural crest development and craniofacial morphogenesis. Here, we carried out whole-genome shotgun sequencing for the snai2:eGFP embryos to identify the transgene integration sites. With a 19x sequencing coverage, we estimated that 6 copies of the transgene were inserted into the Xenopus tropicalis genome in the hemizygous transgenic embryos. Two transgene integration loci adjacent to each other were identified in a noncoding region on chromosome 1, possibly as a result of duplication after a single transgene insertion. Interestingly, genomic DNA at the boundaries of the transgene integration loci contains short sequences homologous to the I-SceI recognition site, suggesting that the integration was not random but probably mediated by sequence homology. To our knowledge, our work represents the first genome-wide sequencing study on a transgenic organism generated with I-SceI, which is useful for evaluating the potential genetic effects of I-SceI-mediated transgenesis and further understanding the mechanisms underlying this transgenic method.

Transgenic frogs can be very efficiently generated using I-SceI meganuclease, a nuclease with an 18-bp recognition site. The desired transgene must be flanked by I-SceI sites, in either a plasmid or a polymerase chain reaction (PCR) product. After a short in vitro digestion with the meganuclease, the complete reaction is injected into fertilized eggs, where the enzyme mediates genomic integration by an unknown mechanism. Posttransgenesis development is typically normal, and up to 70% of the embryos integrate the transgene.

OBJECTIVE The aim of the present meta-analysis was to explore the association between FokI polymorphism of the vitamin D receptor gene and lumbar spine disc degeneration. DESIGN The search was performed in PubMed, Scopus, and Web of Science databases up to January 2020. The authors selected nine studies comprising a total of 1549 cases and 1672 controls. The association analysis included the allelic, dominant, recessive, homozygous, and heterozygous genetic models. Odds ratios with 95% confidence intervals were used to evaluate the association. The Newcastle-Ottawa Scale was used to measure the quality of the studies included in the analyses; a cut-off of 6 stars was applied. RESULTS This meta-analysis indicated that FokI polymorphism is significantly associated with lumbar degenerative disc disorder and disc herniation in the homozygous (odds ratio, 1.77; 95% confidence interval, 1.23-2.54; Z test P = 0.002, Q test P = 0.416) and recessive (odds ratio, 1.53; 95% confidence interval, 1.23-1.90; Z test P < 0.000, Q test P = 0.224) models. CONCLUSIONS This study indicates that the vitamin D receptor gene FokI polymorphism may be correlated with the risk of developing a lumbar degenerative disc disorder and disc herniation. However, the small sample population studied and the lack of an evaluation of environmental factors must be taken as limitations in the present meta-analysis.

Background Vitamin D inhibits cell proliferation via the vitamin D receptor (VDR), which may affect breast cancer risk. This study aimed to investigate the association of ApaI and TaqI polymorphisms of the VDR gene with breast cancer risk which followed by stratified analysis. Materials and methods A case-control study was conducted on 150 breast cancer patients and 150 healthy controls. VDR ApaI and TaqI genotyping were performed by PCR-RFLP. Some demographic and pathologic features of patients were extracted from their archived files and then were analyzed by genotypes distributions. Results For ApaI polymorphism, our data showed a significant difference between the patient and healthy groups for mutant allele carriers compared with those with AA genotype. Besides, statistical analysis showed that there was a significant association between the C allele and the increased risk of breast cancer. For TaqI polymorphism, statistical analysis revealed that there was a significant association between CC genotype and increased risk of breast cancer. Also, there was a significant association between the C allele and the increased risk of breast cancer. In a preliminary study, stratified analysis based on the size of tumor and lymph node metastasis revealed no significant association between two ApaI and TaqI variations and these parameters. Conclusions Based on our results, the VDR ApaI and TaqI variations could be considered as genetic risk factors for breast cancer. However, further studies with a larger sample size are required to obtain more accurate outcomes, especially in stratified analysis.

We previously developed a large-scale genome restructuring technology called the TAQing system. It can induce genomic rearrangements by introducing transient and conditional formation of DNA double-strand breaks (DSBs) via heat activation of a restriction enzyme TaqI, which can cleave DNA at 5'-TCGA-3' sequences in the genome at higher temperatures (37-42°C). Such heat treatment sometimes confers lethal damage in certain plant species and TaqI cannot induce rearrangements in AT-rich regions. To overcome such problems we developed an extended TAQing (Ex-TAQing) system, which enables the use of a wider range of restriction enzymes active at standard plant-growing temperatures. We established the Ex-TAQing system using MseI that can efficiently cleave DNA at room temperature (at temperatures ranging from 22 to 25°C) and the 5'-TTAA-3' sequence which is highly abundant in the Arabidopsis genome. A synthetic intron-spanning MseI gene, which was placed downstream of a heat-shock-inducible promoter, was conditionally expressed upon milder heat treatment (33°C) to generate DSBs in Arabidopsis chromosomes. Genome resequencing revealed various types of genomic rearrangements, including copy number variations, translocation and direct end-joining at MseI cleavage sites. The Ex-TAQing system could induce large-scale rearrangements in diploids more frequently (17.4%, n = 23) than the standard TAQing system. The application of this system to tetraploids generated several strains with chromosomal rearrangements associated with beneficial phenotypes, such as high salinity stress tolerance and hypersensitivity to abscisic acid. We have developed the Ex-TAQing system, allowing more diverse patterns of genomic rearrangements, by employing various types of endonucleases and have opened a way to expand the capacity for artificial genome reorganization.

Rapid detection of physiological changes of neuropeptides is of great importance as they are involved in a wide range of physiological processes and behaviors. Abnormalities in their expression level are correlated with various neurological diseases. However, current methods such as radioimmunoassay, enzyme-linked immunosorbent assays and liquid chromatography tandem mass spectrometry relied on cumbersome operation steps and could not rapidly provide the information of their concentration fluctuations. Thus motivated, we developed a target-driven DNA-based molecular machine that could be triggered only in the presence of a specific target neuropeptide. Using arginine-vasopressin (AVP) as a model neuropeptide, we integrated the DNA-based molecular machine with fluorescence signal transduction and amplification technology. The assay was rapid and homogeneous, which offered a linear range of 75-700 pM and a limit-of-detection as low as 75 pM. It holds great potential for further applications in real-time monitoring of the variations of the AVP level in biological samples.

Five 2-substituted 2'-deoxyinosine triphosphates (dRITP) were synthesized and tested as substrates in enzymatic synthesis of minor-groove base-modified DNA. Only 2-methyl and 2-vinyl derivatives proved to be good substrates for Therminator DNA polymerase, whilst all other dRITPs and other tested DNA polymerases did not give full length products in primer extension. The DNA containing 2-vinylhypoxanthine was then further modified through thiol-ene reactions with thiols. Cross-linking reaction between cysteine-containing minor-groove binding dodecapeptide and DNA proceeded thanks to the proximity effect between thiol and vinyl groups inside the minor groove. 2-Substituted dIRTPs and also previously prepared 2-substituted 2'-deoxyadenosine triphosphates (dRATP) were then used for enzymatic synthesis of minor-groove modified DNA to study the effect of minor-groove modifications on cleavage of DNA by type II restriction endonucleases (REs). Although the REs should recognize the sequence through H-bonds in the major groove, some minor-groove modifications also had an inhibiting effect on the cleavage.

HhaI, a Type II restriction endonuclease, recognizes the symmetric sequence 5′-GCG↓C-3′ in duplex DNA and cleaves (‘↓’) to produce fragments with 2-base, 3′-overhangs. We determined the structure of HhaI in complex with cognate DNA at an ultra-high atomic resolution of 1.0 Å. Most restriction enzymes act as dimers with two catalytic sites, and cleave the two strands of duplex DNA simultaneously, in a single binding event. HhaI, in contrast, acts as a monomer with only one catalytic site, and cleaves the DNA strands sequentially, one after the other. HhaI comprises three domains, each consisting of a mixed five-stranded β sheet with a defined function. The first domain contains the catalytic-site; the second contains residues for sequence recognition; and the third contributes to non-specific DNA binding. The active-site belongs to the ‘PD-D/EXK’ superfamily of nucleases and contains the motif SD-X11-EAK. The first two domains are similar in structure to two other monomeric restriction enzymes, HinP1I (G↓CGC) and MspI (C↓CGG), which produce fragments with 5′-overhangs. The third domain, present only in HhaI, shifts the positions of the recognition residues relative to the catalytic site enabling this enzyme to cleave the recognition sequence at a different position. The structure of M.HhaI, the biological methyltransferase partner of HhaI, was determined earlier. Together, these two structures represent the first natural pair of restriction-modification enzymes to be characterized in atomic detail.

Bioorthogonal control of metal ion sensors for imaging metal ions in living cells is important for better understanding of the distribution and fluctuation of metal ions. While bioorthogonal control using external stimuli such as light has been reported, these stimuli are not suitable for investigating many biological systems where light penetration is limited or quantum yield of activation is low. To overcome this limitation, we herein report the endogenous and bioorthogonal activation of a DNAzyme fluorescent sensor containing an 18-base pair (bp) recognition site of a homing endonuclease (I-SceI), since the recognition site of this length is found by chance only once in 7×10(10) bp of genomic sequences, it can thus form a near bioorthogonal pair with I-SceI for DNAzyme activation with minimal effect on living cells. The formation of the recognition site through double stranded DNA hybridization prevents the formation of an active DNAzyme initially. Once I-SceI is expressed inside cells, it cleaves at the recognition site, which allows the DNAzyme to adopt its active conformation. The activated DNAzyme sensor is then able to specifically catalyze cleavage of a substrate strand in the presence of Mg(2+) to release the fluorophore-labeled DNA fragment and produce a fluorescent turn-on signal for Mg(2+). Using this method, we demonstrate the use of I-SceI to activate the 10–23 DNAzyme for imaging of Mg(2+) in HeLa cells with endogenous and bioorthogonal control.

An ultrasensitive strategy based on sandwich immunoassay coupled with isothermal exponential amplification reaction (IMEXPAR) is proposed for the determination of tumor protein Mucin 1 (MUC1). An immuno-PCR plate was prepared from modification of the primary MUC1-antibody (Ab1) onto the inner-well of the PCR plate. A biotinylated secondary MUC1-antibody tagged with the biotinylated EXPAR primer (P-Ab2) was prepared through biotin-streptavidin reaction. In the presence of target MUC1, sandwich-type combinations were specifically formed in the immuno-PCR plate. With further addition of amplification template, polymerase and nicking enzyme, EXPAR was specifically triggered, producing numerous primer replica in minutes, and greatly enhanced fluorescence of SYBR Green I. The proposed strategy has a good linear relationship with the logarithm of the MUC1 concentration ranging from 3 pM to 3 nM with a limit of detection of 1.63 pM (S/N = 3), which is two orders of magnitude lower than those of other methods. Owing to the specificity of immuno-reaction and EXPAR, the selectivity of the strategy is favorable, even if for the homologous protein. The proposed strategy was further applied for the MUC1 determination in human serum, and a satisfactory recovery range of 98.7%–105.3% was obtained. The strategy can be facilely extended to the ultrasensitive determination of various proteins.

For precise genome editing, it is important to control the activity of sequence-specific nucleases. We have constructed a chemically inducible nuclease system based on the dimerization of FKBP and FRB domains in the presence of rapamycin and designated it as a chemically inducible dimerization (CID). The CID was designed to occur at the interlinker section between DNA binding domains and the FokI catalytic domain. Thus, induction of cleavage should occur quickly after addition of rapamycin because components of proteins are already in active form and located in the nucleus. This CID-dependent sequence-specific nuclease has potential to be applied for time-resolved analysis of the mutation induction mechanism in the genome.

The biological functions of DNA are carried out by individual proteins that interact with specific sequences along the DNA in order to prime the molecular processes required by the cellular metabolism. Protein-DNA interactions include DNA replication, gene expression and its regulation, DNA repair, DNA restriction and modification by endonucleases, generally classified as enzymatic functions, or transcription factors functions. To find specific binding target sequences and achieve their aims, in less than one second proteins operate in symbiosis with a crowded cellular environment, identifying extremely small cognate sequences along the DNA chain, which range from 15-20 bps for repressors to 4-6 bps for restriction enzymes. In a previous work, we proposed that the extraordinary ability of proteins to identify consensus sequences on DNA in a short time appears to be dependent on specific quantum signatures such as the entanglement of

The LAGLIDADG family of homing endonucleases (LHEs) bind to and cleave their DNA recognition sequences with high specificity. Much of our understanding for how these proteins evolve their specificities has come from studying LHE homologues. To gain insight into the molecular basis of LHE specificity, we characterized I-WcaI, the homologue of the Saccharomyces cerevisiae I-SceI LHE found in Wickerhamomyces canadensis. Although I-WcaI and I-SceI cleave the same recognition sequence, expression of I-WcaI, but not I-SceI, is toxic in bacteria. Toxicity suppressing mutations frequently occur at I-WcaI residues critical for activity and I-WcaI cleaves many more non-cognate sequences in the Escherichia coli genome than I-SceI, suggesting I-WcaI endonuclease activity is the basis of toxicity. In vitro, I-WcaI is a more active and a less specific endonuclease than I-SceI, again accounting for the observed toxicity in vivo. We determined the X-ray crystal structure of I-WcaI bound to its cognate target site and found that I-WcaI and I-SceI use residues at different positions to make similar base-specific contacts. Furthermore, in some regions of the DNA interface where I-WcaI specificity is lower, the protein makes fewer DNA contacts than I-SceI. Taken together, these findings demonstrate the plastic nature of LHE site recognition and suggest that I-WcaI and I-SceI are situated at different points in their evolutionary pathways towards acquiring target site specificity.

There have been plenty of reports regarding the association between Vitamin D (Vit D) and carotid atherosclerosis and stroke. We aimed to assess the association between FokI and TaqI polymorphisms of vitamin D receptor (VDR) gene and the severity of carotid bulb stenosis and the incidence of carotid bulb calcification in patients with ischemic stroke.This prospective study conducted at Shiraz University of Medical Sciences between February 2020 and August 2020. All consecutive patients with ischemic stroke with more than 50% carotid bulb stenosis in color doppler sonography underwent cervical CT angiography (CTA). Demographics, risk factors of ischemic stroke, serum calcium, phosphate, creatinine, serum 25-hydroxyvitamin D (Vit D) level were investigated by High-Performance Liquid Chromatography (HPLC) method. The severity of stenosis and presence of calcification in carotid bulb ipsilateral was studied in CTA to ischemic stroke. VDR genotypes of FokI and TaqI polymorphisms were determined by the Restriction FragmentLength Polymorphism (RFLP) method.A total of 122 patients were recruited in this study (mean age: 59.1, 66.4% males, 17.2% with carotid artery stenosis of 70-99%. 57% with carotid bulb calcification). There was a significant association between calcification of carotid bulb with FokI CC polymorphisms of VDR gene (P value = 0.037). There was no significant relationship between the severity of carotid bulb stenosis and Fok1 and TaqI polymorphisms of vitamin D receptor gene and their alleles.There may be a biological association between the FokI VDR gene and carotid bulb calcification.

Orientadores: Stephen Hyslop, Carla Beatriz Collares-Buzato Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia Resumo: As peçonhas de serpentes Bothrops são responsáveis por diversos danos locais (na região da mordida) e sistêmicos durante o envenenamento. Dentre as manifestações sistêmicas, a insuficiência renal aguda e um dos mais importantes efeitos tóxicos causados por acidentes botropicos. Esta tese teve como objetivos: 1) investigar a ação da peçonha bruta de B. alternatus em células epiteliais renais MDCK; 2) proceder a purificação e caracterização de uma DNase acida presente nesta peçonha; e 3) determinar a possível ação apoptotica desta DNase sobre células MDCK em cultura. Com relação as ações in vitro do peçonha bruta de B. alternatus, observamos modificações no citoesqueleto, nas junções intercelulares e sobre a morte celular das células MDCK tratadas com 10 ou 100 µg/mL de peçonha bruta. Dentre as modificações observadas, houve uma diminuição da resistência transpitelial, uma redistribuição de algumas proteínas associadas as junções intercelulares acompanhada por um desarranjo do citoesqueleto envolvendo as fibras de estresse na superfície basal e adesão focal associada a F-actina na região de contato celula-matriz. A analise morfometrica mostrou uma diminuição do numero de células entrando em mitose e um aumento do numero de células com núcleos picnoticos ou morfologicamente alterados apos tratamento com o peçonha. Microscopia eletrônica de varredura revelou uma densidade de microvilosidades diminuída, assim como a alteração da morfologia celular normal, de poliédrico para um formato fusiforme, nas células tratadas. O tipo principal de morte celular induzido pelo tratamento com o peçonha bruta foi a necrose, com uma freqüência pequena de indução de apoptose. O pré-tratamento das células MDCK com catalase, superoxido dismutase e L-NAME inibiu os efeitos sobre morte celular causados pelo peçonha bruta, indicando o envolvimento de espécies reativas de oxigênio e nitrogênio nos danos causados pelo envenenamento pela peçonha de B. alternatus. As peçonhas ofídicas possuem uma grande variedade de enzimas que degradam ácidos nucléicos e seus constituintes. As desoxirribonucleases (DNases) são endonucleases presentes em peçonhas de serpentes que hidrolisam acido desoxirribonucleico (DNA). Sua ação no envenenamento ocorre em conjunto com outras enzimas que quebram ligações fosfato (ATPases, 5¿-nucleotidases, fosfodiesterases, ribonucleases). Vários estudos sobre endonucleases em mamiferos sugerem que a DNase II (DNase acida) seria responsável pela fragmentacao do DNA durante a apoptose. E também conhecido que peçonhas são capazes de induzir apoptose em células. Através de uma combinação de cromatografias de troca iônica, gel filtração, afinidade e HPLC, foi purificada uma DNase da peçonha de B. alternatus, com atividade especifica de 3.489 unidades/mg (atividade especifica da peçonha: 65 unidades/mg) e fator de purificação de ~54 vezes. As características bioquímicas desta enzima são: uma massa molecular de ~31 kDa, ausência de subunidades, pI de 4,4-5,2, pH otimo de atividade de 4,7, termo estabilidade ate 40oC. O Km e Vmax são 10.1 µg/mL e 352.5 U/mg, respectivamente. A enzima degrada preferencialmente DNA de dupla fita, com atividade menor sobre DNA desnaturado; também degrada DNA circular (dos plasmideos pGEM e pBR322) mas não degrada RNA ou poly A. E inibida por altas concentrações (100 mM) de cations (Ca2+, Mg2+ e Zn2+), e também por N-etilmaleimida, iodoacetamida, acido aurintricarboxilico e DTT, mas não por EDTA. A enzima e reconhecida por IgG antibotropica em Western blot e no ELISA e por anti-DNase II humana no Western blot. Em celulas MDCK, a DNase produz alterações morfologicas como vacuolacão do citoplasma, retração e destacamento das celulas em monocamada, presença de núcleos condensados e/ou fragmentados. Através de ensaios de viabilidade e citotoxicidade, verificamos que a DNase e citotoxica as células MDCK em doses a partir de 400 U/mL (~20 µg/mL). Alem disso, causa fragmentação de DNA e um aumento no numero de células apoptoticas, em menor proporção, de células em necrose. A via de apoptose estimulada pela enzima envolve a ativação das caspases 3, 8 e 9, e uma diminuição na expressão da proteína anti-apoptotica Bcl-2. Estes resultados mostram que a peçonha de B. alternatus e citotoxica as células MDCK, com parte desta toxicidade mediada pela DNase II. Esta enzima induz apoptose que poderia contribuir para a toxicidade geral da peçonha Abstract: Bothrops snake venoms are cytotoxic to a variety of cells (endothelial, smooth muscle, renal and inflammatory cells), and may cause cell death by apoptosis. The venom components implicated in apoptosis include metalloproteinases and L-amino acid oxidase. In contrast, although acidic deoxyribonucleases (DNase II) have been implicated in DNA fragmentation during apoptosis in mammals, nothing is known of the involvement of venom deoxyribonucleases in this phenomenon. In this thesis, we 1) investigated the cytotoxicity of Bothrops alternatus venom in Madin-Darby canine kidney (MDCK) epithelial cells, 2) purified and characterized an acidic DNase from this venom, and 3) assessed the apoptotic activity of this DNase in MDCK cells. Treatment with B. alternatus venom (10 and 100 µg/mL) markedly decreased the transepithelial electrical resistance of cultured cells, and caused redistribution of some junctional proteins followed by cytoskeletal rearrangement involving stress fibers at the basal cell surface and focal adhesion-associated F-actin in the cell-matrix contact region. There was a decrease in the number of mitotic cells and an increase in the number of cells with pycnotic or morphologically altered nuclei. Scanning electron microscopy revealed a decrease in microvillar density and alteration in the normal cell morphology from polyhedric to fusiform. Staining with annexin V-FITC and electrophorese of cellular DNA suggested that cell death was predominantly by necrosis. Pretreating the cells with catalase, superoxide dismutase or L-NAME significantly attenuated the venom-induced cell death, indicating the possible involvement of reactive oxygen and nitrogen species in this phenomenon. DNase II was purified from B. alternatus venom by a combination of ion exchange and gel filtration chromatographies (specific activity = 1.9x103 units/mg vs. 36.1 units/mg for venom, purification factor = 51.2, with a protein yield of 1.75%). The molecular mass of 26.4 kDa (SDS-PAGE) was unaffected by dithiothreitol or i-mercaptoethanol, indicating a single-chain protein. Immunoblotting with affinity-purified IgG from commercial bothropic antivenom also yielded a single protein band with the same molecular mass. The enzyme was also recognized by antibothropic IgG in ELISA and crossreacted with anti-human DNase II in western blots. The isoelectric point determined by 2Dgel electrophoresis was ~5.0. DNase II cleaved double-stranded DNA, denatured DNA and circular DNA (from the plasmids pGEM and pBR 322), but there was no degradation of RNA. The enzyme was active in the pH range of 4.5-5.5, with an optimum at 4.7; activity was lost at >50oC. The Km and Vmax were 10.1 µg/mL and 352.5 U/mg, respectively. Enzymatic activity was inhibited by aurintricarboxylic acid (25 µM), iodoacetamide (1 mM), DTT (1 mM) and Ca2+, Mg2+ and Zn2+ (100 mM), but not by EDTA (5 mM). In MDCK cells, DNase II produced cytoplasmic vacuolization, cell shrinkage and cell detachment from the substrate, as well as condensed and/or fragmented nuclei. DNase was cytotoxic to MDCK cells at > 400 U/mL (~20 µg/mL), caused DNA fragmentation, and increased the proportion of apoptotic cells. The apoptotic pathway stimulated by this enzyme involved the activation of caspases 3, 8 and 9, and a decrease in the expression of the anti-apoptotic protein Bcl2. These results show that B. alternatus venom is cytotoxic to MDCK cells, with part of this toxicity probably being mediated by DNase II. This enzyme induces apoptosis that could contribute to the general cytotoxicity of the venom Doutorado Bioquímica Doutor em Biologia Funcional e Molecular

Persistent hepatitis B virus (HBV) infection remains a serious medical problem worldwide, with an estimated global burden of 257 million carriers. Prophylactic and therapeutic interventions, in the form of a vaccine, immunomodulators, and nucleotide and nucleoside analogs, are available. Vaccination, however, offers no therapeutic benefit to chronic sufferers and has had a limited impact on infection rates. Although immunomodulators and nucleotide and nucleoside analogs have been licensed for treatment of chronic HBV, cure rates remain low. Transcription activator-like effector nucleases (TALENs) designed to bind and cleave viral DNA offer a novel therapeutic approach. Importantly, TALENs can target covalently closed circular DNA (cccDNA) directly with the potential of permanently disabling this important viral replicative intermediate. Potential off-target cleavage by engineered nucleases leading to toxicity presents a limitation of this technology. To address this, in the context of HBV gene therapy, existing TALENs targeting the viral core and surface open reading frames were modified with second- and third-generation FokI nuclease domains. As obligate heterodimers these TALENs prevent target cleavage as a result of FokI homodimerization. Second-generation obligate heterodimeric TALENs were as effective at silencing viral gene expression as first-generation counterparts and demonstrated an improved specificity in a mouse model of HBV replication.

NANOG is an embryonic transcription factor, which gets reexpressed in cancer stem or tumor initiating cells. NANOGP8, a retrogene belonging to the NANOG family, is predominantly expressed in cancer cells and shows very high similarity with NANOG both at the nucleotide and at the protein level. The high similarity makes it extremely challenging to distinguish between these two transcription factors. Here we describe a highly efficient restriction endonuclease-based assay, which is performed on cDNA and allows to distinguish NANOGP8 from NANOG. This assay is critical to understand the specific role of NANOGP8 in cancer stemness, which in turn helps to unravel the therapeutic potential of targeting this undruggable transcription factor through gene therapy, for treatment of various cancers.

DNA indexing is based on a presynthesized library of oligonucleotide adaptors (256 in total), named indexers, and type-IIS restriction endonucleases. It enables amplification and direct analysis of large DNA fragments with low overall redundancy and without subcloning. Here, we describe a detailed protocol for PCR-based amplification of DNA fragments followed by DNA sequencing by indexer walking and provide helpful hints on its practical use. The proposed protocol can be applied to the sequencing of plasmids, cDNA clones, and longer DNA fragments. It can also be used for gap filling at the final stage of genome sequencing projects.

Restriction endonucleases (REs) are intra-bacterial scissors that are considered tools in the fight against foreign genetic material. SspI and BsmAI, examined in this study, cleave dsDNA at their site of recognition or within a short distance of it. Both enzymes are representatives of type II REs, which have played an extremely important role in research on the genetics of organisms and molecular biology. Therefore, the study of agents affecting their activity has become highly important. Ionizing radiation may damage basic cellular mechanisms by inducing lesions in the genome, with 5′,8-cyclo-2′-deoxypurines (cdPus) as a model example. Since cdPus may become components of clustered DNA lesions (CDLs), which are unfavorable for DNA repair pathways, their impact on other cellular mechanisms is worthy of attention. This study investigated the influence of cdPus on the elements of the bacterial restriction–modification system. In this study, it was shown that cdPus present in DNA affect the activity of REs. SspI was blocked by any cdPu lesion present at the enzyme’s recognition site. When lesions were placed near the recognition sequence, the SspI was inhibited up to 46%. Moreover, (5′S)-5′,8-cyclo-2′-deoxyadenosine (ScdA) present in the oligonucleotide sequence lowered BsmAI activity more than (5′R)-5′,8-cyclo-2′-deoxyadenosine (RcdA). Interestingly, in the case of 5′,8-cyclo-2′-deoxyguanosine (cdG), both 5′S and 5′R diastereomers inhibited BsmAI activity (up to 55% more than cdA). The inhibition was weaker when cdG was present at the recognition site rather than the cleavage site.

A specific type II restriction endonuclease T.Smu451I has been purified to electrophoretic homogeneity from the frozen cells of soil bacterium Sphingobacterium multivorum 451 (formerly Flavobacterium multivorum 451), using ultrasonic grinding, nucleic acid removal by streptomycin sulfate, protein precipitation by ammonium sulfate and phosphocellulose P-11, DEAE-Cellulose DE-52, Hepharin-Sepharose CL-6B chromatography, and elucidated several characteristics of T.Smu451I. The molecular weight of the enzyme determined by gel filtration and SDS-polyacrylamide gel electrophoresis was calculated to be 45,000 ± 2000 D (dimer) and 23,000 ± 1000 D (monomer), respectively. The isoelectric point (pI) of T.Smu451I is 5.4. T.Smu451I recognizes pentanucleotide palindromic sequences 5'-GGNC↓C-3' and cleaves between C and C in position shown by arrow to produce 3'-cohesive terminus of trinucleotide. Therefore, T.Smu451I is a neoschizomer of T.AsuI.

Interactions between distant DNA segments play important roles in various biological processes, such as DNA recombination. Certain restriction enzymes create DNA loops when two sites are held together and then cleave the DNA. DNA looping is important during DNA synapsis. Here we investigated the mechanisms of DNA looping by restriction enzyme SfiI by measuring the properties of the system at various temperatures. Different sized loop complexes, mediated by SfiI-DNA interactions, were visualized with AFM. The experimental results revealed that small loops are more favorable compared to other loop sizes at all temperatures. Our theoretical model found that entropic cost dominates at all conditions, which explains the preference for short loops. Furthermore, specific loop sizes were predicted as favorable from an energetic point of view. These predictions were tested by experiments with transiently assembled SfiI loops on a substrate with a single SfiI site.

Biochemical reactions occurring inside cells have significant stochastic signatures due to the low copy number of reacting species. Kinetics of DNA cleavage by restriction endonucleases are no exception as established by single-molecule experiments. Here, we propose a simple reaction scheme to understand the role of the cofactor magnesium ion in the action of the endonuclease ApaI. The methodology is based on the waiting time distribution of cleavage product formation that enables us to determine the corresponding rate both analytically and numerically. The theory is developed at the single-molecule level and then generalized to the biologically relevant case of a population of DNA-endonuclease complexes present inside a cell. The theoretical rate versus cofactor concentration curve is matched with relevant single-molecule experimental data that reveals positive cooperativity of cofactor binding and provides a reliable estimate of model parameters. Furthermore, a parameter range is identified where the dispersion of the waiting time, measured using the coefficient of variation, is significantly lower than the Poisson limit and becomes minimum at the in vivo magnesium ion concentration level. Such low dispersion can play a role in the robust DNA-scissoring activity of ApaI under in vivo conditions.

Single base mismatch can always connect with various gene-related diseases, whose determination has aroused widespread interest. So far, various methods have been developed to determine the common base mismatch. However most of them are complex, time-consuming. Herein, we report a novel method, which only need one conventional endonuclease (NEase) and achieve site-specific cleavage in a programmable way, to detect single base mismatch, termed aligner-mediated cleavage-based single base mismatch discrimination (AMCMD). The DNA aligner (DA) is in a stem-loop structure, consistent with an incomplete recognition site of NEase on its stem and a 5′-side arm complementary to the target sequence (TS). Once TS contains matched base and hybridizes with DA, the complete recognition site of NEase is formed, and the TS will be cleavaged with fast speed, while converse is not. Based on it, the method can clearly distinguish mismatched and complementary bases. Without sample pre-processing, we were able to obtain and verify all the test result in about 30 min through the polyacrylamide gel electrophoresis analysis. This endows the proposed method with a simpler advantage. Then we combined AMCMD and EXPAR to create a new method for single base mismatch discrimination, the short sequence obtained by AMCMD as a target to trigger EXPAR, with a detection limit at 1pM level. Another process with human serum underlines that AMCMD is compatible with the complex biological sample, thus it has the potentials for practical applications.

Nicking endonucleases (NEs) become increasingly attractive for their promising applications in isothermal amplification. Unfortunately, in comparison with their applications, their catalytic mechanism studies have relatively lagged behind due to a paucity of crystal structure information. Nt.BstNBI is one of those widely used NEs. However, many aspects of its catalytic mechanism still remained to be explored. Herein, we employed only rolling circle amplification (RCA) assay as a major analytic tool and succeeded in identifying the potential binding positions and regions of the DNA substrate based on locked nucleic acid modification, DNA duplex length of substrate, and substrate mismatch designs. Based on these data, we, for the first time, revealed that Nt.BstNBI was likely to recognize six adjacent positions of the recognition sequence (G1rt, A2rt, G3rt, A2rb, C3rb, and T4rb) in the major groove and hold three positions of the cleavage sequence (N3ct, N4ct, and N7cb) in the minor groove of DNA duplex for nicking. Moreover, this work also demonstrated the unexpected efficiency of RCA to study the macromolecular interaction for certain kind of nucleases in an easy and high-throughput way.

Objectives Removal of selection marker genes from transgenic plants is highly desirable for their regulatory approval and public acceptance. This study evaluated the use of two nucleases, the yeast homing endonuclease, I-SceI, and the designed zinc finger nuclease, CCR5-ZFN, in excising marker genes from plants using rice and Arabidopsis as the models. Results In an in vitro culture assay, both nucleases were effective in precisely excising the DNA fragments marked by the nuclease target sites. However, rice cultures were found to be refractory to transformation with the I-SceI and CCR5-ZFN overexpressing constructs. The inducible I-SceI expression was also problematic in rice as the progeny of the transgenic lines expressing the heat-inducible I-SceI did not inherit the functional gene. On the other hand, heat-inducible I-SceI expression in Arabidopsis was effective in creating somatic excisions in transgenic plants but ineffective in generating heritable excisions. The inducible expression of CCR5-ZFN in rice, although transmitted stably to the progeny, appeared ineffective in creating detectable excisions. Therefore, toxicity of these nucleases in plant cells poses major bottleneck in their application in plant biotechnology, which could be avoided by expressing them transiently in cultures in vitro. Electronic supplementary material The online version of this article (10.1186/s13104-019-4304-2) contains supplementary material, which is available to authorized users.

A simple and sensitive electrochemical method was developed for ampicillin detection based on the protective effect of aptamer-antibiotic conjugate towards endonuclease DpnII activity. Without ampicillin, DNA aptamer firstly hybridizes with the capture probe to form double strand DNA (dsDNA) structure. Then, dsDNA is cleaved by DpnII restriction endonuclease to form two dsDNA fragments. In which, one fragment is released from electrode surface and the other fragment is kept on electrode surface. Then, the dsDNA fragment kept on electrode surface is further digested by Exo III, which leads to the release of the dsDNA fragment from electrode surface. Thus, the electrochemical signal increases due to the decrease of the interface electron transfer resistance causing by the release of dsDNA from electrode surface. However, the formation of dsDNA is blocked when forming aptamer-ampicillin conjugate, which makes the obstruction of the digestion of DpnII and Exo III towards capture probe. Thus, a weak electrochemical signal is achieved due to the increase of the interface electron transfer resistance causing by the dsDNA on the electrode surface. Based on the relationship between ampicillin concentration and the decrease of the electrochemical signal, antibiotic is detected with low detection limit of 32 pM under optimal conditions, which is lower than the mandated maximum residue limit of European Union (9.93 nM). The developed method also presents good detection selectivity. Moreover, the applicability is confirmed by detecting antibiotic in milk and water samples with satisfactory results.

Genome editing for therapeutic applications often requires cleavage within a narrow sequence window. Here, to enable such high-precision targeting with zinc-finger nucleases (ZFNs), we have developed an expanded set of architectures that collectively increase the configurational options available for design by a factor of 64. These new architectures feature the functional attachment of the FokI cleavage domain to the amino terminus of one or both zinc-finger proteins (ZFPs) in the ZFN dimer, as well as the option to skip bases between the target triplets of otherwise adjacent fingers in each zinc-finger array. Using our new architectures, we demonstrate targeting of an arbitrarily chosen 28 bp genomic locus at a density that approaches 1.0 (i.e., efficient ZFNs available for targeting almost every base step). We show that these new architectures may be used for targeting three loci of therapeutic significance with a high degree of precision, efficiency, and specificity., Genome editing often requires cleavage within a narrow sequence window. Here the authors develop an expanded set of zinc finger nuclease architectures that increase the available configurations by a factor of 64 and can target almost every base at loci of therapeutic significance.

Background & objectives : There is a paucity of information on association between dental fluorosis, osteoporosis and periodontitis. The aim of this pilot study was to evaluate oestrogen receptor (ER). Rsa 1 gene polymorphism in osteoporosis periodontitis patients with and without dental fluorosis. Methods : Twenty one primary osteoporotic patients suffering from periodontitis with dental fluorosis and 20 primary osteoporotic patients suffering from periodontitis without dental fluorosis participated in this study. Periodontitis was diagnosed based on age, gender T-scores using clinical parameters such as plaque scores, gingival bleeding scores and probing pocket depth, clinical attachment level (CAL) and severity of dental fluorosis. DNA was genotyped at the RsaI RFLP (in exon 5) inside the ER gene to study ER Rsa I gene polymorphism in osteoporosis periodontitis patients with and without dental fluorosis. Results : Patients with dental fluorosis had higher degree of osteoporosis than those without fluorosis. CAL was significantly higher (P

Enzyme filamentation is a widespread phenomenon that mediates enzyme regulation and function. For the filament-forming sequence-specific DNA endonuclease SgrAI, the process of filamentation both accelerates its DNA cleavage activity and expands its DNA sequence specificity, thus allowing for many additional DNA sequences to be rapidly cleaved. Both outcomes-the acceleration of DNA cleavage and the expansion of sequence specificity-are proposed to regulate critical processes in bacterial innate immunity. However, the mechanistic bases underlying these events remain unclear. Herein, we describe two new structures of the SgrAI enzyme that shed light on its catalytic function. First, we present the cryo-EM structure of filamentous SgrAI bound to intact primary site DNA and Ca

Molecular self-replication is a fundamental function of all living organisms with the capability of templating and catalyzing its own synthesis, and it plays important roles in prebiotic chemical evolution and effective synthetic machineries. However, the construction of the self-replication system in vitro remains a great challenge and its application for biosensing is rare. Here, we demonstrate for the first time the construction of an in vitro enzymatic nucleic acid self-replication system and its application for amplified sensing of human 8-oxoguanine DNA glycosylase (hOGG1) based on autocatalytic self-replication-driven cascaded recycling amplification. In this strategy, hOGG1 excises 8-oxoguanine (8-oxoG) to unfold the hairpin substrate, activating the autonomous biocatalytic process with molecular beacons (MBs) as both the fuels for producing nucleic acid templates and the generators for signal output, leading to the continuous replication of biocatalytic nucleic acid templates and the repeated cleavage of MBs for an enhanced fluorescence signal. This strategy exhibits an extremely low detection limit of 4.3 × 10

Crossover recombination during meiosis is accompanied by a dramatic chromosome reorganization. In Saccharomyces cerevisiae, the onset of meiotic recombination by the Spo11 transesterase leads to stable pairwise associations between previously unassociated homologous centromeres followed by the intimate alignment of homologous axes via synaptonemal complex (SC) assembly. However, the molecular relationship between recombination and global meiotic chromosome reorganization remains poorly understood. In budding yeast, one question is why SC assembly initiates earliest at centromere regions while the DNA double strand breaks (DSBs) that initiate recombination occur genome-wide. We targeted the site-specific HO endonuclease to various positions on S. cerevisiae’s longest chromosome in order to ask whether a meiotic DSB’s proximity to the centromere influences its capacity to promote homologous centromere pairing and SC assembly. We show that repair of an HO-mediated DSB does not promote homologous centromere pairing nor any extent of SC assembly in spo11 meiotic nuclei, regardless of its proximity to the centromere. DSBs induced en masse by phleomycin exposure likewise do not promote homologous centromere pairing nor robust SC assembly. Interestingly, in contrast to Spo11, HO-initiated interhomolog recombination is not affected by loss of the meiotic kinase, Mek1, and is not constrained to use the meiosis-specific Dmc1 recombinase. These results strengthen the previously proposed idea that (at least some) Spo11 DSBs may be specialized in activating mechanisms that both 1) reinforce homologous chromosome alignment via homologous centromere pairing and SC assembly, and 2) establish Dmc1 as the primary strand exchange enzyme.

Identification of gene variation is of great importance for attaining information related to disease susceptibility. A highly sensitive and specific surface plasmon resonance (SPR) method for quantification of the apoE gene and genotype discrimination was demonstrated. The complementary sequences with the specific recognition sites of GCGC bases upon hybridization to the preimmobilized biotinylated probes could be cleaved by the restriction enzyme HhaI, while the existence of the single-base mismatch (GTGC) prevented the cleavage reaction. In both cases, the incorporation of streptavidin increased the sensitivity of the SPR assay, and the detection levels of 10 fM and 50 fM for the complementary and single-base mismatched sequences were attained, respectively. The sensing protocol is simple, label-free, and quantitative, thus avoiding the complicated polymerase chain reaction (PCR) amplification procedures. The proposed method serves as a viable means for facile and sensitive analyses of apoE genes in four unamplified genomic DNA extracts.

This novel total internal reflection fluorescence microscopy-based assay facilitates the simultaneous measurement of the length of the catalytic cycle for hundreds of individual restriction endonuclease (REase) molecules in one experiment. This assay does not require protein labeling and can be carried out with a single imaging channel. In addition, the results of multiple individual experiments can be pooled to generate well-populated dwell-time distributions. Analysis of the resulting dwell-time distributions can help elucidate the DNA cleavage mechanism by revealing the presence of kinetic steps that cannot be directly observed. Example data collected using this assay with the well-studied REase, EcoRV - a dimeric Type IIP restriction endonuclease that cleaves the palindromic sequence GAT↓ATC (where ↓ is the cut site) - are in agreement with prior studies. These results suggest that there are at least three steps in the pathway to DNA cleavage that is initiated by introducing magnesium after EcoRV binds DNA in its absence, with an average rate of 0.17 s-1 for each step.

Development of primordial germ cells (PGCs: precursors to adult gametes) is a key process in vertebrate sexual differentiation. Marsupials are ideal to investigate this phenomenon because much of PGC migration and development unusually occurs postnatally in pouch young. However, investigation of the molecular dynamics underpinning PGC development is restricted to one marsupial model species: the tammar wallaby (Macropus eugenii). Given the reproductive diversity among clades, marsupial PGCs likely exhibit diversity in molecular patterns that could help uncover their developmental dynamics. Here we characterise PGC marker expression (SSEA1 and DDX4) in developing ovaries of the brushtail possum, Trichosurus vulpecula. Female germ cells expressed DDX4 from 6 days postpartum (dpp) and almost all germ cells expressed DDX4 by meiosis (40 dpp), consistent with M. eugenii and eutherian mammals. In contrast, PGCs and oogonia expressed SSEA1 from 12 dpp, throughout proliferation and until entry into meiosis (40-63 dpp). SSEA1 expression was temporally distinct from that of M. eugenii, in which SSEA1 expression persists only until 14 dpp, indicating differential expression between marsupial species at equivalent stages of germ cell development. Hence, the molecular characteristics of M. eugenii germ cells cannot be assumed for all marsupials, as at least one key molecule exhibits species-specific expression.

Protein-DNA interactions play a fundamental role in all life systems. A critical issue of such interactions is given by the strategy of protein search for specific targets on DNA. The mechanisms by which the protein are able to find relatively small cognate sequences, typically 15-20 base pairs (bps) for repressors, and 4-6 bps for restriction enzymes among the millions of bp of non-specific chromosomal DNA have hardly engaged researcher for decades. Recent experimental studies have generated new insights on the basic processes of protein-DNA interactions evidencing the underlying complex dynamic phenomena involved, which combine three-dimensional and one-dimensional motion along the DNA chain. It has been demonstrated that protein molecules spend most of search time on the DNA chain with an extraordinary ability to find the target very quickly, in some cases, with two orders of magnitude faster than the diffusion limit. This unique property of protein-DNA search mechanism is known asfacilitated diffusion. Several theoretical mechanisms have been suggested to describe the origin of facilitated diffusion. However, none of such models currently has the ability to fully describe the protein search strategy.In this paper, we suggest that the ability of proteins to identify consensus sequence on DNA is based on the entanglement of π-π electrons between DNA nucleotides and protein amino acids. The π-π entanglement is based on Quantum Walk (QW), through Coin-position entanglement (CPE). First, the protein identifies a dimer belonging to the consensus sequence, and localize a π on such dimer, hence, the other π electron scans the DNA chain until the sequence is identified. By focusing on the example of recognition of consensus sequences by EcoRV or EcoRI, we will describe the quantum features of QW on protein-DNA complexes during search strategy, such as walker quadratic spreading on a coherent superposition of different vertices and environment-supported long-time survival probability of the walker. We will employ both discrete- or continuous-time versions of QW. Biased and unbiased classical Random Walk (CRW) has been used for a long time to describe Protein-DNA search strategy. QW, the quantum version of CRW, have been widely studied for its applications in quantum information applications. In our biological application, the walker (the protein) resides at a vertex in a graph (the DNA structural topology). Differently to CRW, where the walker moves randomly, the quantum walker can hop along the edges in the graph to reach other vertices entering coherently a superposition across different vertices spreading quadratically faster than CRW analogous evidencing the typical speed up features of the QW. When applied to protein-DNA target search problem, QW gives the possibility to achieve the experimental diffusional motion of proteins over diffusion classical limits experienced along DNA chains exploiting quantum features such as CPE and long-time survival probability supported by environment. In turn, we come to the conclusion that, under quantum picture, the protein search strategy does not distinguish between one-dimensional (1D) and three-dimensional (3D) case.SignificanceMost biological processes are associated to specific protein molecules binding to specific target sequences of DNA. Experiments have revealed a paradoxical phenomenon that can be synthesized as follows: proteins generally diffuse on DNA very slowly, but they can find targets very fast overwhelming two orders of magnitude faster than the diffusion limit. This paradox is known asfacilitated diffusion. In this paper, we demonstrate that the paradox is solved by invoking the quantum walk picture for protein search strategy. This because the protein exploits quantum properties, such as long-time survival probability due to coherence shield induced by environment and coin-position entanglement to identify consensus sequence, in searching strategy. To our knowledge, this is the first application of quantum walk to the problem of protein-DNA target search strategy.

Transcriptional regulation of the Saccharomyces cerevisiae HO gene is highly complex, requiring a balance of multiple activating and repressing factors to ensure that only a few transcripts are produced in mother cells within a narrow window of the cell cycle. Here, we show that the Ash1 repressor associates with two DNA sequences that are usually concealed within nucleosomes in the HO promoter and recruits the Tup1 corepressor and the Rpd3 histone deacetylase, both of which are required for full repression in daughters. Genome-wide ChIP identified greater than 200 additional sites of co-localization of these factors, primarily within large, intergenic regions from which they could regulate adjacent genes. Most Ash1 binding sites are in nucleosome depleted regions (NDRs), while a small number overlap nucleosomes, similar to HO. We demonstrate that Ash1 binding to the HO promoter does not occur in the absence of the Swi5 transcription factor, which recruits coactivators that evict nucleosomes, including the nucleosomes obscuring the Ash1 binding sites. In the absence of Swi5, artificial nucleosome depletion allowed Ash1 to bind, demonstrating that nucleosomes are inhibitory to Ash1 binding. The location of binding sites within nucleosomes may therefore be a mechanism for limiting repressive activity to periods of nucleosome eviction that are otherwise associated with activation of the promoter. Our results illustrate that activation and repression can be intricately connected, and events set in motion by an activator may also ensure the appropriate level of repression and reset the promoter for the next activation cycle., Author summary Nucleosomes inhibit both gene expression and DNA-binding by regulatory factors. Here we examine the role of nucleosomes in regulating the binding of repressive transcription factors to the complex promoter for the yeast HO gene. Ash1 is a sequence-specific DNA-binding protein, and we show that it recruits the Tup1 global repressive factor to the HO promoter. Using a method to determine where Ash1 and Tup1 are bound to DNA throughout the genome, we discovered that Tup1 is also present at most places where Ash1 binds. The majority of these sites are in “Nucleosome Depleted Regions,” or NDRs, where the absence of chromatin makes factor binding easier. We discovered that the HO promoter is an exception, in that the two places where Ash1 binds overlap nucleosomes. Activation of the HO promoter is a complex, multi-step process, and we demonstrated that chromatin factors transiently evict these nucleosomes from the HO promoter during the cell cycle, allowing Ash1 to bind and recruit Tup1. Thus, activators must evict nucleosomes from the promoter to allow the repressive machinery to bind.