scholarly journals Further Probing of Cu2+-Dependent PNAzymes Acting as Artificial RNA Restriction Enzymes

Molecules ◽  
2019 ◽  
Vol 24 (4) ◽  
pp. 672 ◽  
Author(s):  
Olivia Luige ◽  
Merita Murtola ◽  
Alice Ghidini ◽  
Roger Strömberg
Keyword(s):  
Peptide Nucleic Acid ◽  
Cleavage Site ◽  
Restriction Enzymes ◽  
Rna Cleavage ◽  
Artificial Enzymes ◽  
Rna Sequences ◽  
Specific Manner ◽  
A Site ◽  
Fold Excess ◽  
Insight Into

Peptide nucleic acid (PNA)-neocuproine conjugates have been shown to efficiently catalyse the cleavage of RNA target sequences in the presence of Cu2+ ions in a site-specific manner. These artificial enzymes are designed to force the formation of a bulge in the RNA target, the sequence of which has been shown to be key to the catalytic activity. Here, we present a further investigation into the action of Cu2+-dependent PNAzymes with respect to the dependence on bulge composition in 3- and 4-nucleotide bulge systems. Cu2+-dependent PNAzymes were shown to have a clear preference for 4-nucleotide bulges, as the cleavage of 3-nucleotide bulge-forming RNA sequences was significantly slower, which is illustrated by a shift in the half-lives from approximately 30 min to 24 h. Nonetheless, the nucleotide preferences at different positions in the bulge displayed similar trends in both systems. Moreover, the cleavage site was probed by introducing critical chemical modifications to one of the cleavage site nucleotides of the fastest cleaved 4-nucleotide RNA bulge. Namely, the exclusion of the exocyclic amine of the central adenine and the replacement of the 2′-hydroxyl nucleophile with 2′-H or 2′-OMe substituents in the RNA severely diminished the rate of RNA cleavage by the Cu2+-dependent PNAzyme, giving insight into the mechanism of cleavage. Moreover, the shorter recognition arm of the RNA/PNAzyme complex was modified by extending the PNAzyme by two additional nucleobases. The new PNAzyme was able to efficiently promote the cleavage of RNA when fully hybridised to a longer RNA target and even outperform the previous fastest PNAzyme. The improvement was demonstrated in cleavage studies with stoichiometric amounts of either PNAzyme present, and the extended PNAzyme was also shown to give turnover with a 10-fold excess of the RNA target.

scholarly journals Zn2+-Dependent Peptide Nucleic Acid Based Artificial Ribonucleases with Unprecedented Efficiency and Specificity

2021 ◽  
Author(s):  
Olivia Luige ◽  
Partha Pratim Bose ◽  
Rouven Stulz ◽  
Peter Steunenberg ◽  
Omar Brun ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Peptide Nucleic Acid ◽  
Rna Cleavage ◽  
Artificial Enzymes ◽  
Site Specificity ◽  
Artificial Ribonucleases

We present Zn2+-dependent dimethyl-dipyridophenazine PNA conjugates as efficient RNA cleaving artificial enzymes (10-minute RNA cleavage half-lives). These PNAzymes display site-specificity and cleavage of clinically relevant RNA models

Use of stereoisomers of zacopride to analyze actions of 5-hydroxytryptamine on enteric neurons

1991 ◽  
Vol 260 (1) ◽  
pp. G80-G90 ◽  
Author(s):  
P. R. Wade ◽  
G. M. Mawe ◽  
T. A. Branchek ◽  
M. D. Gershon
Keyword(s):  
Receptor Antagonist ◽  
Enteric Neurons ◽  
Myenteric Neurons ◽  
Substituted Benzamide ◽  
A Site ◽  
Ics 205 930 ◽  
Fold Excess ◽  
Insight Into

Two subtypes of excitatory 5-hydroxytryptamine (5-HT) receptor, 5-HT1P and 5-HT3, are found on type 2-AH neurons of the guinea pig myenteric plexus. The 5-HT1P receptor mediates a slow and the 5-HT3 receptor a fast depolarization of these cells, however, the role of these receptors in the physiology of the gut is unknown. Renzapride (BRL 24924), a substituted benzamide, has previously been found to antagonize responses of myenteric neurons mediated by both 5-HT1P and 5-HT3 receptors. The effects on myenteric type 2-AH neurons of a structurally similar benzamide, zacopride, which unlike renzapride has S and R stereoisomers, were investigated to gain further insight into 5-HT receptor function. In contrast to renzapride, S-, but not R-zacopride, was found to mimic the 5-HT1P receptor-mediated slow response to 5-HT. Desensitization of 5-HT1P receptors with 5-HT inhibited slow depolarizing responses to S-zacopride, and desensitization with S-zacopride antagonized slow responses to 5-HT. Responses to S-zacopride were also inhibited by renzapride and the 5-HT1P receptor antagonist N-acetyl-5-hydroxytryptophyl-5-hydroxytryptophan amide (5-HTP-DP). S-zacopride, like renzapride and 5-HT, presynaptically inhibited nicotinic fast excitatory postsynaptic potentials, an effect that can be mediated by 5-HT1P or 5-HT1A receptors. Both S and R stereoisomers of zacopride antagonized 5-HT3 receptor-mediated fast responses to 5-HT. Unlike 5-HTP-DP, neither zacopride or its stereoisomers nor renzapride inhibited the binding of 5-[3H]HT to 5-HT1P receptors. [3H]zacopride (5-10 nM) was found to bind to a site in the gut from which it could be displaced by a 1,000-fold excess of renzapride and S-zacopride (but not R-zacopride) greater than 5-HTP-DP much greater than the 5-HT3 receptor antagonist ICS 205-930. These observations suggest that, in addition to 5-HT3 receptors, there is a benzamide binding site on myenteric neurons that interacts with, but is distinct from, the 5-HT recognition site of 5-HT1P receptors. Benzamides may affect coupling of the 5-HT1P receptor to its effector.

scholarly journals Development of Fragility Curves for Piping and Slope Stability of River Levees

Water ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 738
Author(s):  
Nicola Rossi ◽  
Mario Bačić ◽  
Meho Saša Kovačević ◽  
Lovorka Librić
Keyword(s):  
Slope Stability ◽  
Fragility Curves ◽  
Safety Margin ◽  
Water Levels ◽  
Flood Event ◽  
Soil Parameters ◽  
Design Code ◽  
A Site ◽  
Insight Into

The design code Eurocode 7 relies on semi-probabilistic calculation procedures, through utilization of the soil parameters obtained by in situ and laboratory tests, or by the means of transformation models. To reach a prescribed safety margin, the inherent soil parameter variability is accounted for through the application of partial factors to either soil parameters directly or to the resistance. However, considering several sources of geotechnical uncertainty, including the inherent soil variability, measurement error and transformation uncertainty, full probabilistic analyses should be implemented to directly consider the site-specific variability. This paper presents the procedure of developing fragility curves for levee slope stability and piping as failure mechanisms that lead to larger breaches, where a direct influence of the flood event intensity on the probability of failure is calculated. A range of fragility curve sets is presented, considering the variability of levee material properties and varying durations of the flood event, thus providing crucial insight into the vulnerability of the levee exposed to rising water levels. The procedure is applied to the River Drava levee, a site which has shown a continuous trend of increased water levels in recent years.

scholarly journals “IF YOU DON’T KNOW ME BY NOW…”

2021 ◽  
pp. 1-28
Author(s):  
Ellen M. Whitehead ◽  
Allan Farrell ◽  
Jenifer L. Bratter
Keyword(s):  
Race And Ethnicity ◽  
Mate Selection ◽  
Racial Identities ◽  
Hispanic Origin ◽  
Socially Constructed ◽  
Attitudinal Factors ◽  
A Site ◽  
Intimate Partnerships ◽  
College Educated ◽  
Insight Into

ABSTRACT The racial composition of couples is a salient indicator of race’s impact on mate selection, but how well do those in intimate partnerships know the racial identities of their partners? While prior research has revealed that an individual’s race may be perceived differently than how they identify, most of what is known comes from brief interactions, with less information on established relationships. This study examines whether discrepancies in the reports of a person’s race or ethnicity can be identified even within intimate relationships, as well as which relational, social, and attitudinal factors are predictive of divergent or concordant reports. We draw on the Fragile Families and Child Wellbeing Study (n=3467), a U.S.-based dataset that uniquely provides both the father’s self-reported race and Hispanic origin and the mother’s report of the father’s race and ethnicity. We compare reports of the father’s race/Hispanic origin from both parents to assess the extent of mismatch, and we distinguish between whether mothers view the father’s race as similar to or different from her own. We find roughly 14% of mothers provide a race and Hispanic origin that is inconsistent with the father’s report, with a large share reflecting differences in the self-identified and perceived race of fathers who are reported as Hispanic. Among mismatched reports, mothers are more likely to report a race/ethnicity for the father that matches her own, depressing the number reporting interracial unions. Perceptions of racial homogamy are especially likely when mothers view racial sameness as important to marriage. Further, mismatches are more common in the midst of weak relational ties (i.e. non-marital relationships) and are less common when both parents are college-educated. These findings reveal that intimate unions are a site where race is socially constructed and provide insight into how norms of endogamy manifest within formed relationships.

scholarly journals Rab1-AMPylation by Legionella DrrA is allosterically activated by Rab1

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jiqing Du ◽  
Marie-Kristin von Wrisberg ◽  
Burak Gulen ◽  
Matthias Stahl ◽  
Christian Pett ◽  
...  
Keyword(s):  
Legionella Pneumophila ◽  
Adenosine Monophosphate ◽  
Vesicular Trafficking ◽  
Bacterial Protein ◽  
Post Translational Modification ◽  
Allosteric Control ◽  
Rab Protein ◽  
Biochemical Characterisation ◽  
A Site ◽  
Insight Into

AbstractLegionella pneumophila infects eukaryotic cells by forming a replicative organelle – the Legionella containing vacuole. During this process, the bacterial protein DrrA/SidM is secreted and manipulates the activity and post-translational modification (PTM) states of the vesicular trafficking regulator Rab1. As a result, Rab1 is modified with an adenosine monophosphate (AMP), and this process is referred to as AMPylation. Here, we use a chemical approach to stabilise low-affinity Rab:DrrA complexes in a site-specific manner to gain insight into the molecular basis of the interaction between the Rab protein and the AMPylation domain of DrrA. The crystal structure of the Rab:DrrA complex reveals a previously unknown non-conventional Rab-binding site (NC-RBS). Biochemical characterisation demonstrates allosteric stimulation of the AMPylation activity of DrrA via Rab binding to the NC-RBS. We speculate that allosteric control of DrrA could in principle prevent random and potentially cytotoxic AMPylation in the host, thereby perhaps ensuring efficient infection by Legionella.

scholarly journals Structure of a canonical RNase YoeB bound to the ribosome

2014 ◽  
Vol 70 (a1) ◽  
pp. C207-C207
Author(s):  
Yun Chen ◽  
Shu Feng ◽  
Katsuhiko Kamada ◽  
Han Wang ◽  
Kai Tang ◽  
...  
Keyword(s):  
Specific Activity ◽  
Base Catalysis ◽  
Mass Spectrometry Data ◽  
Catalytic Core ◽  
General Base ◽  
Rna Hydrolysis ◽  
70S Ribosome ◽  
A Site ◽  
Insight Into

As a typical endoribonuclease, YoeB mediates cellular adaptation in diverse bacteria by degrading mRNAs on its activation. Although the catalytic core of YoeB is thought to be identical to well-studied nucleases, this enzyme specifically targets mRNA substrates that are associated with ribosomes in vivo. However, the molecular mechanism of mRNA recognition and cleavage by YoeB, and the requirement of ribosome for its optimal activity, largely remain elusive. Here, we report the structure of YoeB bound to 70S ribosome in pre-cleavage state, revealing that both the 30S and 50S subunits participate in YoeB binding. The mRNA is recognized by the catalytic core of YoeB, of which the general base/acid (Glu46/His83) are within hydrogen-bonding distance to their reaction atoms, demonstrating an active conformation of YoeB on ribosome. Also, the mRNA orientation involves the universally conserved A1493 and G530 of 16S rRNA. In addition, mass spectrometry data indicated that YoeB cleaves mRNA following the second position at the A-site codon, resulting in a final product with a 3'–phosphate at the newly formed 3' end. Our results demonstrate a classical acid-base catalysis for YoeB-mediated RNA hydrolysis and provide insight into how the ribosome is essential for its specific activity.

A reactive center loop–based prediction platform to enhance the design of therapeutic SERPINs

2021 ◽  
Vol 118 (45) ◽  
pp. e2108458118
Author(s):  
Wariya Sanrattana ◽  
Thibaud Sefiane ◽  
Simone Smits ◽  
Nadine D. van Kleef ◽  
Marcel H. Fens ◽  
...  
Keyword(s):  
Cleavage Site ◽  
Serine Proteases ◽  
Protein C ◽  
Activated Protein C ◽  
Reactive Center Loop ◽  
Physiological Processes ◽  
Naturally Occurring ◽  
Reactive Center ◽  
Insight Into

Serine proteases are essential for many physiological processes and require tight regulation by serine protease inhibitors (SERPINs). A disturbed SERPIN–protease balance may result in disease. The reactive center loop (RCL) contains an enzymatic cleavage site between the P1 through P1’ residues that controls SERPIN specificity. This RCL can be modified to improve SERPIN function; however, a lack of insight into sequence–function relationships limits SERPIN development. This is complicated by more than 25 billion mutants needed to screen the entire P4 to P4’ region. Here, we developed a platform to predict the effects of RCL mutagenesis by using α1-antitrypsin as a model SERPIN. We generated variants for each of the residues in P4 to P4’ region, mutating them into each of the 20 naturally occurring amino acids. Subsequently, we profiled the reactivity of the resulting 160 variants against seven proteases involved in coagulation. These profiles formed the basis of an in silico prediction platform for SERPIN inhibitory behavior with combined P4 to P4’ RCL mutations, which were validated experimentally. This prediction platform accurately predicted SERPIN behavior against five out of the seven screened proteases, one of which was activated protein C (APC). Using these findings, a next-generation APC-inhibiting α1-antitrypsin variant was designed (KMPR/RIRA; / indicates the cleavage site). This variant attenuates blood loss in an in vivo hemophilia A model at a lower dosage than the previously developed variant AIKR/KIPP because of improved potency and specificity. We propose that this SERPIN-based RCL mutagenesis approach improves our understanding of SERPIN behavior and will facilitate the design of therapeutic SERPINs.

scholarly journals Impact of a Single Nucleotide Change or Non-Nucleoside Modifications in G-Rich Region on the Quadruplex–Duplex Hybrid Formation

Biomolecules ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1236
Author(s):  
Dorota Gudanis ◽  
Karolina Zielińska ◽  
Daniel Baranowski ◽  
Ryszard Kierzek ◽  
Piotr Kozłowski ◽  
...  
Keyword(s):  
Target Sequence ◽  
Rich Region ◽  
Rna Sequences ◽  
Single Nucleotide ◽  
Alternative Structures ◽  
Single Nucleotide Change ◽  
G Quadruplex ◽  
Quadruplex Formation ◽  
Target Rna ◽  
Insight Into

In this paper, a method to discriminate between two target RNA sequences that differ by one nucleotide only is presented. The method relies on the formation of alternative structures, i.e., quadruplex–duplex hybrid (QDH) and duplex with dangling ends (Dss), after hybridization of DNA or RNA G-rich oligonucleotides with target sequences containing 5′–GGGCUGG–3′ or 5′–GGGCGGG–3′ fragments. Using biophysical methods, we studied the effect of oligonucleotide types (DNA, RNA), non-nucleotide modifications (aliphatic linkers or abasic), and covalently attached G4 ligand on the ability of G-rich oligonucleotides to assemble a G-quadruplex motif. We demonstrated that all examined non-nucleotide modifications could mimic the external loops in the G-quadruplex domain of QDH structures without affecting their stability. Additionally, some modifications, in particular the presence of two abasic residues in the G-rich oligonucleotide, can induce the formation of non-canonical QDH instead of the Dss structure upon hybridization to a target sequence containing the GGGCUGG motif. Our results offer new insight into the sequential requirements for the formation of G-quadruplexes and provide important data on the effects of non-nucleotide modifications on G-quadruplex formation.

Moving into Nanotechnology Roles to Mimic and Boost Enzyme Activity

2018 ◽  
pp. 421-440
Author(s):  
Maria Laura Soriano
Keyword(s):  
Enzyme Activity ◽  
Catalytic Activity ◽  
Enzyme Immobilization ◽  
Mesoporous Materials ◽  
Specific Activity ◽  
Artificial Enzymes ◽  
Catalytic Nanoparticles ◽  
Solid Liquid ◽  
By Products ◽  
Insight Into

A new tendency toward the design of artificial enzymes based on nanostructures (nanodots, nanofibers, mesoporous materials) has emerged. On one hand, nanotechnology bestows self-catalytic nanoparticles with a specific activity to achieve efficient reactions with low number of by-products. On other hand, the nanoparticles may behave as nanometric scaffolds for hosting enzymes, promoting their catalytic activity and stability. In this case, enzyme immobilization requires the preservation of the catalytic activity by preventing enzyme unfolding and avoiding its aggregation. These approaches render many other advantages like hosting/storing enzymes in nanotechnological solid, liquid, and gel-like media. This chapter focuses on the most up-to-date approaches to manipulate or mimic enzyme activity based on nanotechnology, and offers examples of their applications in the most promising fields. It also gives new insight into the creation of reusable nanotechnological tools for enzyme storage.

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